Life' s molecules dictated by physical chemistry (Introduction)

by David Turell @, Tuesday, August 03, 2021, 15:38 (81 days ago)

Molecules make quantum processes decisions for 3-D shape:

https://physicstoday.scitation.org/doi/full/10.1063/PT.3.4808

"When a molecule reaches a point in its configuration space where the energies of two quantum states cross, it has a choice to make: It can continue along in the state it was in, or it can cross over to the other one. Understanding what happens at those crossroads—known as conical intersections—has been a long-standing challenge in chemical physics. In some molecular systems, most molecules make the switch; in others, most don’t. And there’s no reliable means of predicting which systems are which.

"The problem is that everything happens so fast. Electrons and nuclei alike rearrange rapidly at a conical intersection. Their motions become strongly coupled, and the Born–Oppenheimer approximation—the principle that nuclear and electronic degrees of freedom can be treated separately—breaks down. Because the Born–Oppenheimer approximation is the foundation of nearly all conventional quantum chemical calculations, theorists are left with few tools for describing dynamics at conical intersections. And experimental studies on such rapid time scales aren’t much easier.

"Now, Kristina Chang of the University of California, Berkeley, her advisers Daniel Neumark and Stephen Leone, and their colleagues have developed a system of ultrafast lasers that can directly observe molecules passing through a conical intersection.

***

"Conical intersections are thought to be critical to many of the ways in which molecules convert or make use of energy, especially in living things. Examples include photosynthesis, human vision, and DNA’s mechanism for resisting UV damage.

"Nature has evolved a genetic code consisting of just four DNA bases: adenine, cytosine, guanine, and thymine. Plenty of other molecules exist that could fit just as easily inside DNA’s double helix. For example, 2-aminopurine is structurally identical to adenine except for the placement of an NH2 group, and it pairs with thymine just as well as adenine does. Nature’s choice of adenine over 2-aminopurine seems to have come down to how the molecules respond to UV light.

"When adenine absorbs a UV photon—a frequent occurrence in our sunlit world—it returns to its ground state within a picosecond; 2-aminopurine, on the other hand, takes tens of thousands of times as long.3 The longer a molecule remains in an excited state, the more opportunity the excitation energy has to initiate a reaction that can lead to a genetic mutation. In fact, biologists sometimes use 2-aminopurine as a substitute for adenine in experiments when they want to induce mutations deliberately.

"Adenine’s short excited-state lifetime is attributable to a conical intersection that efficiently funnels molecules from the excited state to the ground state. It’s not much of an exaggeration, therefore, to say that life on Earth as we know it owes its existence to conical intersections."

Comment: God, as an organic chemist, knew how to create a stable DNA for our basic code. DNA is not an accident of chance mutations.

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