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Lab Story: Strong Effects of Weak Interactions

A lot of us know that one molecule of water is made of one oxygen atom and two hydrogen atoms, joined together by two covalent bonds. How are water molecules bound together in forming liquid/solid water? The scientific community has spent decades coming up with ways to find out and define interactions between atoms within a molecule and also intermolecular interactions. Prof Elangannan Arunan of the department of Inorganic and Physical Chemistry (IPC) in the Indian Institute of Science, Bangalore has highly rated work in this field to his credit.

He has made fundamental contributions to what is now called the ‘carbon bond’, which is a new type of interaction between carbon and electron-attracting elements like oxygen. Earlier, he headed an international group of experts to rework the definition of hydrogen bond. Prof. Arunan’s group has built the first and only molecular beam microwave spectrometer in India, a device that can probe into rotational motion of molecules.

Understanding the nature of the chemical bond in its myriad manifestations is the main focus of their work, says Prof. Arunan. “Seventy five years after (Linus) Pauling’s seminal work on the nature of chemical bond, the topic is still debated fervently. That tells us how important the bond is to chemistry.” We can run more accurate simulations of macromolecules, as our knowledge of molecular interactions grows. Many old ideas and metrics need refinement in the wake of results of new experiments, he says.

Atoms form chemical bonds by redistributing electrons in their outermost orbit. Atoms achieve a stable configuration called the octet by doing so. Octet is having eight electrons in the outermost shell. Bonds formed by a transfer of an electron from one atom to another atom making them positively and negatively charged ions respectively, are called ionic bonds. This transfer of electrons leads to an octet configuration for both atoms. When bonds are formed by sharing of electrons, they are called covalent bonds. In this arrangement, both atoms can use both electrons to achieve an octet configuration. Many times, sharing is not uniform. Such molecules are polarised and have partially charged positive and negative sites.

One must understand, however, that even a neutral molecule is not without interactions with other molecules (or light) around it though atoms have stabilised substantially by forming a bond and achieving an octet configuration. They can attract each other due to charge separation in polarised molecules. They are generally weak and become insignificant at high temperatures. After J van der Waals, a theoretical physicist who did pioneering work on gases and liquids, these interactions were named van der Waals interactions.In 1920, the ‘hydrogen bond’-- an interaction between hydrogen and oxygen atoms of two neighbouring molecules of water – was discovered.

These interactions are significantly stronger than, for example, interaction between two H2S molecules. They are found to be directional in nature through X-ray crystallography, a technique to know positions of atoms in a solid sample. Early experiments found the directional bonding in ice but not solid H2S, which meant that sulphur doesn’t form hydrogen bonds. Prof Arunan’s group performed experiments using molecular beams whose results suggested that water and H2S dimers did have directional bonds. Confusions about the nature of hydrogen bonds persisted, even in the international scene, until 2004, when Prof. Arunan headed a project backed by the International Union of Pure and Applied Chemistry (IUPAC) to redefine the hydrogen bond in light of recent research.

The new definition should reconcile all the experimental facts -- sometimes contradictory, like in the case of H2S. Instead of looking at the bond-breaking energies, the group looked at energy of “torsional strain” due to rotation about the hydrogen bond. Groups of atoms are free to rotate about the bond joining them. This relative motion is called torsion/internal rotation. Among the configurations obtained by internal rotation, some are more favourable energetically than others as they avoid repulsions due to proximity. It means there is an energy barrier to change from one configuration to another. When this rotational energy of molecules is greater than the barrier, they can overcome the barrier and move freely. This was perhaps why solid H2S did not show hydrogen bonding.

To the surprise of Prof. Arunan’s group, high-pressure crystallographers from the University of Edinburgh had published results from measurements on H2S at much lower temperature i.e. thermal energy would not be enough to cross the barrier for internal rotation! The authors of that publication -- mark the pleasant coincidence -- had written that H2S is a model system in which hydrogen bond goes from non-existence to weak to structurally influential. When H2S has enough thermal energy to overcome the barrier, it keeps tumbling, and on an average it looks like a sphere. (Imagine how a fan looks when stationary and when rotating) But when it is cooled sufficiently, the motion is “frozen” and conditions are right to form the hydrogen bond.

It means that hydrogen bond can form in some molecules when conditions are suitable. Whether the hydrogen bond exists or not has to be backed by evidence. The taskgroup Prof Arunan headed emphasised the need for evidence in their definition.

Prof Arunan’s group is presently working to refine the idea of van der Waals radius, which is the closest distance two atoms can approach each other without forming a bond. “The term radius is itself a misnomer,” says Arunan because a covalent bond is directional, and atoms that have already formed bonds (think of a large molecule) can come closer without reacting. The closest distance can also depend on the direction of approach. Prof Arunan also works in a shock wave-laboratory in the Aerospace department of IISc, addressing some fundamental questions on gas ignition. “That has more immediate applications, because many agencies like ISRO, DRDO are interested in it. Some have also asked me if we can detect explosives using microwave spectroscopy. Other techniques can do this better than microwave spectroscopy and so it is not being pursued in microwave laboratories much now”.

About Prof. Arunan’s lab: Prof. Elangannan Arunan is a professor at the department of Inorganic and Physical Chemistry (IPC) in the Indian Institute of Science.

Web: www.ipc.iisc.ernet.in/arunan.html

Email: arunan@ipc.iisc.ernet.in

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