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

More than 1/3rd of Americans and ½ of Germans live within 75 km of a nuclear power plant

Anant Babu Marahatta
Sendai, Japan

Disaster is a disaster. This time, Japan is victimized. No one knows, such catastrophe may happen anytime, anywhere, in the world.　

The current world news is about the crippled Fukushima based Japanese nuclear power plants which was hit by a 9.0-magnitude quake on March 11 of 2011 and then, about 25 minutes later, a devastating tsunami. About 172,000 people lived in the 30-km zone of these plants.

The Japanese government has declared the 20-km evacuation area around the crippled Fukushima No. 1 nuclear power plant a “no-go zone”. It has also urged the residents to abide by the order for their own safety or possibly face fines or detention. Under a special nuclear emergency law, people who enter into the zone will now be subject to fines of up to ¥100,000 and possible detention of up to 30 days.

In order to aware this potential risk of this scenario to the world, a current study released by “Nature” on Friday, 22nd April 2011, shows that about 90 million people worldwide live within 30 kilometers of a nuclear reactor, equivalent to the exclusion zone around Japan's crippled Fukushima plants. The United States alone has nearly 16 million people within this range, followed by more than 9 million each in China, Germany and Pakistan, and 5 to 6 million in India, Taiwan and France.

When the radius is expanded to 75 km, the number of people potentially at risk in case of a nuclear accident jumps to nearly half a billion. More than 110 million are in the U.S., 73 million in China, 57 million in India, 39 million in Germany and 33 million in Japan.
Let’s look at another way; more than 1/3rd of Americans live within 75 km of a nuclear power plant, and nearly half of all Germans.

It does suggest how many people will be at risk if something does go terribly wrong, as happened in Fukushima a month ago and in Chernobyl 25 years ago.

Sources:
‘The Japan Times” daily newspaper.
www.nature.com

A Chemical to capture radioactive substances: "Fukushima-reactors issue"

Anant Babu Marahatta
Tohoku university
Japan

Nuclear energy can be both beneficial and harmful, depending on the way in which it is used. We routinely use X-rays to examine bones for fractures, treat cancer with radiation, and diagnose diseases with the help of radioactive isotopes. Approximately 17% of the electrical energy generated in the world comes from nuclear power plants. 'Nuclear reactors produce electricity so cheaply that it is not necessary to meter it. The users pay a fee and use as much electricity as they want. Atoms provide a safe, clean and dependable source of electricity. '

On the other hand, nuclear hazard which literally means “risk or danger to the human health or to the environment caused by radiation emitted by the radioactive nuclei of a given substance, or the possibility of an uncontrolled explosion originating from a nuclear fusion or fission reaction of atomic nuclei”, that appeared in the Japanese “Fukushima nuclear plants” is the latest example of its negative impact. .

The contamination of the coolant (by radioactive iodine, cesium, and strontium), a mandatory process during nuclear chain reactions, caused by the “Fukushima nuclear reactors leakage” is the current issue of the world. To remove such radioactive substances, recently, a Japanese chemist and a domestic company have jointly developed a powdery chemical that can capture and precipitate radioactive substances in water.

This powder, made of various chemicals and minerals, including zeolite, can remove radioactive substances such as iodine, cesium and strontium, a professor at Kanazawa University said. The powder was able to remove almost 100 percent of cesium when 1.5 grams of the powder were mingled with 100 milliliters of water in which cesium had been dissolved at a density of 1-10 ppm. It has been confirmed to have the ability to remove iodine even at a density of 100 ppm. It is reminded that the densities of radioactive substances seeping into the water at the Fukushima No. 1 nuclear complex are estimated at around 10 ppm. This powder could be used in the ongoing effort to deal with contaminated water at the crippled Fukushima nuclear plant

What a problem oriented research; isn't it?

DEATH BY OXALIC ACID

Anant Babu Marahatta
Tohoku University
Japan
Oxalic acid is a constituent of many house hold products. It is found in many disinfectants, household bleach, metal cleaning liquids, antirust products and furniture polishes. Oxalic acid is a crystalline, colorless substance and is efflorescent. This means it tends to become powdery on account of loss of water of crystallization. It has got its name from the Greek word Oxalis, which means sorrel. It occurs in sorrel plant and because of this the French chemist Lavoiser in 1787 named it as Oxalic acid. It occurs in the leaves and young stalk of Rhubarb, Spinach and even Cabbage. Sorrel is succulent acid herb used in salads.

Accidental poisoning has been known to occur after a hearty meal of rhubarb or sorrel .Food rich in oxalate can also lead to kidney stones because kidney stones are generally made up of oxalates. Crystals of oxalic acid are similar in appearance to those of magnesium sulphate (Epsom salt) and zinc sulphate. Because of this similarity, cases of accidental poisoning have occurred. Magnesium sulphate in doses of 15g is used as a laxative (to facilitate the evacuation of Bowels) and is non toxic. Since oxalic acid, a dangerous poison is so similar looking to Epsom salt-a commonly used drug as laxative medicine-it is necessary to be able to differentiate between the two. If the doctor or nurse fails to differentiate between the two, accidental poisonings may occur. Two patients at the mental hospital in Scotland had died in 1956 after receiving doses of oxalic acid which was mistaken for Epsom salts. Similarly zinc sulphate is also commonly used drug and looks very similar to the dangerous poison, oxalic acid. Thus in order to remain in the safe side, it is very much essential to be able to differentiate between them.

HOW DO DOCTORS DIFFERENTIATE BETWEEN THE TWO?

Since if we taste a small amount of crystal of each, oxalic acid is sour in taste and magnesium sulphate is nauseatingly bitter and zinc sulphate is metallic bitter. But surely, this is not the best method to find out the poison. The reaction of oxalic acid is strongly acidic but that of zinc sulphate is slightly acidic and magnesium sulphate is neutral. On application of heat, Oxalic acid sublimes while the rest of the two salts remain fixing. When each salt is allowed to react with sodium carbonate, oxalic acid shows effervescence but no precipitate while the other two salts show no effervescence but a give white precipitate of metal carbonates. But perhaps the easiest test is to see whether stains of ink will disappear by a solution of one of these salts or not. Since, a solution of oxalic acid makes the stain disappear ,the other two salts can not do that That is why oxalic acid is used in products like ink removers and furniture polishes. It is also used in households as a “bleach” to remove stains or to clean metals notably brass or leather and also used in calico-printing (cotton cloth especially plain white and unbleached).


CAN OXALIC ACID BE USED FOR HOMICIDE?

No that is not possible .because of its sour taste; it has not been used for homicide. Oxalates have however been used to procure abortion by vaginal injection.

HOW DOES OXALIC ACID AFFECT THE HUMAN BODY?

Oxalic acid has both a local and systemic action on the body. By local action, i.e. the action on stomach and intestinal walls with which it comes in contact. By systemic effect i.e. remote effects on organs with which it does not really come in contact. Oxalic acid readily corrodes the mucus membrane of the digestive tract. Unlike corrosive mineral acids and alkalis, oxalates do not lose their poisonous properties when diluted. On the contrary, dilute solution of oxalates can cause grave systemic effects. Oxalic acid however rarely damages the skin.

As far as systemic effects are concerned, large doses of oxalic acid can cause death due to shock. Oxalates can readily combine with the Calcium ion in the body tissues, causing a precipitous fall in the level of ionized calcium. This can cause muscle irritability, tetany and convulsions and irregular action and slowing of the heart. Since all muscle cells in the body are very much dependent on calcium for their proper functioning and it includes heart muscle too.

WHAT ARE THE SIGNS AND SYMPTOMS OF OXALIC ACID POISONING?

The symptoms of the oxalic acid poisoning depend on the size and concentration of the dose. A large concentrated dose would kill with in a couple of hours by shock or hypocalcaemia (lowering of calcium levels in the blood).A large dilute dose would cause kidney failure. There is immediate sour or bitter taste associated with a burning sensation in the mouth, throat and food pipe because of the corrosive action of the oxalic acid. There is eructation (formal belching-emit wind noisily through the mouth), distension(Swell out by pressure) of abdomen, thirst, nausea and vomiting. The vomit has a coffee ground appearance because the oxalic acid badly corrodes the stomach walls. There may be bloody vomiting for the same reason. Finally shock supervenes and death occurs. Acute poisoning occurs when the moderately large dose is taken and in such cases, the person survives up to 48 hrs. The symptoms are muscle irritability, tenderness, tetany, convulsions, numbness (paralyzed) and tingling (feel a slight stinging) of the finer tips and legs, cardiac irregularity, slowing of the heart, ventricular fibrillation (irregular and fast beating of the ventricles of the hearts).Delayed poisoning may occur when a smaller dose is taken. This may lead to renal failure and uremia. Death occurs with in 5-14 days.

HOW EXACTLY DID THE DOCTOR MAKE OUT THAT IT WAS THE CASE OF OXALIC ACID POISONING?

The person poisoned with the oxalic acid runs down the strange streaks from the angles of the mouth. Due to corrosion, there is whitening or yellow-white discoloration of the lips, lining of the mouth and upper surface of the tongue. The lining of the stomach in oxalic acid poisoning is blackened by the production of acid haematin. There may be superficial corrosion. The stomach may contain fresh or altered blood. Furthermore crystals of calcium oxalate can be demonstrated in scrapings of the stomach mucosa. The kidneys of a person dying of oxalic acid poisoning are congested and swollen with oedema (accumulation of excess fluid in body tissues). The renal tubules even contain the oxalate crystals. Thus doctors may sure it is the case of oxalic acid poisoning.