Hello! I am new to using Avogadro so I am in the process of learning how to navigate this software. I wanted to start making 3D molecules so I can edit them into Wikipedia pages. I would like to achieve the image quality seen when viewing a 3D molecule image on a Wikipedia page. Yesterday I built the Fluorodeoxyglucose (18F) molecule and I had a few questions:
Can isotopes be added? I need to add the ^18F radioisotope of Fluorine.
Are there options to make the Van der Waals spheres smoother? Are there any anti-aliasing options?
Any other tips for exporting my molecules so they can have the same image quality as seen on Wikipedia?
Thanks in advance, I’m hoping to use this software plenty of times in the near future.
What would you want for a depiction of \ce{^{18}F} to look like? How does the isotope look any different than another F atom? Or put another way, what would you want to see?
Based on your comment about “making spheres smoother,” I gather that you’re using v1.2. You can change the quality in the settings. Or you can update to 1.99 which includes perfect spheres and real-time shading:
It’s been a while, but the Wikichemistry folks seemed pretty friendly and willing to share tips. Feel free to ask what they’ve been using. At one point, I think they had a specific style with Jmol or POV-ray. It probably wouldn’t be too hard to copy the colors, for example.
@Hypothanos The difference in bond strength and bond length of a \ce{C-H} bond, and a \ce{C-D} (with \ce{D} as a frequently accepted alternative to describe deuterium, or \ce{^2H}) is relatively large because e.g., the atomic mass is about twice as much as for “normal” \ce{^1H} hydrogen (or protium). Now compare e.g., the two naturally occurring stable isotopes of chlorine: \ce{^{35}Cl} (abundance of about 75%) vs. \ce{^{37}Cl} (about 25%): the difference of the isotopic atomic masses is about 5% only (NIST data). Depending on the sample, it can affect e.g., IR spectroscopy (example) and the difference can influence molecular structures, and reactivity (kinetic isotope effect). But the smaller the difference between the isotopes in question, the less prominent the effect.
Now the interest in the artificial \ce{^{18}F} isotope in comparison to the naturally occurring \ce{^{19}F} is because of its radiochemistryin addition to normal chemistry. In structure formulae, this particular isotope is marked as such, as a label (example fluorodeoxyglucose F18). In ball-and-stick structure visualizations, sometimes \ce{^2H} is indicated by a different color (if at all, example) – in tracer molecules (like FDG) the fluorine typically is this particular that a discern to standard fluorine is not necessary, either.
To obtain a recent version of modern Avogadro, visit either the landing page of the forum, or its presence on GitHub.
