Computational Chemistry 1.8 - Bond Angles

Short lecture on bond angles in molecules.
If an atom is bonded to two different atoms, the three atoms form a bond angle. We can measure a bond angle by computing the dot product of the two unit vectors of the bonds as they point away from the central atom.
Notes Slide: i.imgur.com/mF4...
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[@rafael_l0321]

So, the calculated angle for water was 109°, but we know that the actual value is closer to 104°. Was the xyz file generated from Avogadro? Shouldn't the optimized structure have the proper 104° angle? Thanks for the videos, I'm going through the playlist

[@ima_haider]

Should it not be N(N-1)(N-2) / 6, As we are selecting triplets from N atoms at a time. And we will take combination N C 3 which will simplify to N(N-1)(N-2) / 6, the similar approach used for finding complexity of pairs in bonds.

[@alexhuynh5850]

if you are having issues with the run command, I used % and it worked for some reason

[@faycalaissabrahim8036]

where are you runing molecules from !? to put them in vmd is that from avogadro ?

[@hanaahassanin3089]

your videos are very usefull. is there any text books or lecture nots that would help in this?

[@TMPChem]

Hi Hanaa. There isn't really a textbook on this particular chapter per se, as it is primarily based on a set of online notes here (vergil.chemistry.gatech.edu/resources/programming/geom-project.pdf). As for physical chemistry textbook recommendations in general, that can be found here: kzbin.info/www/bejne/fqqTh4Gka8qqi7c

[@hanaahassanin3089]

Thank you

[@zamzamali4842]

Thank you for your videos!! What course should be taken to understand the math?

[@TMPChem]

Hi Zamzam. Math prerequisites for pchem typically include algebra, trigonometry, and the basics of calculus. Depending on the course, professor, and intensity you may benefit from studying linear algebra, differential equations, and/or vector calculus. The computational chemistry course will eventually include quite a bit of advanced math, but this first chapter is mostly geometry. I believe I first encountered dot products in multi-variable calculus (often called calc 3 in the US). If you're looking for review sources outside of math courses or Khan Academy I would recommend "Mathematics for Physical Chemistry" by McQuarrie.

[@senthilcaesar]

What is the Prerequisite for Computational Chemistry ?

[@TMPChem]

Computational chemistry is a somewhat interdisciplinary topic which doesn't necessarily have additional prerequisites relative to physical chemistry. Most students in such a course are typically physical chemistry graduate students, but we also see students from biology, chemical engineering, physics, and other technical disciplines. The first three chapters (i.e. what exists as of the time of this comment) doesn't require any additional background knowledge. The later chapters (if I ever get around to completing them, ugh) will be substantially more mathematically demanding, and require the quantum chemistry playlist as a prerequisite.

[@senthilcaesar]

I am excited to start learning . Thank you

[@amritasharma3392]

Why is there a dot product and not cross product?

[@amritasharma3392]

Are you a student or professor?

[@TMPChem]

Dot product is introduced in this video because it is necessary to compute bond angles. Cross product will be introduced in the next video on torsion / dihedral angles, where it is necessary. We can compute the dot product and cross product of any pair of vectors that we choose, but typically in programming we only do what necessary to achieve the desired result of the program. There was a cross product function in this program, but only because I created the smaller programs used in these earlier videos by removing functions from the final program at the end of this chapter (Rotational Constants), and must have forgotten to remove that function, as it isn't yet necessary.

[@TMPChem]

Neither at this exact moment. I have completed most of my PhD and am currently on a leave of absence while I pursue some business opportunities.

[@amritasharma3392]

I am studying cellular biology, so very little background on physics r computer science. My questions might annoy you, I am sorry about that

[@TMPChem]

No problem. That's why they're here. If you've got a question other viewers probably do too. It benefits everyone to have additional clarification through forum-like comments. For simulations in chemical biology the primary tool of the trade at the atomistic level is molecular mechanics, as is discussed extensively in the next chapter. Should have strong overlap with the types of things you'd encounter in a graduate computational biology course.

[@amritasharma3392]

And what are a and b?

[@TMPChem]

a and b are generic 3-dimensional vectors. You can represent a 3-d vector as an arrow, pointing a certain direction in 3-d space, with a certain length (magnitude). If two unit vectors (vectors of length 1) point in the same exact direction, their dot product is 1. If they point in exact opposite directions, their dot product is -1. When they point 90 degrees relative to one another, they are "independent" a.k.a. "orthogonal" and their dot product is zero. See the Math Review video on Vectors for more info.

[@terriblast8076]

This topic is interesting but the way you present it. the color of slides are terrible :). Thats why i have to pause it :) and find another video :)

[@TMPChem]

Best of luck to you Terri.