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EPNOE Online Seminar on Computational Resources

14 jun 2024

EPNOE has recently organized a seminar on the usefulness of molecular simulation of starch and cellulose.

On the 13th of June of 2024, Roberto J. Aguado (LEPAMAP-PRODIS) introduced the first EPNOE Online Seminar on Computational Resources, featuring talks by Dr. Jeff Sanders (Schrödinger) and Dr. Yu Ogawa (CNRS). At least this time, the seminar was only available for EPNOE members. Fortunately, this includes every single researcher at the University of Girona, and especially the LEPAMAP-PRODIS staff.

Dr. Sanders, the product manager and scientific lead of Schrödinger's Consumer Packaged Goods group, gave an insightful talk on amylose as host molecule for diverse guest compounds. He presented molecular simulations modeling the encapsulation of (mostly) lipophilic molecules, including aromas, flavoring agents, bioactive compounds... by starch. The practical applications of this for the food and pharmaceutical industry are evident.

Then, Dr. Ogawa modeled cellulose I crystals to assess their behavior in the presence of bending stresses at very small scales (nanometers). He exposed notorious differences that depended on where the bending force was applied: (110) plane, (100) plane, etc. Furthermore, he assessed the effects of drying at nanometric scales by progressively removing water molecules. What does happen during drying?

Advertisement of the EPNOE seminar for members.

Although the content of Sanders' and Ogawa's presentations is exclusive to EPNOE members, it is not out of place to explain what this is about. Computational models? Polysaccharides?

Two years after Schrödinger's equation, Walter Heitler and Fritz London spent an entire night calculating the Hamiltonian and different bonding properties of the hydrogen atom. When the first computers appeared, chemists jumped at the opportunity to use them to... well, get a bit more sleep.

Using a computer had become common practice among scientists from all disciplines by the time the Quantum Chemistry Program Exchange emerged, and among the information they exchanged, code and software played an essential role. Of course, there was no internet, and this code was carried around printed or on massive floppy disks.

The seventies saw the creation of Gaussian, the MM1 force field, Gamess... and in 1980, the first issue of the Journal of Computational Chemistry appeared. Now, not only Wiley, but also ACS, Elsevier, Springer, Taylor & Francis... have journals dedicated to computational chemistry or computational materials science.

A slide from R.J. Aguado's introduction.

In 2013, Karplus, Levitt, and Warshel were awarded with the Nobel Prize in Chemistry for the development of multiscale models for complex chemical systems. And complex chemical systems include us living beings, biochemistry, biological macromolecules... yes, polysaccharides too.

Now, we have many companies (including Schrödinger and Gaussian), research groups, software packages to try computational chemistry or computational materials science. You have molecular dynamics, DFT, artificial intelligence, combinations thereof… Major goals are saving money, resources, exposure to chemical risks, and interaction with whiny co-workers.

However, nobody said this was a piece of cake. Having successful runs has no meaning if you do not apply proper models, a proper force field, a topology backed by previous literature, etc. So the machine won’t do everything for you and you need to have your chemistry, your physical chemistry, even your computer science… in order.

In the particular case of polysaccharides, we are talking macromolecules that get many of their most relevant properties from their supramolecular structure. Cellulose chains will be forming elementary fibrils, amylose and amylopectin will form starch granules, etc. And this brings it some complexity to be overcome. But with this challenge comes an opportunity, and we hope that seminars like this one have motivated some people to take it.

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