RealAtoms reinvents the molecular model kit

Founders Ulrich Fekl and Joshua Moscattini aspire to create a new standard for chemistry model kits

RealAtoms reinvents the molecular model kit

Around this time of year, students purchase molecular model kits from the bookstore. These kits come with parts to create ball-and-stick models, but they are rigid and rather unreflective of the dynamic reactions taught in courses like organic chemistry.

“You have a visual picture of atoms shuffling around, and it’s very hard to communicate it in undergraduate classes,” says Professor Ulrich Fekl of UTM’s Department of Chemical and Physical Sciences. 

For instance, in existing model kits, the carbon atom can only form four bonds, and the models are unable to show chemical reactions and intermediates. 

As such, teaching reactions and mechanisms becomes difficult for instructors, who could resort to animations and videos, but this approach lacks a tactile experience. 

This lack of flexibility is what inspired Fekl and U of T alum Joshua Moscattini to found RealAtoms

“I always have this mental picture of atoms rearranging and it’s really, really smooth, and there is something enjoyable and memorable about touching models,” says Fekl. But “rearranging and the tactile experience don’t mesh with the existing kits.”

RealAtoms is a dynamic molecular model kit developed with the goal of being able to model and visualize organic and inorganic chemistry reactions, including their intermediates. 

The kit comes with 12 hydrogens, six carbons, one nitrogen, and two oxygens. The carbons, nitrogen, and oxygens all have the same composition and can be used interchangeably. 

“We call it the molecular reaction kit,” says Fekl.

Fekl developed prototypes of the molecular kit with support from his department, its Chair Claudiu Gradinaru, as well as the Impact Centre.

Moscattini, who is a sessional instructor at U of T and Professor at Seneca College, used his ten years of design experience to help develop RealAtoms using 3D Design. 

With RealAtoms there are more possibilities. SN2 reactions can be observed in the hands of the user. The atoms of this kit are capable of showing the entire process from a nucleophilic attack, a five-coordinate carbon representing the intermediate, and finally the exit of the leaving group. 

The Walden inversion — the conversion of a molecule from one enantiomer to another — cannot be demonstrated using current model kits, but can be done with RealAtoms with ease. 

The kit can also be used for inorganic studies. The atoms in the kit are also able to form transition metal complexes and show square planar and octahedral geometries, and can be used to create lattice structures, and organic and inorganic molecules. 

Unlike typical ball-and-stick models, parts in the RealAtoms kit contain magnets enclosed in ABS plastic. According to Fekl, magnetic model kits can already be purchased, but the magnets in the kits don’t contribute to their function.  

The magnets used in RealAtoms are functional and allow users to quickly assemble and change a molecule’s geometry. 

The model kit also allows users to feel the resistance when rotating bonds. 

The model clearly shows that the single bonds of sp3 hybridized carbons can freely rotate, while the double bonds of sp2 hybridized carbons, which cannot rotate. 

To form molecules with double or triple bonds, traditional ball-and-stick models would require completely different sticks to form them. The molecule must also be taken apart in order to transition between the different geometries. 

However, the atoms in the RealAtoms model kit contain plane surfaces along with concave and convex surfaces. These surfaces, contributed by Moscattini, lock in the orientation of a molecule to prevent rotation around the double bond. 

Fekl and Moscattini hope to create a new standard for organic and inorganic model kits. 

The model kit became commercially available for the first time at the 2018 Canadian National Exhibition. Moscattini delivered a pitch that won the Kids Technology Pitch Competition. It is also currently being used in a study at Seneca College to investigate the benefits of model kits in chemistry education. 

“The overall goal, I think, is for this to be the new standard in terms of organic model kits and inorganic kits,” says Moscattini. “We’re aiming for that, to have it in classrooms across Canada and the rest of North America.”

Researchers model chemical bonds using quantum computers

The multi-qubit simulation of a quantum chemistry calculation is a world first

Researchers model chemical bonds using quantum computers

A group of researchers including Alán Aspuru-Guzik, U of T professor and Canada 150 Research Chair in Theoretical & Quantum Chemistry, has achieved a world first in quantum chemistry.

A recent study in Physical Review X published the findings of a quantum computer used to calculate the ground-state energy of molecular hydrogen (H2) and lithium hydride (LiH). Ground state refers to the lowest possible energy level of electrons in an atom or molecule.

Although these bonds have been simulated before, this is the first time a multi-qubit — pronounced ‘cue-bit’ — system has been used. While qubits are the basic unit of quantum information, classical computing uses basic units known as bits, which are unable to solve complex computations.

Quantum chemistry is a subfield of chemistry that uses quantum mechanics to model physical systems like chemical bonds and reactions. Quantum chemistry uses ground states, transition states, and excited states to model bonds and reactions.

Where transition states signify the highest possible energy levels in a given molecule or atom, excited states include all energy levels when moving between ground and transition states.

Many advances have been made in the field of quantum chemistry in years prior. In 2010, the hydrogen atom was simulated using photonic and nuclear magnetic resonance experiments.

In 2013, another photonic experiment was used to simulate the hydrohelium cation HeH+. In 2015, the dissociation curve of the same cation was modelled.

We saw the first scalable quantum chemistry simulator on a superconducting platform in 2016, and in 2017, three molecules — H2, LiH, and beryllium hydride, or BeH2, — were simulated on a superconducting qubit platform.

However, these experiments involving ion-trap implementation were limited to a single qubit.

In contrast, this experiment used the trapped-ion model, which was implemented in conjunction with the variational quantum eigensolver (VQE) algorithm. This algorithm was used to calculate the molecular ground-state energies of H2 and LiH, which were then used to simulate their respective bonds.

In effect, the ions are isolated in free space using electromagnetic fields and, once stabilized, they are used to store qubits. This allows quantum information to be transferred through the motion of the ions in a shared trap.

Lasers are used to induce coupling between the internal qubit states and the external motional states for multi-qubit experiments. In other words, the ions become excited and move from a lower energy state to a higher one, which leads to an increase in ion size and allows them to start interacting. The more qubits involved, the more data is shared.

This groundbreaking study is an indication that data processing and collection through quantum computers could become faster, leading to practical applications in many areas from medicine to artificial intelligence.

Currently, even the largest supercomputers are struggling to accurately model molecules. The researchers chose to model H2 and LiH because they are easily understood molecules, and can be modelled using classical computers. Modelling simple bonds helps to pinpoint the accuracy of quantum computing and refine its applications to chemistry.

Simulations of said molecules would allow scientists to model and understand different chemical reactions with lower energy pathways. This would enable the design of new catalysts — substances that increase the rate of reactions — by reducing the amount of energy needed to start them.

The production of new catalysts could lead to the development of new fertilizers, better batteries, and organic solar cells.

The high speed afforded by quantum computing could also benefit the medical field. Masses of data produced through biomedical research on genomes could be more easily shared and handled by scientists. This, in turn, could lead to advances in personalized medicine, useful in treating diseases such as cancer.

More research is still needed to limit errors and their consequences, especially as the VQE method is vulnerable to calibration errors early on, and some errors cannot directly be recovered from.

But with developments in machine learning, scientific discoveries in fields like chemistry can be made much more quickly, and can lead to more advancements.

The newcomers at the table

Now that the seventh row of the periodic table is complete, what’s next?

The newcomers at the table

On December 30 2015, the scientific community received a late Christmas present from the International Union of Pure and Applied Chemistry (IUPAC): the recognition of four new elements, which completes the periodic table. A joint Russian-American research team is credited for the discovery of elements number 115, 117, and 118, and the discovery of element number 113 is accredited to a Japanese research team.   

Though the hardest part of discovering new elements is over, the researchers will have the task of giving suitable names to the elements. The  IUPAC regulations state that elements must be named after “one of their chemical or physical properties, a mythological concept, a mineral, a place or country, or a scientist.” Once everything is commercialized, we can expect the new periodic tables to appear in new chemistry textbooks. 

However, according to Robert Batey, the Chair of the U of T chemistry department, the U of T community should not expect to see the periodic tables around the chemistry department change any time soon.

Since the new elements were created synthetically through nuclear reactions using particle colliders, it is unlikely that they will be found naturally on Earth. The instability of the newly discovered elements makes it unlikely that practical uses will emerge from their discovery.

“The amount of element produced is so tiny that it really doesn’t have any practical benefit. It is more of an intellectual development more than anything else,” said Batey.

The completion of the seventh row of the periodic table is certainly a great achievement for the scientific community. The table allows scientists to predict the chemical and physical properties of each element according to their position in the table. It is the first time since 2011 that the table has been updated.

Dmitri Mendeleev was the first to compose a periodic table, in 1869, which characterized elements according to the element’s atomic number.

Now that the seventh row is complete what happens next is the question on everyone’s minds. There certainly has been speculation about the uncharted eighth row. At least until element number 120, all the elements can be arranged according to blocks (s-, p-, d-, and f-) on the periodic table. Batey has suggested that the real excitement would be caused by a discovery beyond element number 120. This would mean creating a whole new g-block for the element, prompting chemists and physicists to redesign the periodic table. 

However there is no need to wait in anticipation, as there is no timeline for when scientists will discover g-block elements. Though there have been predictions about elements that are heavy but stable enough to exist for a longer period of time, it may be the case that these elements are too unstable to make. “Maybe this is it,” says Batey, “maybe this is the end, we’ve reached it, the rest can’t be made, but my gut feeling is probably that’s not the case.” 

The Japanese Riken Lab expressed the same opinion as they announced that they would continue the pursuit of discovering new elements. Since there is no chemistry for the g-block elements, it would be a redefining moment for the world if chemists and physicists ever reach that region of the periodic table.