Introducing biochemistry (Introduction)

by David Turell @, Tuesday, January 18, 2022, 20:04 (131 days ago)

An oddball molecule demonstrate how organic molecules can change shape:

"Shape-shifter molecules are in never-ending motion. Their structure fluctuates because the carbon bonds that hold them together constantly break up and form again. Researchers have now found a way to "tame" a shape-shifter molecule called bullvalene. In the journal Angewandte Chemie, they report that integrating the molecule into a coordination cage enables its shape-shifting behavior to be restricted through molecular recognition. Such form capturing could play a role in responsive materials.

"Chemical bonds between carbon atoms can be strong, as in the hydrocarbon gas ethane, or strained, as in triangular cyclopropane, or they can fluctuate between both kinds, such as in the organic hydrocarbon compound bullvalene.

"This molecule, discovered around 1960, fascinates chemists because its structure is in constant motion. Its outer shape remains the same, but the bonds between the carbon atoms continually change. This prevents the molecule from performing reactions that lead to defined substances. What is a nightmare for some chemists, others see as an opportunity because bond fluctuation also means that the molecule can react very quickly to external stimuli.


"'The key to the restriction of bullvalene's fluctional motion was the use of negative ions such as chloride or iodide," Fallon explains. "When these ions were added into the cage mixture, a significant convergence from over 200,000 possible isomers to only one dominating cage form occurred." As a driving force, the team identified molecular recognition, which is a term used to describe specific interactions between molecules and ions. This specific interaction led to the formation of a dominating cage isomer where four bullvalenes, held together on the top and bottom by metal ions, were arranged around the negative ion like curved struts of a basket."

Comment: this article is to show how organic molecules can change shape and be controlled by ions carrying specific charges plus or minus. This is not a natural molecule but used for illustration. Natural molecules must fold and/or bend to be functional, controlled in the same way as this article illustrates. Be sure to download to see the illustration. In life trillions of molecules must change shape trillions of times in nanoseconds. Being free to make mistakes in their liquid environment, it is not surprising mistakes occur.

Introducing biochemistry: revisiting chirality

by David Turell @, Friday, April 29, 2022, 18:52 (30 days ago) @ David Turell

Organic molecules have handedness. That is they are either right handed or left handed:

"Chirality, while not a rarity in the world of molecules, is nevertheless a special property. If a molecule is chiral (from the Greek word chiros = hand), it exists in two mirrored versions that are very similar but not identical—like two hands that can be folded together, but cannot be placed congruently on top of each other. This is why we speak of right-handed and left-handed molecules, or enantiomers, which means "opposite shape" in Greek.

"An international team of scientists from the Fritz Haber Institute of the Max Planck Society and the Prokhorov General Physics Institute of the Russian Academy of Sciences has found a way to address these molecules separately. Since chiral molecules are very similar to each other, this is a real challenge. "The trick is to expose them to electromagnetic radiation in a way so that only one 'hand,' i.e., one enantiomer, responds. This allows us to specifically control right- or left-handed molecules and learn more about them," says Dr. Sandra Eibenberger-Arias, head of the Controlled Molecules group at the Fritz-Haber-Institut.

"Learning this is important because enantiomers sometimes have very different biological and chemical qualities, for which explanations are sought. Take, for example, the chiral molecule carvone: one "hand" smells like mint, the other like caraway. Or the notorious sedative thalidomide, which is named after its active ingredient, a chiral molecule: while one form had the intended sedative effect, the other caused birth defects. Eibenberger-Arias' group studies the physical properties of chiral molecules. "Theory predicts a small energy difference between the two enantiomers, due to what is called parity violation. However, this has not been shown experimentally so far," explains JuHyeon Lee of the Fritz-Haber-Institut, first author of the published results, which appeared in the journal Physical Review Letters."

Comment: All essential amino acids in life are left-handed, but DNA is right-handed. This complicates the theories about origin of life. In nature in the universe amino acids are equally present. So how did life form in specified ways? For me, by design

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