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.

Japan and US: You must construct “Onkalo”- Fukushima Issue

Anant Babu Marahatta
Sendai, Japan
(News analysis)

Being one of the eyewitnesses from Sendai, Japan, I should proudly say that it was not so big issue about the ~9 M mega-quake that shook some of the major cities of northeast-Japan including Sendai of Miyagi prefecture on March 11, 2011, as all the skyscrapers are still standing unlike the case in Haiti few months ago. Even the mechanical damage caused by the big Tsunami, the consequence of that tremor, has been stopped broadcasting by the world’s leading news networks as well as covering by the front pages of the leading newspapers.

However, the major technical damage of the Tsunami which is being faced by the Fukushima based nuclear power plants, each has the capacity of storing 100s of tons of nuclear fuel, has been publishing with the greatest priority. It is reminded that the storage of all the crippled power plants had contained tons of nuclear fuel and were fully operated during the time of Tsunami. Thus, it is not surprising to mention “Japan is having a big nuclear disaster and crisis” which has presented the crucial question to the world “what to do with nuclear energy?” and I believe (& you too) the world has seriously begun thinking about it.

The current situation of the nuclear disaster in the world after receiving ‘Fukushima-nuclear plants threats’, can be envisioned by this news headline “In search of a nuclear disposal site” published by the “Japan Times” on 7th April 2011. It's every nation's responsibility to construct permanent nuclear waste repositories on its own territory. It is a praiseworthy work that around 300 km northwest of Finland's capital, an island named “Helsinki” houses the potential site for one of the world's first permanent underground high-level nuclear waste repositories “Onkalo” (Finnish language for “hiding place”).The repository is hundreds of meters deep and is designed to store high-level nuclear waste for at least 100,000 years. Research is still under way, but the dumping of the spent fuel is scheduled to begin around 2020.

Even though, Aomori prefecture of Japan is housing “Rokkasho reprocessing plant” for low-level as well as a temporary storage space for high-level radioactive waste, it is not enough at all for the final repository. It must be appreciated that US had spent much time and money in order to develop a permanent repository for spent nuclear fuel and other high-level nuclear waste at Yucca Mountain in Nevada, but the project was scrapped by the Obama administration amid local opposition.
Come on Japan & US !! You are the leaders of the world but why are you still operating massive nuclear power plants without installing proper safety measures? It's too late but for the safe future, you have to construct the final repository for the nuclear waste.

Diamondoids: Potential candidate for the Nanotech.

Anant Babu Marahatta
Tohoku University
Sendai, Japan

One of the current aspects of chemistry is being a watch-dog of the nanoworld which is a major discipline in Nanotechnology. In the context of building materials for nanotechnology components and in “bottom-up” approaches of chemistry, diamondoids have been of great interest in recent years.

Most generally, diamondoids refer to structures that resemble diamond consisting of a number of six-member carbon rings fused together. They are strong, stiff structures containing dense, 3-D networks of covalent bonds, formed chiefly from first and second row atoms with a valence of three or more. Various hetero-atoms which might include N, O, Si, S, and so forth, some time, act as the major substituent.

Here is the animation obtained by the Molecular Dynamics simulation of the diamondoids.



The carbon-carbon framework of them constitutes the fundamental repeating unit in the diamond lattice structure. More explicitly, they consist of repeating units of ten carbon atoms forming a tetra-cyclic cage system. Above figure illustrates the smaller diamondoid molecules, with the general chemical formula C(4n+6)H(4n+12): adamantane (C10H16), diamantane (C14H20), triamantane (C18H24) and so on. Graphite, Carbon nano tubes consisting of sheets of carbon atoms rolled into tubes, spherical buckyballs (Fullerene) are also included in the class of diamondoids materials.

They are ultra stable, saturated organic compounds (hydrocarbons) with unique structures and properties. The cage nature of them (polymantanes, adamantologues) is very promising architectures for modeling nano structures. This family of compounds (with over 20,000 variants) is one of the best candidates that offer the possibility of producing a variety of molecular machinery shapes including molecular rotors, gyroscopes, propellers, ratchets, gears, toothed cogs, etc. They are heavily used in drug-delivery, drug targeting, DNA directed assembly, molecular building blocks for synthesis of high temperature Polymers and in host-guest chemistry for modeling supramolecular complexes.


References:
Advances in Chemical Physics Vol. 136, pp. 207-258, 2007
and
www.diamantane.info/index.html