Computational Chemistry 1.4 - Drawing Molecules

Short lecture demonstrating the use of Avogadro.
Avogadro can be used to generate an initial guess structure of any molecule with any elements, bond structure, or bond types. Optimization and other manipulations can help to greatly improve the initial structure.
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-- Equipment --
Microphone: Blue Yeti USB Microphone
Drawing Tablet: Wacom Intuos Pen and Touch Small
Drawing Program: Autodesk Sketchbook Express
Screen Capture: Corel Visual Studio Pro X8

[@738shani]

Thanks for all of your videos, great contribution to science...

[@zra8997]

i am watching all of your videos. thank you so much. soooooo helpful.

[@carloscalderon686]

Great content, thanks for your hard work and greetings from Mexico.

[@Everson_Computational]

Great video.

[@Professional_chemist]

Wonderful videos :)

[@sumonhati6839]

If you draw a molecule that has charge (suppose hydroxyl ion or oxygen with negative charge, nitrogen with positive charge), can we put that charge while drawing? Thank you.

[@noongull8041]

Wow 👍

[@hkharis07]

Hi, please reply is it fine if we select hypercam or avogadro to draw molecules and optimise their structure before molecular modeling study?

[@ammarahmed3970]

Respected Sir can we follow this whole procedure for GaussView , because we dont have Avogadro

[@houssemblueflash1744]

Kindly does anyone have a script to draw many molecules in the same time ?

[@Greenbeanandcheese]

what is the difference between UFF and MMFF94?

[@TMPChem]

Hi Eduardo. These are two different molecular mechanics energy functions, as discussed in video 2.2 of this course. The main difference is that UFF (universal force field) has atomic parameters for all atoms on the periodic table, whereas MMFF94 (Merck molecular force field 1994) is primarily concerned with organic molecules, and thus primarily covers atoms in the upper p-block plus hydrogen and a few others (as you would expect a pharmaceutical company to primarily be concerned with). MMFF probably gives somewhat better results for many common organic molecules, but in many cases we need to switch to UFF to guarantee force field parameters exist for all of our atoms. Though it's all very qualitative and empirical anyway, so don't tie yourself in knots over the choice of force field for such a quick initial structure. We're mainly trying to approach the ballpark of reasonable in such a hand-drawing.

[@hasibulalam6172]

Why don't we use gussian software

[@bonbonpony]

05:40 What about representing resonant structures, aromaticity, or delocalized bonds?

[@TMPChem]

Hi Bon Bon. For something like Avogadro, or simple molecule drawing programs, we're often not super concerned with representing organic chemistry valence bond theory concepts such as these, so they may not be great tools for it. I suspect other programs may be helpful for those (perhaps Spartan?), but the programs that I'll present here are typically 1) free, and 2) created by physical chemists. In physical chemistry we note that valence bond theory is a convenient, helpful approximation, whereas molecular orbital theory is much more predictive, and closer to the underlying laws of quantum mechanics, where such concepts become much more ambiguous.