Thursday, October 26, 2017

physical chemistry - Confusion about direction of dipole arrow in alpha-helices and other molecules


I understand that molecular dipoles are electric dipoles. And electric dipole moment vectors point from the negative to the positive charge.



In class we learned to draw these special molecular dipole arrows (with a "plus" at the beginning) that point from the positive to the negative partial charge. I also see these arrows all over the internet, e.g.:



But for alpha-helices, the dipole moment points from the C to the N terminus. And the detail always shows the arrow pointing from the oxygen (negative) to the hydrogen (positive):



Should I just accept that even though an alpha-helix is a molecule like water, the "standard" way to draw its molecular dipole arrow is in the opposite direction than what people normally draw for water and other small molecules?


Edit: Another image, from a recent publication, but without macro-dipole arrow...:


enter image description here




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