Showing posts with label Chemistry. Show all posts
Showing posts with label Chemistry. Show all posts

Friday, November 23, 2012

In Summary: Khan Academy Videos For Organic Chemistry

In Summary – Khan Academy for Organic Chemistry

In six previous posts I went through all 73 videos by Khan Academy for organic chemistry. In this final post I wrap up what I’ve learned from watching them, from the perspective of someone who teaches introductory college-level organic chemistry.

Six previous posts:?[1?2?3?4?5?6]

Contents

What’s great about Khan Academy?What does Khan Academy cover?What’s missing?What’s done the best?What are the biggest weaknesses?How useful is Khan Academy for a typical college student learning organic chemistry?Towards version 2.0

1. What’s Great About Khan Academy?

First of all, KA gets one really big thing right: teaching a subject as a series of 10 minute videos that gradually walk through a subject. There is a huge desire for this type of instruction and the value of discovering a popular working model for delivering educational videos cannot be understated.

His style is also very approachable and non-threatening. He doesn’t make you feel stupid. This alone is a huge part of the appeal. The tools he uses are very simple and accessible to everyone. He’s also an excellent illustrator.

Thirdly, I think it’s commendable that Sal Khan just decided to start making videos on a lot of topics without asking anyone’s permission. In some circles, his videos have been unpopular with academics. Here is a particularly lazy criticism of KA. Memo to instructors who complain about KA: you have the tools to make better videos: why aren’t you doing it?

What Does Khan Academy Cover?

I count 73 videos for organic chemistry.

These can be broken down into the following categories:

Nomenclature [27]: Alkanes, alkenes, R/S nomenclature, E/Z nomenclature, alcohols, ethers, epoxides, benzene derivatives, amines, aldehydes, ketones, carboxylic acids, anhydrides, esters, amides, acyl chlorides

Structure and bonding [5] hybrid orbitals, pi bonds, alcohol properties [hydrogen bonding], resonance, Huckel’s rule

Conformations [3] Newman projections [2 videos], chair/boat shapes for cyclohexane

Stereochemistry [4] Intro to chirality, chiral examples (2 videos), enantiomers/diastereomers/constitutional isomers

Reactivity: [8] mechanisms, Markovnikov’s rule, steric hindrance, sn2 stereochemistry, solvent effects, nucleophile strength, nucleophilicity vs. basicity, carboxylic acid derivative reactivity

Reactions: [24] HBr with alkenes, H3O(+) with alkenes, polymerization of alkenes w/ acid, SN2, SN1, E2, E1, free radical alkane chlorination, epoxide ring opening, bromination of aromatics, Friedel Crafts acylation, keto-enol tautomerism, acid-base of carboxylic acids, Fischer esterification, acid chloride formation with SOCl2, amide formation from amine and acyl chloride, aldol reaction.

Addenda [2]

What does a typical introductory organic chemistry course cover that is NOT included in Khan Academy?

If I had to name my top 10 omissions, they would be this:

no discussion of organic acids and base; i.e acidity, basicity, conjugate acid, conjugate base, pKa, how to determine if an acid base reaction is favorableevaluation of resonance forms; what makes one resonance form more stable than another? Not discussed.no discussion of the stereochemistry of the E2 reactiononly 3 alkene addition reactions covered [out of >15] ; no examples with stereochemistry. Missing examples like bromination, hydroboration, epoxidation, etc.no discussion of alkynes or their reactionsno discussion of carbocation rearrangementsno discussion of oxidation/reductiononly one video devoted to the concept of aromaticity, not enough to understand it; only 2 reactions of aromatic derivativesonly 3 videos on reactions of aldehydes, ketones, and carboxylic acid derivativesno discussion of the Diels-Alder or related reactions; no discussion of molecular orbitals

Of the material covered by the KA videos, what’s done the best?

The videos on nomenclature are useful for those who have never encountered these functional groups before. They provide accurate methods for naming these molecules. There was only one major mistake and this was corrected. A few minor mistakes (see notes on individual videos).

The videos on structure and bonding, including hybrid orbitals were done well.

The drawings of Newman projections were done well and have nice descriptions of how to convert a line diagram into a Newman projection.

What are the biggest weaknesses? What could be done better?

The videos on reactions tend to be shallow. There is a lot of imprecise language (e.g. “guy” instead of, say “nucleophile”). Chemical reactivity is? largely explained in an ad hoc fashion rather than in a way that ties back to fundamental concepts of physics. ?There’s an opportunity to explain a lot of organic chemistry by understanding the key factors that stabilize negative and positive charges; that isn’t done here. Arrow pushing is not done correctly. Stereochemistry? is arguably the major theme of first-semester organic chemistry, but its involvement in reactions is almost completely ignored.

What the videos really lack is a consistent description of chemical reactivity rooted in a small number of fundamental physical principles.

How Useful is Khan Academy For A Typical College Student Learning Organic Chemistry?

As they stand right now, KA videos are in no way a standalone alternative to a college-level course in introductory organic chemistry. If you watch all 73 videos, you will in no way have “learned” organic chemistry.

They are a useful supplement for nomenclature, structure and bonding, and some aspects of conformations.

For someone who finds their university lecturer intimidating, the videos on reactions and reactivity can be a light introduction to some of the topics covered in an introductory course.

Towards Version 2.0

Two questions for the future:

1) What is the minimum number of 10-15 minute videos required to teach the core concepts of Org 1 and Org 2 in a manner that would, say, prepare students for a standardized exam like the ACS?

2) What is the optimal order of those videos? Can we test outcomes to see if there is an optimal way in which these topics can be presented?

I look forward to further improvement of the organic chemistry video content at KA.

Tagged as: khan academy, video


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Khan Academy Videos for Organic Chemistry, Part 6

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In this post (the 6th of 6) we finish up going through all the Khan Academy videos for organic chemistry [videos 65-73]. For previous posts in this series, see [1 2 3 4 5]

Video #65 – Keto-Enol Tautomerism
Length: 8:03
Summary: 3-methyl 2-butanone is drawn, and the mechanism for its conversion into its enol form is shown via protonation of the carbonyl oxygen and deprotonation.
Key concepts/Skills:?keto-enol tautomerism, constitutional isomers.
Nitpicky criticisms:?A little bit of vaugeness about where H3O(+) comes from; there shouldn’t be too much in water at pH 7. Might help to say the reaction is assisted by adding acid. Could help to mention what factors favor the keto over the enol, or to give students a typical value for the position of equilibrium [about 104 favoring keto, for instance].
Red flags:?None, this is fine [except for arrows]

Video #66 – Carboxylic Acid Introduction
Length: 8:51
Summary:?A generic carboxylic acid is drawn, and the acid-base reaction between it and water is shown. It’s demonstrated that the stability of the conjugate base is due to resonance. ?Formic acid, acetic acid, and oxalic acid are also drawn.
Key concepts/skills:?acidity, resonance stabilization, carboxylic acids
Nitpicky criticisms:?It’s said that carboxylic acids are more acidic than alcohols. By how much? It would also be good to explicitly say that “the stronger the acid, the weaker the conjugate base”. When the Arhennius definition of an acid as a proton donor is mentioned [1:05] I think he means Bronsted.
Red flags:?Nothing except for the arrow pushing

Video #67 – Carboxylic Acid Naming
Length: 5:26
Summary:?Butanoic acid, hexanoic acid, 3-methyl hexanoic acid, and (E)-3-heptenoic acid are drawn and named.
Key concepts/Skills:?Carboxylic acid nomenclature
Nitpicky criticisms:?It’s fine. One weird thing though – around 5:15 it’s said that “this is only true if you’re assuming that I drew it in the actual 3 dimensional configuration in some way”. Not sure what is meant by this.
Red flags:?None

Video #68 – Fischer Esterification
Length: 17:12
Summary:?Heptanoic acid is drawn with ethanol and H2SO4. Reaction really begins at 5:00. Protonation of carbonl oxygen, addition of ethanol, ethanol losing proton, protonation of OH, and loss of water. Formation of ethyl heptanoate.
Key concepts/Skills:?Equilibrium, carboxylic acids, addition, elimination.
Nitpicky criticisms:?“Fischer”, ahem. The video begins with “let’s think about what might happen if we do this”. Little pet peeve of mine – we can appreciate things looking backward, but it’s difficult to look forward using first principles. The discussion up to 5:00 probably could have been skipped, since it’s just discussing the acidity of H2SO4.?Would be good to mention that acid makes the carbonyl group a better electrophile; also, an opportunity is missed to explain why the nucleophile attacks the carbon instead of the (positively charged) oxygen. It’s said that we’ve seen this “many, many times” in SN2 reactions but this is actually his first time drawing the addition mechanism in carbonyls. It’s good to mention the reaction is in equilibrium, but it would be better to mention *why* equilibrium favors formation of the ester. Finally I know I’m a grouch, but I just don’t like statements like “protons are flying around everywhere” (11:25).
Red flags:?The elimination step at 14:00 is drawn as a bimolecular mechanism, which is incorrect. Deprotonation should be shown as a separate step.

Video #69 – Acid Chloride Formation
Length: 11:48
Summary:?The mechanism for formation of acetyl chloride from acetic acid using SOCl2 is shown.??
Key concepts/skills:?Conversion of carboxylic acids to acid chlorides
Nitpicky criticisms:?Would be good to mention why Cl is a good leaving group. Why do we lose oxygen and not Cl in the elimination step? It would be good to mention that the gas SO2 is formed and this will drive the reaction to completion. The last step shouldn’t have an equilibrium arrow.?Heh, nobody would perform this reaction in a beaker [9:15] ?it stinks too much!
Red flags:?Just the arrow pushing (as always)

Video #70 – Amides, Anhydrides, Esters, and Acyl Chlorides
Length: 8:48
Summary:?The structures of acetamide, N-methyl propanamide, methyl ethanoate, acetic anhydride, ethanoic anhydride, propanoic anhydride, acetyl chloride, and ethanoyl chloride are drawn.
Key concepts/Skills:?Nomenclature of amides, esters, anhydrides, and acid chlorides
Nitpicky criticisms:?None
Red flags:?None

Video #71 – Relative Stability of Amides, Esters, Anhydrides, and Acyl Chlorides
Length: 11:09
Summary:?Acetamide, methyl acetate, acetic anhydride, and acetyl chloride are drawn, along with their resonance forms. The higher reactivity of anhydrides is rationalized as being due to the lower stability of the resonance form.
Key concepts/Skills:?drawing resonance structures, understanding stability of resonance structures.
Nitpicky criticisms:?If nitrogen is electron rich – more electronegative than carbon, then why might it give up its electrons? [2:44]. ?Finally, for the ester, he mentions the real reason why oxygen is less nucleophilic than nitrogen – because it is more electronegative. This is the first time this is mentioned in the whole video series. How does one differentiate between “quite stable” and “just stable”? Would be better just to show an arrow beginning with “most stable” on the left going to “least stable” on the right. Finally, he says “we’ll explore some of the mechanisms in the next few videos”, but in fact it’s just mentioned in one video.

I think ranking leaving group ability is a more powerful way to explain the relative reactivity of carboxylic acid derivatives than the relative stability of resonance forms, but overall this is a useful video.
Red flags:?No resonance structure is drawn for acetyl chloride because it is said that it “has no resonance structure” ; instead of saying it “has no resonance structure”, which is not true, it would be better to say that the resonance form is not “significant”; also, chlorine is less electronegative than oxygen, so the answer is not electronegativity (9:20) but poor orbital overlap.

Video #72 – Amide Formation From Acyl Chloride
Length: 9:01
Summary:?The reaction between butanoyl chloride and dimethylamine is shown to give N,N-dimethylbutanamide.
Key concepts/Skills:?Reactivity of acyl chlorides, nucleophilic acyl substitution.
Nitpicky criticisms:?Another instance of “Let’s think about what might happen….”. The “stability” argument from the previous video is used to explain the reactivity of acyl chlorides relative to amides, but leaving group ability is more valuable. Compare Cl(-) as a leaving group versus Me2N(-)! This explains everything.
Red flags: Just arrow pushing.

Video #73 – Aldol Reaction
Length: 11:41
Summary:?The aldol addition reaction between two aldehydes RCH2CHO in the presence of NaOH is shown.
Key concepts/Skills:?Enolates, addition reactions, aldol reaction, acidity of alpha protons, enolates as nucleophiles.
Nitpicky criticisms:?It’s said that this is a review of previous discussions of enolate ions, but in fact this is the first description of them. It would be better to consistently show the aldehyde hydrogen.
Red flags:?The arrow pushing here makes it look like the carbonyl carbon is the nucleophile, which isn’t the case [6:32].

And that’s it: 73 videos for organic chemistry from Khan Academy. Again, lots of nomenclature videos here, plus a few on reactions. Kind of disappointing that there’s so few on the reactions of aldehydes, ketones, and carboxylic acids; nothing on reduction, oxidation, extensions of enolate chemistry… a lot of work still left to do, in other words. ?In the next post I’ll write an overall summary of these videos that answers the question, “How useful are Khan Academy videos for learning organic chemistry?”.

Tagged as: khan academy, videos


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#ChemCoach : Online Organic Chemistry Tutor

Early morning in Jerusalem, 2010

For any readers who are interested in chemistry as a career, blogger SeeArrOhh of Just Like Cooking is running a blogging carnival called #ChemCoach where chemists talk about their careers and how they got there. If you’re at all interested in the huge variety of jobs that people with a chemistry background do, I highly recommend checking out the main post here?, which links to over 20 entries by a variety of very interesting people.?This is my entry.

My current job:?I work independently as an online organic chemistry tutor. Basically I run a small business.

What I do in a standard “work day”. It depends on the time of year, but I spend a considerable portion of most days in Skype chats with students who are taking organic chemistry classes. Summers are pretty quiet on the tutoring front, but the months from October through May are often pretty full. ?I’ve worked as much as 11 hours in one day, but I find that the maximum I can tutor in one day and stay sane is about 8 hours.

When I’m not tutoring I’m writing articles for my blog, or developing study materials that I think will be useful for organic chemistry students. I spend a lot of time in ChemDraw!

What kind of schooling/training/experience helped me get there? My background is in total synthesis. I have a Ph.D. in organic chemistry and worked as a postdoctoral fellow for four years (two separate postdocs). My first postdoc was a very traditional total synthesis postdoc at a high powered institution. The second postdoc I took in Jerusalem in order to finally be able to live with my wife (we did 6.5 years of long distance before that – long story).

I finished my first postdoc just in time for the recession. ?We moved to Jerusalem in late ’08 and the recession really changed my focus. Not only did it make “getting a job” harder, I saw how precarious even the careers of my friends with “safe” jobs in pharma could be with plant closings and mergers. I didn’t want to be in the position where an individual could walk into my office and fire me or tell me I had to move cities. My solution was to start my own business on the side. ?In ’09 I started a spectacularly unsuccessful scientific editing service called WriteChem that never got a client. Later that year I was doing some organic chemistry tutoring in person, but the language barrier ?meant that I didn’t have many students. Sometime around January 2010 I saw Chatroulette and saw how easy it was to connect to people all over the world with online video. So it struck me – why not tutor people online through Skype?

In order to attract people to tutor I thought I’d need a website. ?I remember seeing Tenderbutton?and Not Voodoo?in ’06 and thinking that someone needed to build a site that combined the best features of them. Four years later, nobody had really done it yet, so that “someone” turned out to be me. I figure that if I created something truly valuable to people, everything will eventually work out. And so far it has.

The best thing about my work is that ?it allows me to work independently, have flexible hours, and live anywhere. And I get to meet all these great people.

How does chemistry inform my work? I talk and write about chemistry every hour of the day. It probably helps my teaching that many of the reactions I talk to students about I’ve run personally. Beyond undergraduate tutoring, it’s fun to get inquiries from people I never would have expected, like graduate students, chemists in private industry and in law enforcement (I had one person ask me about doing a series of sessions for a city crime lab). ?On another note, ?I find that the methodical habits and attention to detail that were valuable for being a successful chemist transfer well to running a small business. I still run “experiments” but they’re of a different kind.

A unique, interesting or funny anecdote about my career: You never know what you’re going to get with a Skype chat. I’ve worked with women breast-feeding their crying babies (camera off) , people who keep chickens, people in airports.
Living in Jerusalem was fun. In the last few months we lived just outside the gates of the Old City. In order to hit the North American evening crowd, I’d wake up at 1:30 am, tutor from 2am to 8am [I'd quit my postdoc by this point], go for a run through the Old City, sleep until noon, write / tutor for the next several hours, eat dinner, and go to bed at 9pm.
I’d be tutoring at 4am (that’s early evening EST)? and the Call To Prayer would suddenly blare out from each of the three mosques in the adjoining valley. That always got a reaction. Sessions would also get interrupted by the noises from fighting street cats. I actually miss that now.

For more posts in the #chemcoach series, check out SeeArrOh’s blog

Tagged as: stories, teaching, tutoring


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Success Stories: How Stu Aced Organic Chemistry


I recently got an email from a reader, Stu (not his real name) who told me he got an A in Organic Chemistry 1, and was on pace to do the same in Org 2. I asked him if he’d be willing to share with the readers of this blog how he did it. I think you’ll agree that this is a story of tremendous dedication, hard work, and attention to detail. The rest I’ll leave to Stu [note: emphasis and subtitles have been added by me]
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How I Got An A In Organic 1
I guess I should start off with quantifying what I did in organic 1 and so far in organic 2, then I can describe how I did it.
So, this summer in organic 1 we had a quiz (mostly review stuff from gen chem, i.e. acid base chemistry, lewis structures, etc:10%), HW (25%), 2 tests (20% each) and a final (25%).
Each of the tests had 5 (out of 100) extra credit points, no extra credit for the quiz, just a hair of extra credit for the HW, which was through Sapling. The extra credit was a nice boost, making available 105 points but only grading 100 of those. So, any scores that I mention are uncurved but do include the 5 extra credit point
I got a 100% on everything except for the first exam. My initial grade was an 83%, but I submitted for a regrade and got an 87%. More on this later..
So far in Organic 2, we just took our first exam last week and I scored a 99.5%.
Now how I did it:
1. Course Preparation
I don’t really have one overarching strategy, and I wouldn’t say that my strategy is the most elegant or efficient, but I would say that I am getting there. Especially in the beginning, in was more of “siege” tactics than anything.
My one bad habit (?) with classes is getting ahead of the class pace, sometimes learning all of the subject during a semester break. So, knowing about the reputation that organic chemistry had, I decided to “run into the burning building”, for lack of better words, and tackle it head on rather than fear it. I guess you could say that my first step was to get into the right mindset.
Next, I started early, before the semester started. This way, I was able to stay about 4-5 chapters ahead of the lecture. What I would do is pre-read the chapter to know what was going on, then read it again slowly and doing all of the problems. If there was a word or concept I didn’t know, I would not move forward until I understood and mastered it. I sketched out just about every mechanism and molecule I could find. I have notebooks full of molecules and mechanisms. This was a serious time investment.
So anyway, I probably spent about 10-20 hours on each chapter, depending on the difficulty. A lot of this was time well spent, although some of it was wasted since later on in lecture the teacher would emphasis certain parts while skipping others, want us to know about certain reactions/mechanisms but not even mention others. Although my approach was not efficient, I did reach a level pretty close to mastery on those concepts once I stepped into lecture. This allowed me to fully understand everything the teacher was talking about, and to ask relevant questions.
2. Exam Preparation
About a week or two before an exam, I would take the list of “suggested book problems” that our teacher gave us and would rework those problems for the relevant chapters. Keep in mind that I had already done these problems, but by this point it was sometimes 3-4 weeks previously. Any problems I had trouble with would go onto a list and I would keep reworking them until they got eliminated from the list.
The book “Organic Chemistry as a Second Language” was a HUGE help, especially for IR and NMR. I only skimmed the textbook chapters on these subjects, as this book was more pointed and relevant.
3. Organizing Notes and Reactions
A day or two after lectures, I would compile all of my notes. Concepts would do into an outline form Word document. Reactions go into my reaction notebook. Here is a description of my reaction notebook:
4 sections:
?A chronological list of reactions with starting material, conditions, and products. Any reactions whose mechanisms were discussed in class have a *A list of mechanismsA list of reactions organized by common starting product, i.e. Reactions starting with Alkenes, starting with Primary R-OH, Secondary R-OH, Epoxides, Oxidizing Primary R-OH, etcA list of reactions organized by common ending product (retro) i.e. Reactions ending with Alkenes, Primary R-OH, Alkanes, etc
The reactions in lists 1,3,4 are all cross indexed. For example, hydroboration might be listed as #28 in each list. This makes it easy to identify errors, omissions, demo molecules that could be improved. Most of the molecules were ones given in lecture. Some of them used prototype molecules. I did this if I wanted to demonstrate a particular stereochemistry concept, or showing how different reagents lead to different products with the same molecule, etc.
My main study of reactions was with lists 3+4. I have found that identifying reactants and products is usually pretty easy if you know one or the other and the conditions, but remembering all of the conditions can be a challenge, so that is what I focused on.
4. Learning Reactions
What I would do this these lists is get a piece of paper, cover up all of the conditions, and see how many I could write out on the paper. Any that I missed would get an X next to them. I would keep going through the lists, repeating just the incorrect ones, until all of the Xs were gone. Then I would go through each group again. If I could do them all perfectly, that group got a tick mark. Then, wait a while, come back to it. If I could still do the group perfectly again, another tick mark. Once I got to 5 tick marks for each group, remembering all of the reactions was no sweat.
Me and a friend of mine traded synthesis problems for a while. I found that I learned a lot just by writing them and seeing all of the different ways I could move functional groups in 2 steps, 3 steps, etc.
This reaction notebook has been an awesome help, but unfortunately it wasn’t until I was quite a way into Organic 1 that I figured it out. Better late than never!
5. Keeping Track of Mistakes
Another thing I did was I kept a list of every mistake I did on every exam. This included conceptual, technical, and cognitive mistakes.? For example, I did horrible on my first exam, considering the amount of time I invested in it. I wasn’t lacking in the first two categories, but I made a lot of cognitive mistakes. I was a little too overconfident, so much so that I didn’t notice a lot of mistakes I made even though I checked my work a few times. Also, since I wasn’t used to how organic tests were formatted, that threw me off a little bit. I made some really dumb mistakes.
There was one mistake I remember where the question asked to outline the free radical addition of HBr to an alkene. I figured that I would be a hot shot and detail the mechanism, even though that wasn’t asked for. Also, I wasn’t entirely sure how much detail was required when it said “outline”, so I decided to play it safe and prove that I knew what I was talking about. Well, I detailed everything, except that I forgot to draw out the starting alkene!!!!!? This definitely went on the list. The moral of the story was to learn from every mistake. Also, there were a few stereochemistry concepts (particularly meso) that I still wasn’t quite strong enough on, so I had to figure those out, quickly.
6. Final Words of Advice
Another piece of advice is to not get behind and to try to understand everything as it is presented. If something looks foreign, it must be made familiar immediately. Look stuff up, do extra practice problems. I have done probably thousands of problems…way too many than I would even like to think of.
I feel like I am a little more efficient now. When I go into class, I have still read all of the chapter and have done most of the practice problems, or at least the recommended ones. Sometimes, if I don’t do all of the problems in a chapter, I will do ones that are similar to the recommended ones, since they have appeared on tests.? I don’t try to memorize every reactions before lecture, since I don’t know which ones the teacher will want us to know. Memorizing all of them would just be wasted time.
Also, I always consider homework to be “free points” in every class that I take. There is so much time and so many resources available that getting anything else than close to 100% is almost illogical to me.
Anyway, hope this helps. I think that should be the bulk of my approach.
-”Stu”
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