What a clear Chemistry !!

Anant Marahatta
Chemistry Department
Tohoku University
Japan
(ananta037@gmail.com)

It is a fact that if one could direct the computer according to his/her intention, one would get fantastic information about any disciplines of science. Computational chemistry which uses chemical software to compute chemistry behind matter has become fundamental tool in the cutting edge research. Now a day, without the computational approach, the experimental research findings are being difficult to accept by the scientific society. One of the very clear chemistry of single molecule rotation on crystalline surfaces is clarified here.

Fig (a) and (b) explain the alignment of dimethylsulphide (CH3)2 S molecule over Au(111) and over Au(100) surfaces respectively. Over Au (111) surface, one methyl group lies on the three-fold hollow site while another methyl group sits on the top site. In contrary, over Au (100) surface, both methyl groups occupy the hollow site present between atoms. During the rotation, if one CH3 group is passing the atop site while another one is above the hollow site (like in Au(111)), the rotation becomes facile. The opposite is true at Au (100) surface.

What a clear illustration, isn’t it? It’s a challenging finding of computational chemistry over experimental one.


If you are interested to read above chemistry in detail, you are advised to go through
J. Phys. Chem. C 2011, 115, 125–131

Setting up Computational Chemistry (Quantum Chemistry) laboratory? Technical stuffs [Part II].

Anant　Babu Marahatta
Ph.D. student in chemistry
Tohoku University
Japan

(Interested fellows are suggested to read the first part [Part 1] of this article archived herewith before proceeding it).

The designation of the molecular model is another mandatory step before performing any sorts of computer calculations. Several model making software (molecule model builder) are available free of charge. Mercury, RasMol, CHIME, SwissPDB Viewer, Avogadro etc. are some of them. How to handle them is the matter of their practice. It is very essential to know that some of the molecular builders do not support the calculating software. Let’s say in this step that we could model the sample system of our interest and get the Cartesian co-ordinates or Z-matrix of it (generated by the molecular builder) which will be our input for exploring the chemistry behind it.

Let’s move to the calculating software, one of the very well-known is GAUSSIAN (currently Gaussian-09 version for the windows G09W is available) owned by the Gaussian Inc., USA. It is very flexible software developed by the quantum chemists of all around the world. It is very trustworthy for the most accurate calculations especially ab initio, MD simulation and some semi-empirical calculations. Thus, for having the copy of this software, the university must be the member of it and get the license. The normal cost for the single computer license (single CPU version) is $1150 and for the multiprocessor /core version is $1725 (excluding shipping charge). The detail information is available here. http://www.gaussian.com/g_prod/g09.htm
Here is the sample video of "Gaussian in action" to analyze the frequency.

Similarly, individual person can get the license but he or she needs to pay some additional amount provided that Gaussian Inc. trusts him or her.

It is recommended that “GaussView” (currently, GaussView5 for windows GVW5 is available) is very useful molecular builder that supports the Gaussian software windows version. One must get the copy of it too from the Gaussian Inc. The new license costs $875 for the single windows computer and $4025 for the unlimited windows computer provided that Gaussian software has already been installed.

So far, we have installed the very essential software and our computer is ready to compute the chemistry of the input (of the interested molecular system) prepared by using molecular builder. Now, it’s time to know how to handle above installed software, prepare and route proper inputs, submit for the calculations, route the outputs, visualize the outputs and analyze them. The real chemistry starts from here and for it one must be perfect on computational/quantum chemistry.

Setting up Computational Chemistry (Quantum Chemistry) laboratory? Technical stuffs [Part I]

Anant　Babu Marahatta
Ph.D. student in chemistry
Tohoku University
Japan

[Being a 4th year Doctoral student majoring Quantum chemistry, “Nepa Chem’s-facebook-status” on 11th April 2011 motivated me to write this article. It is solely dedicated to our energetic seniors/colleagues who are planning to introduce the Computational Chemistry lab in Nepal.]

[ This informative article is intended to provide some pre-requisites needed to set up very basic computational chemistry (Quantum Chemistry) laboratory. It is not valid to those who want to establish the high-tech lab by installing the supercomputing calculators into the networks which is a very common way in the renowned research institutions. Even though “LINUX” computer operating system with “Emacs”, world's most powerful text editor, is very common to be installed into the computer, the basic computational laboratory can be set up in the absence of them.

Thus, the person who is master on handling the networking systems of the supercomputers (calculators) with the personal computer (local machine) having installed LINUX is assigned as an administrator of the computational chemistry laboratory. Therefore, nominating a technical staff with such assignments is the crucial point to set up the advanced computational laboratory. ]

Let me start by defining computational chemistry, a branch of chemistry that uses principles of computer science to assist in solving chemical problems. Thus the computers with good memory are the very fundamental tools of it.

Now think yourself that how can computers generate a chemistry of the matter? It does suggest that without using any chemistry related software developed by utilizing the results of the theoretical chemistry (quantum and statistical chemistry), computing chemical and physical properties of the matter are impossible. Thus saying “Computers alone don’t calculate chemistry of the matter” is very usual fact. The most essential tool is the chemical software developed by implementing the results of the quantum and statistical chemistry. Just for making quantum chemistry in action, computer is essential. That’s the reason, why computational chemistry most of the time refers to the quantum chemistry as it is governed by the solution of the Schrödinger equations in order to know everything about the system.

On account of setting very simple computational laboratory for conducting normal level calculation of the small molecular system, the general computers which we use in our daily purpose is more than enough. Thus, even the very poor research institutes can afford such computers. Now the problem is about the chemical software to be installed into each assigned computer. As the molecular synthesis is very needful step in experimental chemistry, in computational chemistry too, one must engineer/model the molecule by using computer. This movie is an example of model making processes and the appearance while running the computational calculations.



The software for designing the molecule and computing the calculations will be discussed in part II.

Computational chemistry

Anant Babu Marahatta
Ph.D. student in chemistry
Tohoku University
Japan

Perspectives:
In the real world, “A Digital Laboratory could eventually mean that most chemical experiments are conducted inside the silicon chips instead of the glassware of laboratories. Turn off that Bunsen burner; it will not be wanted in ten years.” This intension of the “1998 Chemistry Nobel Prize Awardees” directed the computational procedures for conducting cutting-edge research. In the present condition, computational procedures have become a “superstar”.

Overview: Computational chemistry is a branch of chemistry that uses principles of computer science to assist in solving chemical problems. It is simply the application of chemical, mathematical and computing skills to the solution of interesting chemical problems.
It uses computers to generate information such as properties of molecules, simulated experimental results, displays almost all the information with the chemical visualization package developed by considering the results of the theoretical chemistry.

Computational chemistry has become a useful way to investigate materials that are too difficult to find or too expensive to purchase. It also helps chemists to make predictions before running the actual experiments so that they can be better prepared for making observations.
Similarly, it can predict unobserved chemical phenomena of the macro molecules like amino acids, protein, DNA, enzymes etc. in the visual form. The following animation has explained about the preliminary processes of molecule modeling, electron density tracing and some prerequisites of the computational chemistry.
To calculate the structures and properties of molecules and solids computationally, several computer software have been developed. Some of the common software includes,
• Gaussian xx, Gaussian 09 currently [Gauss. Inc. USA]
• GAMESS [Gordon research group, Iwa state Univ.]
• MolPro, 2010.1 currently [H.-J. Werner and P. J. Knowles]
• DFTB+ [Bremen Center for Computational Materials Science]
• MOPAC [Stewart Computational Chemistry ]
• Spartan [Spartan Chemical Company, Inc.]
• Sybyl [Tripos, a Certara company]
• SIESTA[Spanish Initiative for Electronic Simulations with Thousands of Atoms]
The employed computational methods rely on the software installed and can cover both static and dynamic situations. In all cases, the computational time and other resources (such as memory and disk space) increase rapidly with the size of the system being studied. That system can be a single molecule, a group of molecules, or a solid. In order to perform the calculation in an efficient way with extremely low computational cost, proper selection of the computational method is mandatory.