Designing Small Molecules for Big Assemblies


This story is about dendrimers – man-made, nanoscale molecules with fascinating nature of self-assembly. They are used in designing exotic gels to fabricate novel smart materials for futuristic applications

In 1959, in a lecture entitled There is Plenty of Room at the Bottom, the renowned physicist Richard Feynman said,

. . . But I am not afraid to consider the final question as to whether, ultimately, in the great future, we can arrange the atoms the way we want; the very atoms, all the way down!

What Feynman did in his lecture was to explore the possibility of advanced synthetic chemistry by direct manipulation of individual atoms and molecules. The conceptual insight, though revolutionary, was not able to generate enough waves in the scientific community, at least initially. It was not until the late 1980s that the technology could reach a stage where molecules and atoms could really be controlled and engineered by direct engagement in their level. The scale of interest, as one can imagine, is exceedingly small or nano as we know it now. For comparison, human hair is about 80,000 – 100,000 units wide on nanometre scale. The ‘Nano’ revolution ushered in synthesis of several brand new molecules and structures of nano size with remarkable properties and hence diverse applicability. The field of nanotechnology grew rapidly in the years that followed and had already seen two Nobel Prizes by the end of the next decade.

One such man-made nano structure which has received considerable popularity since its synthesis in 1990, is dendrimers and its assemblies. These are nanoscale molecules with beautifully symmetric and repetitively branched structure. A cursory search for `dendrimer’ on the Web of Science (Thomson Reuters) database produces more than 17,500 results. Here at IIT Madras, the efforts to prepare them and other light weight molecules for large assemblies to be used in wide variety of applications is spearheaded by Dr. Edamana Prasad with his group in the Department of Chemistry.

“So, why have we chosen these molecules for our work?” says Dr. Prasad as we speak in his office next to the newly constructed Chemistry department building. Let us consider dendrimers, for instance. These organic molecules closely resemble bio-molecules such as protein in shape, size and weight. Proteins are known to self-assemble and generate unique hierarchic nanoscale structures for performing various functions in the human body. Taking this important clue from proteins, one can in fact, in more or less similar fashion, generate higher order complex structures with useful functionality by properly customised aggregation of dendrimers. “But what useful functionality are we taking about?” was my follow-up question. Vivek, one of Dr. Prasad’s students, promptly replied -“What if I tell you that such appropriately designed big assemblies have self-healing ability and can assist in oil spill recovery too? This is just a couple of their myriad usages.” I was intrigued.

In order to better understand the process of designing them, I stepped into Dr. Prasad’s laboratory and spoke with his PhD students Partha and Madhu. The individual molecules undergo the process of self-assembly to create bigger assemblies. The protagonist of this story, dendrimers, which consist of `chemical shells’,  organise themselves  very beautifully in a symmetric pattern around the core in a spherical form. Each shell is made up of molecules which are functionlised to create a branched structure around the core. This structure is known as dendrimers. The number of branching events from the core to the periphery is known as ‘generations’.  One can easily visualise them as a tree with many branches and sub-branches.  The name has been derived from Dendron which happens to be the Greek work for  ‘tree’.

Incidentally, branching in a tree reminds of fascinating objects called fractals, repeating never-ending patterns which appear self similar on various scales. So, do these dendrimers also show fractal nature? Yes, they do. Dr. Prasad with his former student Dr. Jasmine, reported that a popular class of dendrimers named PAMAM organise themselves in an aqueous medium and show fractal structures. The self-assembly of PAMAM is achieved by electrostatic forces. Fractal dimension is a statistical index to estimate the fractal nature of an object. It essentially quantifies the change in fractal pattern with the change of scale at which measurement is done and if this index is a non-integer (e.g., 1.5), the corresponding structure is a fractal. For PAMAM dendrimer assembly, this index was shown to be a little above 1.5 and therefore, the fractal nature was confirmed. As a direct consequence of fractal nature, their light emission properties show an unprecedented enhancement. Fractals are perhaps the most preferred way of generating captivating complexities in the natural world. It clearly works in the nano world too.

One is then led to think “What holds them together or to be more precise, what kind of forces mediate this self assembly of small molecules?” Partha reminds me of covalent bonds that we encounter in Chemistry 101. A covalent bold is a strong chemical bond which involves the sharing of electron pairs between atoms. But, for these big assemblies, we need the bonding to be of the non-covalent kind which essentially means weak interactions. These forces operate beyond molecular level and are responsible for spatial organisation of complex molecular architecture through self-assembly. Therefore, we name them, supramolecular forces. There are many kinds of them, one, for example is hydrogen bonding.

Dendrimers and other such self assemblies may have multiple supramolecular interactions holding the individual parts together. Note that these interactions are weak in nature, therefore the system is amenable to tuning during synthesis. We need freedom to break and make the bonds easily to control the process. An important way in which some derivatives of dendrimers aggregate themselves is in the form of helical structures. Partha has recently explored the mechanism in minute detail. He has found that such self-assembled systems may exhibit well-defined alignment leading to chirality on the macroscopic level which means that the systems are not identical to their mirror images. This is the origin of the helical structure formed. This understanding of the mechanistic aspect is involved, as Partha says, but crucial to construct supramolecular systems as per the requirement. Now that we are armed with all of this information, it is time to design some gel systems which happen to be a natural consequence of the aforementioned self-assembly.

We all have encountered gels in our daily lives. Butter, jam, shoe polish, hair gel, etc. are some of the gels we use regularly. A gel state is always easier to recognise than define, noted the British scientist Dorothy Jordan Lloyd in 1926. Typically, a liquid system made of two or more components turns into a gel when one of the solute components forms a three dimensional crossed-linked network inside the bulk gas or liquid. Formation of such a solid network within the fluid restricts its flow resulting in a jelly-like substance. Now, if the cross-linking of the network component of a gel is supramolecular in nature, we get supramolecular gels. These gels are formed, for example, as a result of self-assembly of dendrimers in organic and aqueous solvent. In recent years, Dr. Prasad has been actively pursuing the study of the formation and properties of these `physical’ gels.

Research interests in the Dendrimers laboratory, Department of Chemistry at IIT Madras.

“The two kinds of supramolecular gels that we use in our study are – hydrogels and organogels”, informs Dr. Prasad. As the names suggest, hydrogels have water as their solvent while organogels are formed when an organic solvent (which has carbon) is a component of the gel. Dr. Rajamalli, a former research scholar in Dr. Prasad’s lab has investigated both the gels in a series of publications. Organogels have stimuli responsive character, which means that an external or internal physical stimulus can prompt such gels to tune their properties.

Dr. Rajamalli was able to design and synthesise an `instant’ organogel based on a class of dendrons with specific kind of linkages. The gel may be used detect the presence of fluoride ions which has an important role in biological systems. When the gel comes into contact even with small concentration of fluoride ions, a gel-solution transition occurs which changes the colour of the solution from deep yellow to bright red and hence the presence can be detected by `naked eye’. A similar gel formation which was induced by metals, was also prepared to detect lead ions as reported last year by Dr. Prasad with his post-doctoral scholar Vidhya Lakshmi.

More recently, Madhu has prepared an interesting three-component organogel. This organogel consists of one-dimensional nano fibres. One of the components possesses cholesterol which is a biocompatible molecule and is, in fact, known for its ability to form one-dimensional structures and gels. Cholesterol effectively guides the process of supramolecular structure formation by stabilising various hydrogen bonds and regulating positive and negative charge transfer in the system. These charges originate from the other chemical components of the system. Therefore, in the presence of an applied potential, the system exhibits electric conductivity. Such a system has been synthesised for the very first time here in this lab. Dr. Prasad’s student, Sitakant continues this work to understand the mechanism of conduction in detail.

Vidhya Laksmi and Madhu have also synthesised another promising organogel which can assist in recovery of spilled oil from water. In marine areas, accidental oil spill is a major concern as it has detrimental effects on the surrounding ecosystem. Our friends in the lab observed that when a customised dendron-based solution or geletor comes into contact with oil on sea water surface, a robust gel system is formed by readily absorbing the oil floating atop. This gel is hydrophobic (water-hating) in nature and attains a wafer-like form almost instantaneously and floats on the water surface. These wafers of the gel can then removed, manually or mechanically. Oil is easily retrieved by heating the wafer gels. Surprisingly enough, geletor remains intact and can be re-used up to five or six times with reasonable success. It is a highly efficient process of oil spill recovery.

Such a dendron based geletor has been synthesised for the first time in this lab. In addition, the geletor is useful for its anti-wetting and self-cleaning properties and in the formation of invisible ink. It is indeed fascinating to note what hatred for water can do. But as we shall see, love for water could also be equally rewarding. Hydrogels consist of hydrophilic (water-loving) structures in them. These three-dimensional structures are cross-linked enabling the gel system to hold large amounts of water.

Hydrogels are soft, flexible and resemble living tissues. Here, in the Dendrimers laboratory, these hydrogels have been studied for their magnificent luminescence properties by Dr. Rajamalli, Supriya, and Sadeepan. Dr. Prasad’s research student, Prashant is attempting to use a hybrid hydrogel medium to enhance the photoluminescence properties of lanthanide ions by a phenomenon called resonance energy transfer (RET)}. Versatile and stable light emission are highly desired for optoelectronic applications and in cellular bioimaging. However, as it happens, these are not the only compelling features of hydrogels.

Dr. Prasad’s student, Vivek explains that hydrogels have this remarkable ability of self-healing which means two or more separate fragments of the gel can stick together spontaneously   as fresh bonds are created in the process. This is something like the flour dough we make to cook chapati. Two pieces of dough easily stick together if kept close enough to create a larger piece. Hydrogels are soft, flexible and closely resemble living tissues and, therefore, have several biomedical applications. These gels are currently used in reconstructive tissue engineering, wound dressing, contact lenses, etc.

Vivek has recently synthesised a novel three-component hydrogel with some commonly available chemicals. Many of the known hydrogels have this self-healing ability only in acidic medium which limits their usage. The hydrogel synthesised by Vivek maintains its self-healing property even in a medium which is neither acidic or alkaline, such as water. Perhaps the most important use of this hydrogel is in the purification of water. When heavy metals ions (which are toxic in nature) and organic residues present in water come into contact with the gel, they get collected on the gel’s surface. The gel can then be easily removed,  leaving pure water behind.  The gel also has robust mechanical strength and high swelling capacity which are two highly sought-after features of hydrogels from the point of view of applications.

These supramolecular big assemblies that we have seen so far are truly striking. A significant application of supramolecular hydrogels is in drug delivery – an increasingly popular method of targeted administration of medicine in the body. It is one of the on-going works in the Dendrimers lab and Dr. Prasad’s  student Ramya walks me through the details. “We are working on a control release system”, she apprises me. A popular alternative approach of drug delivery is by using macromolecules such as higher generation dendrimers. In these dendrimers, as we have seen earlier, a series of chemical shells are attached on many levels. Such an arrangement gives it a spherically symmetric three-dimensional shape, much like a flower. The structure is highly porous and consists of many empty pockets in which a drug is loaded. The drug get released slowly as and when required. But, there are some serious issues that need to be resolved.

 Dr. Edamana Prasad working with his students in the newly established Laser Flash Photolysis Laboratory at IIT Madras.
Dr. Edamana Prasad working with his students in the newly established Laser Flash Photolysis Laboratory at IIT Madras. Photo taken by Vivekanandan N.


Higher generation dendrimers are difficult to synthesise in a laboratory. In addition to that, some of these dendrimers are cytotoxic in nature, i.e., they can kill the living cells. Ramya is attempting to resolve these by using low generation dendrimers or dendrons. The structures of such dendrons are flat fibers and not a three-dimensional morphology. Therefore, to hold the drug, she uses a gel system created by an intelligent combination of water and an organic solvent. The gel thus formed is the same hybrid hydrogel which we saw earlier. In the presence of the appropriate solvent and water, the dendrons self assembles in the form of long fibres, entangled with each other. The drug is loaded with the solvent in the gelation process itself and resides inside those fibres.  The initial results do indicate that it is an effective control mechanism for the diffusion of drugs. Ramya is now beginning to study the biological aspects of her findings, in collaboration with Dr. Vignesh Muthuvijayan from the Department of Biotechnology, IITM. She is hopeful that the stability of this system and its nature would be favourable for drug delivery applications.

Interestingly, there exists another kind of dendrimers called  Janus type dendrimers named after the Roman God with two faces, one looking towards the future and one at the past. Janus dendrimers have an amphiphilic nature, i.e., they consist of both water-loving and water-hating parts. Dr. Prasad’s student Prabakaran is interested in synthesising them and in studying their self-assembly properties.  These dendrimers tend to form vesicle in a mixture of solvents, can form hydrogel, thermo-reversible organogels and also exhibit liquid crystal behaviour. No wonder that these gels find potential applications in the fields of drug delivery, gene delivery and sensors.

Dendritic structures can be good host systems for metal nano particles and quantum dots. Quite interestingly, Dr. Prasad with his student, Tufan Gosh, has recently shown that some graphene quantum dots (GQDs) immersed in aqueous solutions under certain conditions can be stable even in the absence of dendritic support and emit bright and  pure white light. These GQDs are zero dimensional and have tuneable luminescence properties. On investigation, it was found that it is an assembly of those GQDs that forms in the solutions which generates this white light emission when suitably excited. The process of aggregation of GQDs is similar to that of dendrimers. The work has convincingly demonstrated that pure white light emission can obtained by a well-designed nanoscopic assembly of a single material, GQDs in this case. Dr. Prasad’s research students, Kaviya and Lasitha, in similar manner, use metal nano particles and nano-scale assemblies as sensors and catalysts.

Laser beam at 532 nm in the experimental apparatus.
Laser beam at 532 nm in the Laser Flash Photolysis Lab.  Image courtesy : Dr. Edamana Prasad

In future, Dr. Prasad’s laboratory envisages to create more fundamental and applied research based on molecular assemblies. One of the major developments in this direction was the recent establishment of an ultrafast kinetic study facility (Laser Flash Photolysis) with the help of funding from the Department of Science and Technology for a group project. This is the first of its kind facility at IIT Madras. The experimental set-up can be utilised to analyse electron transfer kinetics which mostly occur from the electronically excited state of the molecules at nano-second time scale. Dr. Prasad and his group are now heading to analyse the electron transfer kinetics in molecular assemblies such as gels, which is an unexplored area in the frontier research.

Therefore, we discovered that big assemblies with incredible features can be achieved by intelligent design of small molecules. The gels that we encountered find major applications in the development of smart materials. These are novel materials which tune their properties under the influence of external stimuli such as temperature, pressure, electric field, nature of the ambience etc. They are immensely useful  in fabrication of sensors. The self-healing ability provides the material long lasting durability. On the other hand, biomedical applications of these gels are only limited by our imagination. From drug and gene delivery to tissue engineering and biosensors, the list is long and rapidly expanding. Water purification and oil spill recovery may be categorised as their non-trivial fields of usage. They also pave the way for new generation of optoelectronics. The development of organic light emitting devices, light harvesting systems, photovoltaic cells, etc. can greatly benefit from their versatile light emitting properties. There is no doubt that these supramolecular big assemblies are playing an important and decisive role in shaping future – the great future that Feynman talked about in his lecture more than five decades ago.



Dr. Edamana Prasad is an Associate Professor in the Department of Chemistry at IIT Madras. He worked at Photosciences and Photonics Laboratory, NIIST Thiruvananthapuram (CSIR, Govt. of India) and obtained his PhD (Chemistry) in 2000. His research interests include study of aggregation kinetics in dendrimers, finding the mechanism of supramolecular self-assembly in dendrimers, and determining the excited state dynamics in self-assembled systems.Dr. Prasad is also  working as the Head of the Teaching Learning Centre  at IIT Madras.


Meet the Author

SwetSwetamber Das is a PhD student in the Department of Physics at IIT Madras. Working on this article exposed him to the fascinating world of Chemistry.  He feels grateful to Immerse and Dr. Edamana Prasad for it. He is also exploring his newly found interest in the history and culture of the Indian subcontinent. He is an Assistant Editor of Scholarpedia. For comment or criticism, he can be reached at


Cover image obtained from “Dendrimers Market”, NANOTECHMAG Issue 14 (2014)