Tag Archives: porphyrins

Using a new computer program to ‘paint’ the structure of molecules in the style of a famous Dutch artist

Leave a reply
Figure 2: a) “Neoplastic” diagram of the porphyrin core of the classic nonplanar 2,3,7,8,12,13,17,18-octabromo-5,10,15,20-tetraphenylporphyrin (CCDC: RONROB), alongside two representations of this same molecule—b) the crystal structure thermal ellipsoid plot and (c) skeletal model.28 This porphyrin shape is primarily saddled and a little ruffled, resulting in S4 symmetry … [downloaded from https://onlinelibrary.wiley.com/doi/10.1002/ange.202403754]

A July 12, 2024 news item on ScienceDaily describes a fascinating computer program developed by scientists at Trinity College Dublin,

Scientists from Trinity College Dublin have created a computer program that “paints” the structure of molecules in the style of famous Dutch artist, Piet Mondrian, whose beautiful artworks will be instantly recognizable to many.

Mondrian’s style, whereby he used blocks of primary colors separated by lines of various widths on a white background, has been extensively copied or used as an inspiration in modern culture. But his deceptively simple artworks have also fascinated scientists for decades, finding niche applications in mathematics and statistics.

And now, researchers from the School of Chemistry are opening eyes and minds to the beauty of molecular structure, as well as posing new questions about the form and function of the molecules themselves.

…

A July 15, 2024 Trinity College Dublin press release (also on EurekAlert but published July 12, 2024), which originated the news item, provides more details about the work,

Their computer program, which can be accessed at http://www.sengegroup.eu/nsd, produces a Mondrianesque plot of any molecule. It does so by following an artistic algorithm that marries the laws of chemistry that describe the 3D structure of a molecule based on its components with the 2D style of one of the most influential painters of the Modern era.

For the scientist, it helps to rapidly assess and demonstrate molecular symmetry, allowing for deeper insights than would emerge from traditional representations. And for the artist, it provides a visually pleasing image of contrasting interpretations of symmetry, hopefully providing inspiration for the incorporation of scientific ideas into work. 

Mathias O Senge, Professor of Organic Chemistry in Trinity and Hans Fischer Senior Fellow at the Institute for Advanced Study of TU Munich [Technische Universität München or Technical University of Munich] is the senior author of a just-published article in the leading international journal, Angewandte Chemie, in which this creation is shared with the world. He said:

“For some years we have been working on this project, initially for fun, to output the structure of a molecule in an artistically pleasing manner as a painting in the style of Mondrian. The ‘paintings’ obtained are unique for each molecule and juxtapose what Mondrian and others aimed to do with the De Stijl artistic movement.

“Symmetry and shape are essential aspects of molecular structure and how we interpret molecules and their properties, but very often relationships between chemical structure and derived values are obscured. Taking our inspiration from Mondrian’s Compositions, we have depicted the symmetry information encoded within 3D data as blocks of colour, to show clearly how chemical arguments may contribute to symmetry.” 

Christopher Kingsbury, postdoctoral researcher in TBSI, who conceived the project, is first author of the journal article. He said: “In chemistry, it is useful to have a universal way of displaying molecular structure, so as to help ‘blueprint’ how a molecule is likely to behave in different environments and how it may react and change shape when in the presence of other molecules. But a certain amount of nuance is inevitably lost.

“This concept of increasing abstraction by removing minor details and trying to present a general form is mimicked by the early work of Mondrian and in some senses this is what scientists intuitively do when reducing complex phenomena to a ‘simpler truth’. Thanks to our new approach very complex science is fed through an artistic lens, which might make it more accessible to a wider range of people.”  

In recent years Professor Senge and his team have greatly enhanced our understanding of porphyrins, a unique class of intensely coloured pigments – also known as the “colours of life”. In one piece of work they created a suite of new biological sensors by chemically re-engineering these pigments to act like tiny Venus flytraps and grab specific molecules, such as pollutants. And now the new direction, in which science and art collide, may further develop our understanding of how porphyrins work.

“Great art gives us a new perspective on the world,” added Prof. Senge. “As a pastiche, this art may allow us to look at familiar molecules, such as porphyrins, in a new light, and help us to better understand how their shape and properties are intertwined. More generally, we believe that contemporary initiatives in ‘Art and Science’ require a transformative break of discipline boundaries and merger to ‘ArtScience’. There is a subtle interplay between science and art and mixing of both aspects in our respective fields of endeavour and this should be a focus for future developments in both areas.”

Here’s a link to and a citation for the paper,

Molecular Symmetry and Art: Visualizing the Near-Symmetry of Molecules in Piet Mondrian’s De Stijl by Dr. Christopher J. Kingsbury, Prof. Dr. Mathias O. Senge. Angewandte Chemie DOI: https://doi.org/10.1002/ange.202403754 Volume 136, Issue 25 June 17, 2024 e202403754 First published: 15 April 2024

This paper is open access.

Carbon nanotubes sense spoiled food

Leave a reply

CNT_FoodSpolage

Courtesy: MIT (Massachusetts Institute of Technology)

I love this .gif; it says a lot without a word. However for details, you need words and here’s what an April 15, 2015 news item on Nanowerk has to say about the research illustrated by the .gif,

MIT [Massachusetts Institute of Technology] chemists have devised an inexpensive, portable sensor that can detect gases emitted by rotting meat, allowing consumers to determine whether the meat in their grocery store or refrigerator is safe to eat.

The sensor, which consists of chemically modified carbon nanotubes, could be deployed in “smart packaging” that would offer much more accurate safety information than the expiration date on the package, says Timothy Swager, the John D. MacArthur Professor of Chemistry at MIT.

An April 14, 2015 MIT news release (also on EurekAlert), which originated the news item, offers more from Dr. Swager,

It could also cut down on food waste, he adds. “People are constantly throwing things out that probably aren’t bad,” says Swager, who is the senior author of a paper describing the new sensor this week in the journal Angewandte Chemie.

This latest study is builds on previous work at Swager’s lab (Note: Links have been removed),

The sensor is similar to other carbon nanotube devices that Swager’s lab has developed in recent years, including one that detects the ripeness of fruit. All of these devices work on the same principle: Carbon nanotubes can be chemically modified so that their ability to carry an electric current changes in the presence of a particular gas.

In this case, the researchers modified the carbon nanotubes with metal-containing compounds called metalloporphyrins, which contain a central metal atom bound to several nitrogen-containing rings. Hemoglobin, which carries oxygen in the blood, is a metalloporphyrin with iron as the central atom.

For this sensor, the researchers used a metalloporphyrin with cobalt at its center. Metalloporphyrins are very good at binding to nitrogen-containing compounds called amines. Of particular interest to the researchers were the so-called biogenic amines, such as putrescine and cadaverine, which are produced by decaying meat.

When the cobalt-containing porphyrin binds to any of these amines, it increases the electrical resistance of the carbon nanotube, which can be easily measured.

“We use these porphyrins to fabricate a very simple device where we apply a potential across the device and then monitor the current. When the device encounters amines, which are markers of decaying meat, the current of the device will become lower,” Liu says.

In this study, the researchers tested the sensor on four types of meat: pork, chicken, cod, and salmon. They found that when refrigerated, all four types stayed fresh over four days. Left unrefrigerated, the samples all decayed, but at varying rates.

There are other sensors that can detect the signs of decaying meat, but they are usually large and expensive instruments that require expertise to operate. “The advantage we have is these are the cheapest, smallest, easiest-to-manufacture sensors,” Swager says.

“There are several potential advantages in having an inexpensive sensor for measuring, in real time, the freshness of meat and fish products, including preventing foodborne illness, increasing overall customer satisfaction, and reducing food waste at grocery stores and in consumers’ homes,” says Roberto Forloni, a senior science fellow at Sealed Air, a major supplier of food packaging, who was not part of the research team.

The new device also requires very little power and could be incorporated into a wireless platform Swager’s lab recently developed that allows a regular smartphone to read output from carbon nanotube sensors such as this one.

The funding sources are interesting, as I am appreciating with increasing frequency these days (from the news release),

The researchers have filed for a patent on the technology and hope to license it for commercial development. The research was funded by the National Science Foundation and the Army Research Office through MIT’s Institute for Soldier Nanotechnologies.

Here’s a link to and a citation for the paper,

Single-Walled Carbon Nanotube/Metalloporphyrin Composites for the Chemiresistive Detection of Amines and Meat Spoilage by Sophie F. Liu, Alexander R. Petty, Dr. Graham T. Sazama, and Timothy M. Swager. Angewandte Chemie International Edition DOI: 10.1002/anie.201501434 Article first published online: 13 APR 2015

© 2015 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim

This article is behind a paywall.

There are other posts here about the quest to create food sensors including this Sept. 26, 2013 piece which features a critique (by another blogger) about trying to create food sensors that may be more expensive than the item they are protecting, a problem Swager claims to have overcome in an April 17, 2015 article by Ben Schiller for Fast Company (Note: Links have been removed),

Swager has set up a company to commercialize the technology and he expects to do the first demonstrations to interested clients this summer. The first applications are likely to be for food workers working with meat and fish, but there’s no reason why consumers shouldn’t get their own devices in due time.

There are efforts to create visual clues for food status. But Swager says his method is better because it doesn’t rely on perception: it produces hard data that can be logged and tracked. And it also has potential to be very cheap.

“The resistance method is a game-changer because it’s two to three orders of magnitude cheaper than other technology. It’s hard to imagine doing this cheaper,” he says.