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.

DEATH BY POTASSIUM PERMANGANATE [KMnO4]

ANANT BABU MARAHATTA
Ph.D. student
Tohoku University, Japan

Potassium permanganate is not a new chemical for the chemists as well as for other scientists. It is generally used in even very simple lab. It is a crystalline, colored substance and soluble in water. Its salts are normally stable in crystalline form but Zinc permanganate can become explosive. In fact, storing it in tightly stopper bottles is highly dangerous.

KMnO4 Solution

The color of the solution of KMnO4 is differed depending upon its concentration. If the concentration is about one part per million (1 PPm), the solution has a faint pink color. When the concentration is one part in 76000 (65mg/4.5dm3), the fluid becomes purple. Because of its color, solution has been used for staining purpose too. Those who use the chemical as a stain for flooring and woodwork and work with the concentrated solution must exercise with great care.

Have you ever been shaken by 7.2 M earthquake ? my experience

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

(I am one of the eyewitnesses of the "Sendai catastrophe" occured on March 11, 2011. That time, Sendai was shaken by 9 M earthquake and hit by a giant tsunami which killed ~30,000 people.)

Japan is well known for having a large number of earthquakes though the largest recorded earthquake in the world was a magnitude of 9.5 in Chile on May 22, 1960. According to the tectonic theory of Geology, earthquakes are most frequent where two or more plates meet. The Japanese islands [archipelago in Geography] too are located in an area where several continental and oceanic plates meet which causes the frequent earthquakes. So the meaning of it can further be clarified by saying “Japan sits on the ‘Rings of Fire’"
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I have been living in Sendai, Miyagi prefecture, Japan since 2007 October. In the “Frontiers of Science” course, I was taught about the “Statistical probability theory to predict the percentage of earthquake occurrence” especially in the Miyagi prefecture. The lecture was concluded by disseminating “99% earthquake probability in Miyagi prefecture”. Till that moment, I did not know about this much percentage of probabilities of the temporal occurrence at my residing area; I just happened to know that I will be shaken any time. On the same week, I was asked to attend the training/preparatory session organized by the “Disaster unit” of the local government of the mentioned prefecture. From that moment, I was mentally ready to be shaken by the tremor any time.

It was the year of 2008, June 14, Saturday, 9.30AM JST. All the int’l students were inside the dormitories of “Tohoku University int’l house” and enjoying their weekend. I was also lying on the bed of room 905 located on the 9th floor of the 12 story building. Suddenly, this skyscraper received strong tremble. The intensity of the quake was comparable to that of the “late Michael Jackson’s hip” during his performance. As the building became the branch of the tree “being shaken by monkey”, we people inside the dorm became the ripe fruits being the Monkey’s trial-target. I happened to look outside the window during the quake and noticed that all the parked vehicles were hopping on their seat.Here is the sample video of 6.8 M earthquake occured on July 24, 2008.

As all the people were trained, immediately after the quake, about 300 people gathered at the nearby designated refugee area holding their passport and a bottle of mineral water. The condition of the ladies was pathetic who were gathered there by wrapping their body with a towel. Some were saying “Oh my god!!! What a terrible shake, it’s my first time”, some were shouting “Allah, you saved us!!!” and several were hugging by congratulating each other and saying that “we got new life!!”. Several Chinese and Koreans were shouting in their mother language with horrified face.
Almost all including myself remained at the lobby around 3 hours by chatting about the “aftershock” which was also pretty powerful. You can imagine that how strong the temblor was? The frequency of the shaking in Miyagi prefecture is 6/month in average. The magnitude of around 5 is even excluded by the local media. It has become habitual now.

A short introduction on: Carbon nano tube and the reaction dynamics inside it-Part 2

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

A carbon nanotube may be considered as a hollow cylinder formed by rolling up a graphite sheet. The chirality and diameter of a carbon nanotube is uniquely defined by a vector (n, m), na + mb; where a and b denote the unit vectors of the hexagonal lattice and n and m are integers.

Fig ; 2.  A unit cell of a system of twelve carbon nano tubes and 1540 water molecules.

A short introduction on: Carbon nano tube and the reaction dynamics inside it-Part 1

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

This is the age of science and technology. In the world, many technological devices have been used and constructed which are the blessings of the science. In the field of science, nanotechnology plays crucial role for the innovation of several nano size devices from the nano materials either by modifying their properties or by using them directly.

Generally, nanotechnology is defined as the engineering of functional systems at the molecular scale. In recent years, properties and structures of nano size materials have attracted many people's attention. Their unique properties and small dimensionality give very promising future for various potential applications. Out of the several nano materials, the history of the newly discovered allotropic forms of carbon called “Fullerene” is the recent one. Significant progress has been made toward the understanding of the properties and structures of nano tubes.

FIG.1 [a] A hexagonal graphite sheet to create a zig-zag or armchair nanotube by rolling up along or y axis; [b] A graphite sheet with active –COOH groups; [c] An armchair SWNT with a diameter of 8.15 Å; [d] A hydrophilic SWNT with –COOH groups having an inner diameter of 8.40 Å.

DEATH BY COMMON SALT [NaCl]

Anant Babu Marahatta
Ph.D.student in Chemistry
Department of chemistry, 
Tohoku University, Sendai,Japan

There is no doubt that common salt or sodium chloride (NaCl) is indeed essential to all life. It is the basic milieu of mammals. It occurs as colorless cubic crystals or as white crystalline powder. It is available at everyone’s home as well as in laboratory. No one suspect that it is a poison. One who studied biochemistry must have learnt that salt is a poison and can be used to kill infants. It is indeed a rather safe poison because one doesn’t need to buy anything when salt is administered in larger quantities than required, it can cause death too.

One teaspoonful of salt weighs about 5gms. Normal uptake by adults is about 5 to 15gm daily or about 1-3 teaspoonfuls. Children consume less salt is even necessary for normal growth. The sodium needed for growth is 0.5 mEq/kg from birth to 3 months of age, which decreases to 0.1mEq/kg at 6 months. The average content of sodium in human milk is 7mEq/L and that in cow milk is 21mEq/L.

Since, chemists and biochemists find it easier to talk in terms of equivalent weights. Equivalent weights are actually measures of the characteristic proportions in which the given elements combine .As we all know that 1mEq.sodium equals 23 mg and that of NaCl equals 58.5mg, and 1mEq would be equal to 1/1000 Equivalent weight. Thus, when one says that sodium needed for growth is 0.5 mEq/kg from birth to three months of age; he simply means that for every kg of baby’s weight, 0.5mEq of sodium is needed. Thus if the infant weighs, say, 4kg he would need 4 x 0.5 or about 2mEq of sodium. Since 1mEq of sodium is 23 mg, it would mean that the infant would need about 46mg of sodium daily. This much sodium would be available from about 117 mg of salt. Similarly we can convert other values given above.

Most people will not believe that common salt is a deadly poison. The only difference between this and other commonly known poisons is that one has to administer rather large quantities. One or two tea spoonfuls of salt would not kill an adult but can easily kill a 6 month old baby. About 40 teaspoons of common salt would kill an adult human being too. The toxic oral dose of salt is 0.5 to 1.0 gm/kg. For a 70 kg man this amount is about 35-70 gm. That means if an adult consumes about 70 gm of salt [or about 14 teaspoons], he would be severely poisoned. The estimated fatal amount, i.e. amount sufficient to kill, is about 1 to 3 gm /kg [remember that weight of one teaspoon common salt is about 5 gm.]. This amounts to about 70 to 210 gm. [about 40 teaspoonfuls] of salt for a 70 kg man.

Interestingly, the Chinese used saturated salt solution for suicide. Salt intoxication and death have occurred when it is used to induce vomiting as well. When some body has consumed a poison, it is imperative to remove as much poison from his stomach as possible. One of the best ways to do this is to make the person vomit. It has been known from the ancient times that a strong solution of common salt induces vomiting and that is why for centuries, it was a favorite method of doctors to induce vomiting for poisoned patients. But now it is known that saturated solution of salt itself can cause salt poisoning, so it is rarely used these days. Thus accidental poisoning and death takes place due to the common salt if the person consuming less harmful poison is induced vomiting by injecting saturated salt solution orally. This is the most common accident frequently observed in the society.

THUS, THIS IS OUR WORK TO MAKE THE SOCIETY AWARE ABOUT THE SALT POISONING. SALT SOLUTION INFACT INDUCES VOMITTING BUT ITS HIGH CONCENTRATION ACTS AS FATAL.


DOCTORAL EVIDENCES OF COMMON SALT POISONING

The stomach contents and the blood analysis of the person poisoned by common salt tell the doctor that salt has been administered to the patient. While examining the brain tissue under the microscope, it has been found the capillaries of the brain are damaged and they are full of blood. There are innumerable bleeding points- technically known as hemorrhages in the brain. Many venous channels of the brain called dural sinuses are blocked. All these findings are strongly in favor of salt poisoning.

Molecular Motors/Rotors/Brakes and Gyroscopes

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

One of the current aspects of chemistry is being a watch-dog of the nanoworld. I wonder how many of you are familiar with the microscopic machinery terms used in Chemistry that concentrates especially in the designation of the Molecular Machine. Some of them are Molecular motors, Molecular Rotors, Molecular Brakes, and Molecular Gyroscopes. You may find several of them by consulting the literatures/text books published so far.

I am sure that all of you [for the beginners only] are familiar with the “molecules” and the macroscopic devices such as Motors or Rotors or Brakes or Gyroscopes. But I think, very few of us [including chemists] have got the concrete knowledge about their applications in the nanoworld or in the Molecular machinery. I, a blog writer of “Nepa Chem”, would like to assure our fellows/readers that the detail explanation with the proper schematic illustrations of all the mentioned molecular machinery devices will be posted in the days to come. For now, let me define them very shortly.

Molecular motors, Molecular Rotors, Molecular Brakes, and Molecular Gyroscopes, all these names are derived from their macroscopic analogues. Synthetic/computational chemists have already synthesized/designed the molecules or supra molecules which resembled mechanically to these macroscopic devices. Thus in this stage, you readers are about to catch the main point. I am sure that you all are thinking like this way; if the synthesized molecules/supra molecules resembled mechanically to that of the macroscopic rotating devices, then these molecules are called Molecular rotors. If the synthesized molecules/supra molecules resembled to that of the macroscopic motors [which contain rotors too, complexity arises], then these molecules are called Molecular motors.

The macroscopic Gyroscopes which are used in aircrafts, ships to route them, contain the mechanical parts like rotating axis-axle, rotating part-rotor and the static framework-stator to uphold the rotor by conserving angular momentum. Hurray!!!!The meaning of the molecular Gyroscope is also clarified!!! Do you agree? If not, your level of understanding is not the worst!!!! …lol….The molecules/supra molecules resembled to those of the Macroscopic Gyroscopes mechanically are called Molecular Gyroscopes. You must be very happy!!!!! Aren’t you? Because whatever you were thinking is correct!!!!

The case of the molecular brake is different. You can imagine yourself!!!! Can you? Do you have driving license? Do you brake [be careful, not break, funny writer, isn’t it?] your car? If not, come here in Japan, I rent a TOYOTA car. Anyway, a “Brake” is a device for slowing or stopping the motion. Wow! So sad!!! There must be some parts in motion before applying brake, unlike in rotors/motors and gyroscopes. Thus the challenging part for the computational chemists/synthetic chemists is that the same molecule must possess dynamic parts as well as brake.

According to my experience, some atoms of the molecules, during the rapid motion of the dynamic parts, migrate towards the active site of the same molecule and the motion of the dynamic parts stopped / braked. However, the automatic migration of the atoms which act as a brake is rare. Some of the external sources [electric field, magnetic field, optical field etc.] that initiate this migrating mechanism must be intruded. So far, laser is one of the predominant sources. Similarly, changing the structure after receiving the impulse is also common braking phenomenon. Here is an example of the molecular brake, thousands of times smaller than the width of a human hair, developed by the researchers in Taiwan. It is powered by light and is the first capable of working at room temperature. The animated view of the schematic illustration of the light-driven molecular brake is posted here!!! Enjoy!!!!!
This molecular brake resembles a tiny four-bladed wheel (a rigid pentiptycene group shown in blue in the illustration below) and contains light-sensitive molecules. The paddle-like structure spins freely when a nanomachine is in motion. Exposing the structure to light changes its shape so that the blades stop spinning, 'the braking effect is on'. The braking power can be turned off and on by altering the wavelength of light exposure.

I hope that you readers are able to get the fundamental concepts about these molecular machines. If you are synthetic /computational chemists, I am sure that you will immediately start designing such molecules and contribute into the nano-world. Good luck from my side!!!!!