Author Archives: Alexander Hasson

Misconduct, Bias or Benign? A Case of Missing Ångströms

An Ångström

An Ångström (Å) is a unit of length equal to 10−10 metres; one ten-billionth of a metre. It sits at a comfortable scale for the atomic world, with the diameter of a hydrogen atom, the length of a chemical bond, all measured in Ångström.

It is not an International System of Units (Système International d’Unités) “SI” unit. In fact, it has been formally deprecated in favour of the nanometre (1 Å = 0.1 nm), and standards bodies such as NIST and the BIPM discourage its use. Yet, in structural biology and chemistry, crystallography, and materials science, the Ångström persists. I would say, partly out of stubbornness, but mostly out of convenience. Saying a protein structure was solved at 2.1 Å feels natural in a way that 0.21 nm does not.

So we keep using it. And because we keep using it, we inherit its quirks and history.

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Chemical Languages in Machine Learning

For more than a century, chemists have been trying to squeeze the beautifully messy, quantum-smeared reality of molecules into tidy digital boxes, “formats” such as line notations, connection tables, coordinate files, or even the vaguely hieroglyphic Wiswesser Line Notation. These formats weren’t designed for machine learning; some weren’t even designed for computers. And yet, they’ve become the wedged into the backbones of modern drug discovery, materials design and computational chemistry.

The emergent use of large language models and natural language processing in chemistry posits the immediate question: What does it mean for a molecule to have a “language,” and how should machines speak it?

if molecules are akin to words and sentences, what alphabet and grammatical rules should they follow?

What follows is a tour through the evolving world of chemical languages, why we use them, why our old representations keep breaking our shiny new models, and what might replace them.

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