Chemical potential: is it there?

I wrote this title because rarely we hear or use the value of chemical potential for chemistry purposes. This became a hot topic (one of the most discussed) in the 2007 IUPAC congress in Torino. Chemical potential is believed as a part of physical and thermodynamical chemistry but less favorable than other terms, such as: entropy, enthalpy. Even, most of students probably never hear the use of this value to calculate their thermodynamic problem. It is more to the ‘ego’ of chemists to describe their ‘own world’ (just an opinion).

IBM-Almaden Kinetics Simulator

Taking from the name of the above software, it will be recognized as the software used for calculating the kinetics of chemical process. However, the next word ‘simulator’ could be taken account as the most important part about what this software can do. This is a simulator program (only) which allows you to calculate simultaneously a set of differential equation of reaction rates. Unfortunately, this software does not have such a ‘databank’ about the kinetic. So, you have to put it by yourself.

Kintecus

For everyone who works in reaction kinetic and pathway, they will be very familiar with this software. Kintecus is known as a program to simulate the chemical kinetics of combustion, biological, nuclear, and air atmosphere in spreadsheet files. Putting spreadsheet as the basis of the interface is nice as most of people are familiar enough with Excel MS. Although it is written not necessary to have MS Excel, it could be better to have at least Excel viewer. The module of the program is activated via macros, so you have to set ‘low’ level of secuirity of your MS Excel.

Transition structure

In reaction kinetic calculation, the transition structure is necessary to calculate the kinetic rate constant. In Gaussian calculation, it is known by the existence of single negative value of frequency. So, it could be TS of rotation, conformation, addition, insersion, and so on. Using Molden software, you can nicely see what happen to the molecule in the negative frequency. I browsed one of the mailing list, and I got a nice explanation about the scientific term of negative frequency written by Christopher Crammer:

Indexing the pdf file

Trouble with many pdf file that you have collected? These proposed softwares could be help you to manage numerous pdf file especially collected papers.

Gaussian error messages

Here, I will put continuously the error messages of Gaussian program and its solution. I collect all these from the internet, mailing list, and also my experiences when I use Gaussian.

Again with IUPAC name

In one of quite crowded mailing list of computational chemistry related subject, one of the topics talked about the software to give a name to the specific molecule following IUPAC rules. It is important since when you find a molecule and you want to publish it, you have to put a correct name written in your manuscript. Here, taken from all the replies of the question, I put all those possible softwares that you can use. Interesting since I never know it before:

Don’t be a copycat!

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.

ONIOM

I was curious to find the simple explanation about this word: ONIOM. You can believe me that (until I wrote this blog), 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.

Multi-Coordinate Driven Reaction Path Search

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.