Molecular Scissors

Anant Babu Marahatta (ananta037@gmail.com)
Tohoku Univ.
Japan

You might wonder to know that molecules work like a scissors in the presence of UV radiation. Such molecules are called “molecular scissors”. Here is an example of it in which an azobenzene moiety acts as a handle, a ferrocene unit acts as a pivot point and two phenyl groups act as the blades.

The conformational changes induced by cis-trans isomerization of the azobenzene switch, due to alternating irradiation with UV and visible light, are translated into a rotational movement around the metal center of the ferrocene unit.

Source: a text book about “Controlled Rotary Motion at the Molecular Level”

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

6.8 M Earthquake at the middle of the symposium

Anant Marahatta
Tohoku University
Sendai, Japan

The “Global Center of Excellence” (G-COE) program of Chemistry Department, Tohoku University, Japan had organized 4 days long int’l symposium from August 17 to 20, 2011. There were around 200 participants from the Graduate school of (Science, Life science, Pharmaceutical science and Engineering). Out of them around 20 were int’l delegates from Korea, Taiwan, Geneva, US, Germany, China, France and Canada. The symposium was divided into Oral and Poster sessions. Only selected candidates were asked to give oral presentation within 25 min. time interval.

It was the third day (August 19) of the symposium. All the events were running smoothly. All the participants were inside the auditorium hall. After the talk about “significance of metal-metal bonding to enhance the catalytic activity of binuclear complex” given by the guy from Germany, the chair person announced the 15 min coffee break. We all had a light snacks.

It was around 14.20, second half of the afternoon session was called and all the participants including Tohoku’s professors entered inside the hall. The guy from Korea was already ready for the presentation. He was from “Pohang University of Science and Technology” South Korea. He at first introduced his university and did not hesitate to tell about “how young is his university (less than 25 years, younger than him)”. His title was “Single Crystal to Single Crystal Post-Synthetic Modification via Framework Constituting Metal Ion exchange”. He was speaking about smart supramolecules with some wonderful videos and illustrations. Suddenly, the one story auditorium hall received quite strong jolt. The high tech. auditorium hall started to produce some noisy sounds (chuii, chuii….sound of glass wares). The speaker said “wow!!, what happened? ” Though this was even not became the news of the Japanese TV and radio channels, the int’l delegates were saying “Oh my god!! Is it called earthquake? What to do? Where are our host students…etc”. By chanting it, they left the hall and reached at the main entrance. The tremor was over within around 5 sec. At the middle of this scenario, the Japanese professors requested all to calm down by announcing not to scare, it’s not a big quake. The speaker started to talk after about 1 min disturbance. My eyes were looking towards the guys from US and Germany. They had made their face horrified. They were talking each other about that tremor. Anyway, the schedule of that day was completed successfully.

I was asked to follow them in excursion on 20 Aug. On that day, they shared about their initial thoughts raised (due to the March 11, 9 M quake) before finalizing the Tohoku’s invitation. If they were correct, they used to think “what to do if earthquake occurred at the middle of the symposium”.

What a coincidence? Isn’t it? They must have got nice experience.

How long will Japan be suffered by the energy crisis?

Anant Marahatta
Tohoku University
Sendai, Japan

One of the major consequences made by the giant tsunami after the scary earthquake occurred on March 11, 2011 is on the Fukushima based nuclear power plants of Japan and damaged the reactors very badly. Immediately after this, the world is forced to think about the nuclear energy consumption in the form of electric energy. Japan has already decided not to depend on nuclear energy but how? Several arguments are being raised.

The Japan government said, "We have a power shortage this year and we are calling for a 15 percent cut in electrical usage." Office buildings are being told to set their thermostats to 82 degrees Fahrenheit. Everywhere, escalators and elevators have been shut down. No Microwaves, ACs, Toasters etc. are allowed to run in the universities, food chain stores, supermarkets, department stores etc. Tohoku University, one of the nation’s high tech university, is asked to minimize the electricity usage as possible as it can. Even though all the lighting systems are set to control automatically, the university has even removed several tubes and fluorescent lamps. All the laboratories are asked to turn on the light after 5 pm if possible. Cafeteria helps this campaign even not tuning TV set.

The Environment Ministry advised workers to use gel sheets or eat foods that cool the body. It also suggested that employees limit overtime hours, work from home and take two weeks of vacation. Since, Japanese are very much hard working peoples and they usually bring lunch packs prepared by them and supposed to use the microwaves present at their offices. But due to the energy crisis, several Japanese are forced to eat without heating. The matter is also concerned about their health.

This sort of campaign is not only for the summer but is going to be a big event to change the way of life in Japan and people's lifestyles. The push to save energy in Japan comes from this Nuclear energy crisis.
How long will Japan be suffered by this crisis?

Molecular Rotor Measures Viscosity of Live Cells

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

Introduction:
Viscosity is one of the major parameters determining the diffusion rate of species in condensed media. In bio-systems, changes in viscosity have been linked to disease and malfunction at the cellular level. These perturbations are caused by changes in mobility of chemicals within the cell, influencing signaling and transport and the efficiency of bimolecular processes.

Observation:

Fluorescence measurements of 1 made in methanol/glycerol mixtures of different viscosities shows that the fluorescence quantum yield increases dramatically with increasing solvent viscosity.The observed increase in fluorescence intensity is consistent with the restricted rotation of the phenyl group in the medium of high viscosity. The rates of radiative and nonradiative decays have been calculated from the measured fluorescence lifetimes and quantum yields. From these results, it has been concluded that, for 1, the nonradiative decay rate increases with decreasing viscosity, and the radiative decay rate remains approximately constant. Thus 1 is truly a molecular rotor which displays both fluorescence intensity and lifetime sensitivity to viscosity of the environment.

For detail, readers are requested to go through J.AM.CHEM.SOC. 2008,130, 6672-6673 if interested.

We must learn “How to love nation” from Japanese devotement

Anant Marahatta
Tohoku Univ.
Japan (ananta037@gmail.com)

After the scary and massive catastrophe on March, 2011 in northeastern Japan, several consequences raised in the world. Germany has already announced to shut down all the nuclear power plants within a decade; China has stopped to increase the number of power plants until the full safety measures are installed into already existed plants and the world’s super power USA has also checked the safety precautions in all the power plants including the biggest one located in the danger zone at California. Experts have already warned the US government and asked for installing safety measures especially in thhe California based reactors.

The victimized country, Japan, has already suspended around 40 reactors out of 50 for close inspection. It has decided to build 20m high seawalls around the reactors located in the danger zones to block them from giant tsunami. The biggest nuclear energy crisis forces to reduce the office hours of world’s largest manufacturers like Sony, Canon, Toyota, Honda, Toshiba and several others. Almost all the companies, universities and many research institutes, supermarket complexes, food-chain stores etc. are asked to minimize the electricity consumption. For it, all Japanese are doing their best by even removing their kitchen wares etc. Most of the chain stores and restaurants are using the play cards holding “Let’s do our level best. Never give up, Tohoku. Let’s build new Japan” at their main entrance. This is a very praiseworthy dedication of the citizens towards their nation.

Since the northeastern part of Japan has been jolting by several aftershocks. Almost every day, the skyscrapers are shaken 3-4 times in an average. After the strongest 9 M tremor on March 11, more than 5 jolts are already categorized into the strong range. They all cross 6 M in strength. The local and central government announce the tsunami warnings immediately after the strong earthquakes. But every Japanese is ready to challenge this horrified situation and gives his/her full support to the government for renovation.

We must learn “How to love nation” from their devotement.

Mixi vs. Facebook in Japan

Mixi, which was launched in February 2004, is the biggest social networking site in Japan. It is growing rapidly. The site has already more than 5 million users. Around 80% of those users are reported as “active”. The name “Mixi” supposedly refers to the fact that “I” can “mix” with other users. To join Mixi, you need to be invited by an existing member. The Mixi URL assigned to you contains a unique user number beginning at 1 and increased sequentially, it’s easy to tell how recently a user joined.

On the other hand, one year since Facebook was introduced to Japanese market; it is obvious that Facebook is not popular at all in Japan, while it is very successful in most of other countries.
Why Facebook is not popular in Japan?

International Collaboration in Science

Anant Marahatta
Doctoral Student (Chemistry)
Tohoku University
Japan
(ananta037@gmail.com)
(Relevant to my collaboration with Germany)

The general meaning of an “international collaboration in science” is explained by these advanced words: global science, global networks, global co-authorships, global interaction, global conference, global sharing, and spreading global hand for helping on different disciplines of science and technologies etc.

Though there is no political institution organizing the sciences on an international level, a self-organized, global network had formed in the late 20th century. It has been found that international collaborations are being doubled from 1990 to 2005. While collaborative authorships within nations have also risen.

This is the century of getting revolution in the world due to the different fields of sciences. If the researchers and scientists of any well developed countries have proudly announced that they are eligible enough to carry out any sorts of revolutionary changes in the field of science, they have initiated to deteriorate their countries themselves. So for getting several supports and ideas, all the countries if possible must be the member of the international collaboration. Any one can analyze that, international collaboration improves all the countries of the world by applying a range of tools including social network analysis and factor analysis, to expose the network.

There has been a rapidly growing literature discussing the increase in international linkages in science. Authors have been approaching the questions from three perspectives: 1) scientific analysis of the increase in the interconnectedness. 2) Social sciences analysis of collaboration in general and international linkages in particular and 3) policy analysis of the implications of linkages for funding and outcomes. The increase in investment in research and development from governments and non-governmental organizations (such as the World Bank) is for using science as a tool to aid development and for contributing to the diffusion of capacity into the collaborating countries. Scientific collaboration may lead to a range of outcomes such as publication of co-authored articles is one of these outputs.

Collaboration in the technology sector refers to a wide variety of tools that enable groups of people to work together. Collaboration encompasses both asynchronous and synchronous methods of communication and serves as an umbrella-term for a wide variety of software packages. Perhaps the most commonly associated form of synchronous collaboration is web conference using tools such as WebEX or Microsoft Live Meeting but the term can easily be applied to instant messaging as well.

According to the available information, at the global level, the network of interactions is shown to be very strong and highly interconnected. Above figure illustrates the association of all the countries of the world in 2000. The main point is that science is a highly interconnected network, with a dense core and a number of periphery countries.

Thus international collaboration seems one of the important tools for making revolutionary change in the world by developing and introducing the multidisciplinary fields.

An argue with CalTech. Chemistry Grad.

Anant Babu Marahatta
Ph.D. student
Tohoku University
(ananta037@gmail.com)

Theme of this article is: “Knowing English is not enough to present Chemistry but one must know Chemistry in English.”
(some thing about Amphidynamic Crystal)

In order to strengthen and enhance the education and research functions of graduate schools of Japanese universities, Ministry of Education, Culture, Sports, Science and Technology (MEXT) introduced the “Global COE (Centers of Excellence) Program in some of the top universities of Japan on 2002. Another main objective is to foster highly creative young researchers who will become world’s leaders in their respective fields through experiencing and practicing research of the highest world standard.Molecular complex Chemistry is one of the fields covered by the GCOE.

Being one of the Chemistry doctoral students of the nation’s high tech. university [Tohoku University] with the nation’s largest chemistry department, I also belong to the network of GCOE program. One of the annual events of the Tohoku Univ. sponsored by this program is to provide a chance for the doctoral students to lead a week long Int’l conference. Including the key speakers and the chairpersons of each section, every participant must be the Ph.D. candidate of Chemistry. The professors only act as a facilitator. He/she never interferes the students’ leadership.

One of the key speakers of the program was from California institute of Technology (CalTech). He was presenting his research work related to coordination chemistry and was chanting the effects of ligands to synthesize the Supramolecules with the metal ions. He was also claiming that his research output is fabulous and praiseworthy. One of the major parts of that molecule was the phenylene ring encapsulated into the cage that can create enough free space for undergoing smooth rotation. He was calling this ring as a “spacer” because the surrounding spokes can control the space around the phenylene. Any way, we around 200 students were listening his interesting speech. Being a chair person of this section, I was feeling that he was pretending some hidden facts behind his research area even though he was very bold and smart guy. He presented well and wrapped his talk by thanking his collaborators.

Then, it’s my time to open the floor for the discussion. I asked the participants for the comments and the queries. Some students asked about the effects of the coordinating efficiency of ligands’ and some other related stuffs. A Tohoku professor was suggesting him about the possibility of changing properties of that supramolecule by changing central metal ions.

Before announcing the next speaker, I raised my query about that spacer so called phenylene ring. I am/ was very much familiar with such molecules having central rotating part encased into the static part. I also knew that such type of molecular crystals with rotating part and static part in a same molecule are called Amphidynamic crystal, but this is a very new type which I encountered while reading a paper published on 2002. My question was “does your molecular crystal belong to Amphidynamic crystal?” But that guy did not understand the last term and instead asked me for the clarification. I just clarified him by reminding the term “Amphibia” and then called the next speaker.

Immediately after this session, the same guy approached and said to me “Knowing English is not enough to present chemistry but one must know chemistry in English.” Excellent understanding!!!! isn’t it?

Small Science Vs. Large Science

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

Science carried out by individuals or small teams of investigators is said to be “small science” and the science carried out for large scientific data gathering programs is said to be “large science”.

Research done by individuals or small teams of investigators has been crucial for many of the important discoveries made in all branches of science. The individual or small group research work has been the first step for bringing up the revolutionary changes in the world. Such type of research facilitates the researcher to concentrate in the particular problem and hence increases the thinking level of the researchers as well. It has been found that the research work performed by the individuals or by the small teams is more accurate and reproducible. Since every branch of science needs accuracy which in fact catalyses the rate of tailoring and building up the new inventions and discoveries. These discoveries provide the fundamental basis for the application of scientific knowledge to national economic and societal goals.

Small science helps to define the goals and directions of large scientific data gathering projects [so called large science]. In turn, these data feed and are often best synthesized and interpreted by the long-term efforts of the small science community. In small science, the rate of manipulation of data is almost nil due to the accuracy which perfectly orients into the solutions of the problems.

Are Carbon Nanotubes the Future of VLSI Interconnections?

Original paper is published by-
K. Banerjee and N. Srivastava
University of California


Summarised by Anant

What is VLSI?
• Very-large-scale integration (VLSI) is the process of creating integrated circuits by combining thousands of transistor-based circuits into a single chip.
• VLSI began in the 1970s when complex semiconductor and communication technologies were being developed. The microprocessor is a VLSI device.
New wiring solutions…!
• Metallic carbon nanotubes (CNTs) are promising candidates that can potentially address the challenges faced by copper and thereby extend the lifetime of electrical interconnects.
• carbon nanotubes (CNTs) have aroused a tremendous amount of interest in their use as building blocks of future integrated circuits due to their outstanding electrical properties

CNT based interconnects can potentially offer significant advantages over copper.
• CNTs exhibit extraordinary strength and unique electrical properties are efficient conductors of heat and are metallic in nature.
•SWCNTs are a very important variety of CNT because they exhibit important electric properties that are not shared by MWCNTs. The remarkable properties of SWCNTs stem from the symmetry and unusual electronic structure of grapheme [one atom thick sheet of graphite].

∙An isolated CNT can carry current densities in excess of 1010 A/cm2 without any signs of
damage even at an elevated temperature of 250 0C. However, the high resistance associated with an isolated CNT (greater than 6.45 KΩ) necessitates the use of a bundle (rope) of CNTs conducting current in parallel to form an interconnection. CNT bundle interconnects have superior performance compared to Cu.

∙For short CNT bundle with small length (L), [especially for L < λCNT], resistance is higher than that of a Cu interconnect because the large contact resistance dominates the overall CNT resistance. However, for long interconnect lengths; i.e. long CNT bundle interconnects have smaller resistance than their Cu counterparts [ L>λCNT].
∙The interconnect delay can be reduced considerably by using densely packed CNT bundle interconnects, so that large power savings can be achieved. CNT bundle interconnects can reduce intermediate level interconnect delay by more than 60% due to their lower resistance.

Reliability and Thermal Analysis
∙Due to strong sp2 bonding, carbon nanotubes are much less susceptible to electro-migration (EM) problems [that plague copper interconnects] and can carry very high current densities. Metallic single-walled CNT bundles have been shown to be able to carry extremely high current densities of the order of 109 A/cm2. Cu interconnects = 106 A/cm2 due to EM.
∙A 100 x 50 nm2 cross-section Cu interconnect can carry current up to 50 μA, whereas a 1 nm diameter CNT can carry upto 20-25 uA current. Hence, from a reliability perspective, a few CNTs are enough to match the current carrying capacity of a typical Cu interconnect.
However, the need to reduce interconnect resistance (and hence delay) makes it necessary to pack several thousands of CNTs in a bundle.
Conclusion
∙There is no any experimental work or theoretical analysis yet about the nature of electromagnetic interactions between non-isolated (or tangled) nanotubes. So the authors have not considered their mutual effect during conduction, however they highlighted that this challengeable investigation should be done before using them in a circuit though these challenges are not expected to cause any fundamental problems.

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.

Practical approaches of Quantum Chemistry [part 4] : Semi-empirical Quantum Chemistry

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

(This article is intended to introduce the semi-empirical techniques of Quantum chemistry) I am a part of it and currently mastering on “Density Functional Tight Binding (DFTB) approximation with and without Gaussian” by implementing them to investigate the rotational dynamics of the crystalline “Molecular Gyroscope”.

(Interested fellows are suggested to read Part 1 to part 3 of this article before proceeding it. And if necessary, you are reminded to consult the article “Computational Chemistry” archived herewith.)

Unlike the ab initio techniques [part 3] which are based entirely on the solution of the Schrödinger equations, semi-empirical techniques employ experimental results. In order to simplify the approximation, such techniques use parameters derived from the experimental data to the Schrödinger equation.

Basically, semiempirical techniques attempt to address the limitations like slow speed and low accuracy by omitting or parameterizing certain integrals based on experimental data, such as ionization energies of atoms, or dipole moments of molecules. As a result, semi-empirical methods are very fast, computationally inexpensive and applicable to very, very large molecules, and may give accurate results. However, accuracy of such methods lacks consistency on many systems.

Following animation explains about the action of the Quantum Molecular Dynamics Simulations of Molecules on a Metal Surface.



In computational chemistry, consideration of the more accurate methods (ab initio techniques) to study the molecular systems consisting thousands of atoms is impossible. The same is valid well to the case of crystalline solid even bearing medium sized molecules due to the inclusion of periodic boundary condition (PBC). In such cases, semi-empirical techniques are the good option. Similarly, in order to obtain the starting structure for an ab initio calculations (eg. Hartree-Fock, Density functional theory etc.), one might run semi-empirical calculations. However, the limitations of them must be considered before selecting the proper one and the level of accuracy depends on the system to be studied.

Semi-empirical methods may only be used for systems where parameters have been developed for all of their component atoms.　In addition to this, types of problems on which they do not perform well include hydrogen bonding, transition structures, van der Waals type interactions and so on. AM1 (Austin Model 1), AM1* (extended AM1), PM3 (Parameterized Model number 3) and MNDO (Modified Neglect of Differential Overlap) are the best known semi-empirical methods which can be run using Gaussian scheme.

The very recent approach “DFTB technique” especially focused to the solid state science has become a very popular for exploring the solid state dynamics computationally. I am also a part of it and mastering on “DFTB with and without Gaussian” by implementing them to investigate the rotational dynamics of the crystalline “Molecular Gyroscope”.

References:
http://www.chm.bris.ac.uk/motm/pentacene/pentacene.htm

Practical approaches of Quantum Chemistry [part 3] : Ab initio Quantum Chemistry

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

(This article is intended to introduce an ab initio technique of Quantum chemistry)

(Interested fellows are suggested to read Part 1 & part 2 of this article before proceeding it. And if necessary, you are reminded to consult the article “Computational Chemistry” archived herewith.)

Basically, the Computational quantum chemistry methods range from highly accurate to very approximate techniques. Ab initio [lat.word-at the beginning] techniques are based entirely on the solution of the Schrödinger equations unlike the empirical or semi-empirical techniques [will be clarified on part 4] which employ experimental results.

More specifically, most ab initio calculations are based on the Born–Oppenheimer approximation, which greatly simplifies the Schrödinger equation by freezing the nuclei in place during the calculation. Such methods converge to the exact solution of the underlying Schrödinger equations by reducing the number of approximations. So the computational cost is the very serious matter. They often take enormous amounts of computer time, memory, and disk space.

For example, the Hartree–Fock (HF) method, a very reasonable ab initio model of quantum chemistry, which does not include full treatment of the effects of electron correlation (the energy contributions arising from electrons interacting with one another) scales as N 4 (where N is the number of basis functions used to create the molecular orbitals) – i.e. a calculation twice as big takes 16 times as long to complete. Density Functional Theory (DFT), which computes electron correlation via general functional of the electron density, scale in a similar manner to HF. However, it is more expensive than equivalent HF calculation due to the introduction of the concept of electron density interactions. Similarly, Moller-Plesset (MPn) Perturbation theories scale as: MP2- N5, MP4 - N6 etc. MP2 model is one of the least expensive ways to improve the HF model and was the first correlation method applied to chemistry. The geometries optimized by it are usually quite accurate.

The following animation illustrates an action of the ab initio technique of Quantum chemistry which explains the double proton transfer in Watson-Crick AT (A=Adenine, T =Thymine) base-pair model of DNA.


Usually, considering the Born–Oppenheimer approximation in order to simplify the Schrödinger equations is okay in ground electronic state which assumes independent motions of electrons and nuclei [but it is not really true]. In practice, however, it is impossible to eliminate all the difficulties arise. Thus, to minimize the errors produced, the empirical or semi-empirical calculations help the quantum/computational chemists by keeping the calculations in track.

……………to be continued………….

The general concept of the empirical or semi-empirical techniques will be posted on part 4.

Reference:
http://www.scidacreview.org/0902/html/qsiman.html

Practical approaches of Quantum chemistry [part 2]

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 before proceeding it).

In order to assist solving Schrödinger equations of the multi electron systems [referred as n body problems], Several Computers / Supercomputers with different mathematical software packages have been developed by applying the results of the theoretical chemistry [refer to an article “Computational chemistry” archived herewith].

By using the solution of the Schrödinger equations, these calculating packages generate information such as properties of molecules and simulate the experimental results. For instance, we can calculate:

• electronic structure determinations [(i.e. the expected positions of the constituent atoms)]
• dipoles and higher multipole moments
• absolute and relative (interaction) energies
• geometry optimizations [the lowest energy and the most stable form]
• frequency calculations [ vibrational and other spectroscopic quantities]

• migrating mechanisms of the active groups
• Dynamics of the molecular rotor, gyroscope, brake, motor etc.
• transition structures
• protein calculations

Here is the video of chaperonin [example of protein] transition from open to closed conformation *.
• reaction mechanisms
• cross sections for collision with other particles
• electron and charge distributions
• potential energy surfaces (PES) **

• rate constants for chemical re actions (kinetics)
• Thermodynamic calculations- heat of reactions, energy of activation etc.
• NMR Calculations etc.

The Computational quantum chemistry methods which range from highly accurate to very approximate techniques will be clarified on part 3.

References:

*Booth et al., 2008 - www.nature.com
**Johnson et al., Chemical & Engineering News (vol.80, No. 2, 2002)

Valentine conversations between HCl and NaOH

(Dedicated to all the valentine couples)

Anant Babu Marahatta
Ph.D. student in Chemistry
Tohoku university
Japan

It is well known that both HCl and NaOH is strong acid and strong base respectively. During their conversations, they themselves confuse each other and request to the phenolphthalein (hph) for checking the neutralization. Here are their detail conversations:

HCl- Hi, how are you today?

NaOH- Hello!! I am ok, what about you? It’s so cold, isn’t it?

HCl- Yeah, you are right. It’s snowing too. The nature also supports the valentine couple like us.

NaOH- I agree. By the way, what’s your plan today? May I know?

HCl- Sure!! I am planning to react with strong base like you in the presence of hph even though we will be completely neutralized /destroyed at the end point.

NaOH- Showing chemical reaction is not a big deal but among us we have to be careful while acting as a titrant and titrand. I mean, who must be kept into the burette?

HCl- Yeah, that’s the good point. But it’s universally accepted that you must be pipetted out and kept into the receiver [conical flask] and I must be poured drop wise from the burette till the pink color of hph created by your OH ion disappeared.You must be shaked uniformly for the vigorous reaction.

NaOH- What do you think about me? I am not like NH4OH. I am as strong as you. One mole [Avogadro’s number] of you can be easily neutralized by one mole of me. Then why should I be kept into the receiver?

HCl- In terms of strength, I agree with your point. But you know, “Acid is acid”. We have to follow the scientific evidences otherwise there will be problematic during complete neutralization processing. And we must use hph properly so that it helps us to detect complete neutralization. It only gives the pink color dropped upon you which can be traced during reaction.

NaOH- Ok, I agree. But if I was made in China, the hph would not be the perfect indicator and I must have been kept into the burette. Any way, it’s out of our discussion.

HCl- In such case, methyl orange could be the best indicator but it is a rare case, however, valid to somebody else. Any way, we are at the end of our discussion now. Good luck!!

-------------Happy Valentine day!!!!-------------

Practical approaches of Quantum chemistry [part 1]

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


Even the high school/senior high school students are acquainted with the “Bohr model” which says electrons are "particles" that revolve around the nucleus in orbits and are quantized so that they can show absorption and emission phenomena.

It is a primitive model of the hydrogen atom though it is verified later after the introduction of the quantum mechanical concept.This model strongly supports the existence of the “Covalent Bond Theory [CBT]” and the “Valence Shell Electron Pair Repulsion theory [VSEPR]” of bonding between the atoms.

The “Quantum model” on the other hand, says that electrons are not particles, but have wavelike characteristics just like photons and their wave length can be explained by the “de Broglie's equation”. In order to calculate the various properties of the electrons, Quantum model developed a famous equation by considering the “de Broglie concept” which is named as a Schrödinger’s equations and appeared as a stepping stone of the Quantum chemistry / Physics. I am sure that most of the chemistry undergrad./ grad. students are encountered with these two forms of Schrödinger equations:
Ĥ ψ = E ψ & Ĥ ψ = iħ (δ/ δt)ψ (time independent and time dependent respectively). These equations model the atoms and molecules with mathematics.

It is well-known for the physical chemists that the quantum n-body problem [many electrons atoms or molecules, beyond Helium] cannot be solved analytically. However, the case for Hydrogen molecular ion [H2+ = 1 electron system] is relatively easy and the results normally agree with the information obtained by the chemical experiments. By considering such agreements, the necessity of the Quantum chemistry arises in order to verify and explore the chemistry of the micro particles which act as a foundation of the matter. The following movie has highlighted about the “Quantum chemistry in action” which explains the equilibrium process between ionized water and hydroxyl radical [OH.] plus hydronium ion [H3O+].



The detailed applications and the general way of simplifying Schrödinger equations will be posted on the days to come. Interested fellows are suggested to visit the site time to time.
---------------------To be continued-----------------------

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.

Supramolecule: Leader of the Nano-world

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

Tailoring “Molecular machine” on the atomic or molecular scale is the current subject of interest in the nano-world. In order to explore the molecular architectures behind it, the first and the foremost motivation came by mimicking the biological systems such as enzymes/catalysts/promoters along with some mechanical devices which leads to supramolecules.

The literal meaning of the supramolecule is “beyond the molecule” and the area of chemistry which mainly concentrates on such system is Supramolecular chemistry. It refers to that sort of molecular system which is made up of a distinct number [more than one] of molecular assemblies. Terms such as molecular self-assembly (1D, 2D & 3D), molecular hierarchy, molecular machine, host-guest chemistry, nanoscience are often associated with this area.

The consideration of the intermolecular [between molecules] interactions and the chemistry involved into it, rather than intramolecular [within molecule], is the major objective of the supramolecular chemistry. In this area, molecule acts as a building block unlike in traditional molecular chemistry [where atom acts as a building block]. In molecular chemistry, the binding forces between the atoms are covalent and ionic. In contrast, the non-covalent interactions such as hydrogen-bonding, dipole-dipole and dipole-quadrupole interactions, van der Waal forces and hydrophilic-hydrophobic interaction are the binding forces which hold the supramolecular assembly together. The following video highlights the procedure of molecules clustering in nanometer range.

“Top Down” and “Bottom Up” approaches in chemistry

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

Who are chemists? Most of you definitely agree with me if I said “Chemists are scientists trained in the field of Chemistry and describe the properties of the matter on the level of molecules and their component atoms.” But if I said “Chemists are ‘tailor’ who make the world fashionable by implementing “top down” and “bottom up” approaches” in chemistry, most of you get confused.

Even though “Top down” and “Bottom up” approaches of chemistry were first applied to the field of nanotechnology in 1989, these terms are not so much familiar among the chemists like us. Thus this article is intended to describe the principles and the perspectives of these approaches which have grown exponentially in the last few decades.

To describe the “top down” approach, let us consider a macroscopic system and break down into the several subsystems and then start analyzing these subsystems and refine them in greater detail until the entire composition is reduced to their base elements. It can be clarified by saying that “top down” is the destructive approach to go insight into the fundamental level [going top to down] and adapt their features to make them functional at a smaller scale. Though it is a traditional way, Chemists sometimes consider the hypothesis which starts at the top with the most general concepts and works down through less general concepts to the most specific details.

On the other hand, the “bottom up” technique is based on the principle of starting from the fundamental [bottom] parts and assembled [going up] them to obtain the desired more complex system [going bottom to up]. Thus, it is the constructive approach to stitch the fundamental parts together and develop the new inventions.

In chemistry, the “bottom up” approach makes the use of atomic/molecular components and assembled them to develop the potential nano-devices. This approach is already implemented even for interconnecting the multiwalled carbon nanotubes into the multilevel interconnects (silicon integrated-circuit) with higher current conducting capacity.

Macroscopic and Microscopic [molecular] Gyroscopes

Anant Babu Marahatta
Ph.D. student in Chemistry
Tohoku University, Japan

Fabricating the nano devices on an atomic and molecular scale (referred as Molecular machine) is the major aspect of the Nanotechnology (sometimes shortened to “nanotech”). One of the recent approaches of the nanotech is “molecular self-assembly” which is governed by the concept “can we directly control matter on the atomic scale?” By considering this sort of challenging prospect, several gyroscopes [as shown in fig.] like molecules have been designing / synthesizing.

The similarities between the macroscopic gyroscope and the molecular gyroscope are solely based on their mechanical parts assembled. The macroscopic gyroscope which is used in aircrafts, ships to route them, contain the mechanical parts like spinning axis-axle, rotating part-rotor and the static framework-stator [gimbal] to uphold the rotor by conserving angular momentum.

Just like this, the molecular gyroscope also possesses the similar fundamental mechanical parts which are labeled in the figure. The rotational dynamics of the rotator enclosed into the case of the stator is controlled by the chemistry of the later. The animated view is included herewith.