Browsing: o-chem help

An often-made SN1 mistake

Hi everybody, just wanted to give out a quick tip when looking at SN1 reactions.  Many students believe that SN1 reactions give totally racemic products, but this is not actually the case. 

We all know that the SN1 reaction proceeds through a carbocation intermediate, which cannot hold the stereochemistry that the carbon atom previously possessed.  (In other words, if you start with a chiral carbon and go through a cation, you will have a trigonal, achiral cation) 

 However, this is not the whole story.  Many times, the leaving group can come back to the cation on the same side.  This partially blocks one face of the cation.  The net result is that your carbocation CANNOT be equally attacked from both sides.  What you get out is both R and S at that carbon, but not in equal ratios.  This means that the SN1 reaction will lose some chirality, but will not usually become totally racemic.

 Good luck on those exams and happy reacting.

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Organic Chemistry Tip of the Week

Hey Everybody–

 Here is a minor distinction between two reactions that I have lately seen some students get crossed up on. 

Cold KMnO4, when reacted with a double bond, give the diol.

Hot KMnO4, when reacted with a double bond, cleaves the double bond to give two carboxylic acids. 

Temperature is the key here, don’t lose points on this.

 For more information on this, please go to organic chemistry

Good luck and happy reacting.

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Starting Organic Chemistry II

Hey Everybody, welcome to semester II.  Hopefully everybody survived the first semester and are ready to clobber “Organic Chemistry Part Deux”.

 One of the questions I get asked alot are about the differences between Semester I and II.  In semester I, you are building the foundation of your house so you need to learn things like nomenclature, stereochemistry, and functional groups.  Most people do some reactions (SN1, SN2, E1, E2) but it is very limited. 

 Semester II will focus on learning reactions.  This is a very good thing for the memorizers out there.  In addition to the simple reactions, you will also have multi-step syntheses and retrosyntheses (working backwards) to complete.  This becomes a big stumbling point for many people, because putting it all together can be difficult.  In future post, I will go over the best way to tackle a multistep problem, but that won’t be until middle semester. 

So until the next post, good luck and happy reacting.

For more information on this, please visit organic chemistry help

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Organic Chemistry Help: Deciphering an NMR

YOUR CLASS NOTES AND EXAMS ARE WORTH MONEY, FIND OUT HOW WITH THIS FREE GUIDE

Happy New Year!  It has been a while since we have put a new organic chemistry post up, so I thought I would put a little guide up now that finals are over.  The question is:  How did you decipher an H1 NMR spectrum?  Well, here is a good, uniform way to tackle the problem. 

 

Step 1: Calculate the degree of unsaturation in the molecule.  This is sometimes called the Sum of Double Bonds and Rings or SODAR.  You will most times be given a molecule formula, and can calculate your total number of double bonds and rings in the molecule using the formula (2#C + 2 – #H – #X + #N)/2 where

 

            #C = the number of Carbons

            #H = the number of Hydrogens

            #X = the number of Halogens

            #N = the number of Nitrogens

 

In this, you do not count the oxygen or sulfur atoms.  For example, the molecular formula C6H6NOCl would be (2*6 + 2 – 6 –1 +1)/2 = 4, meaning that there are 4 double bonds and/or rings.  It is helpful to remember that benzene rings equal to 4 on the SODAR scale, so if you have a SODAR that is 4 or larger, think benzene ring.

 

Step 2: Look for arene protons.  The number of protons between 6ppm-7.5ppm, known as the AR region, can give many clues to your molecule.  A mono-substituted benzene ring will have 5 protons in the AR region.  A di-substituted benzene will have 4 protons in the AR region.  However there are even clues to what type of di-substituted benzene it is.  If the peaks in the AR region are 2 perfect doublets, it is most likely para substituted.  If you have a singlet in the AR region, you most likely have a meta-substituted benzene.  If you just have a mess, it is most likely ortho substituted. 

 

Step 3: Look for the 2 A’s, aldehydes and alcohols.  This is actually simpler than it sounds, and can give you some nice clues.  Aldehydes are sharp singlet peaks that show up past 9ppm.  Alcohols are broad singlets that can show up anywhere in the spectrum, but will “exchange” with D2O, meaning that they will disappear if D2O is added.  Most organic chemistry profs will signify this by writing “exchange” over your spectrum.

 

Step 4:  Add up the integrations in your spectrum and make sure it equals the number of protons that you have.  For example, if you have 10 H’s in your formula, but can only have an integration equal to 5 on your spectrum, you need to realize that each integration is equal to 2 protons.

 

Step 5: Start to make fragments and then add up the fragments.  Using the integration and splitting of each peak, you can start to write down fragments of the molecule.  For example, if you have a singlet with an integration of 3, you know that you have a methyl group (3 H’s) next to something with no protons.  If you have a doublet with an integration of 2, you have a CH2 that is next to a CH.  Once you have all of your fragments, start to piece them together and you will be figure out what your molecule is. 

 For some good practice tests, please see organic chemistry.

 

 

 

 

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Always, sometime, never.

Disclaimer:  This posting applies to Undergraduate organic chemistry.  This does NOT apply to crazy physicists who create all sorts of insanity in a laboratory that cannot exist outside a xenon forcefield.   

I am going to give some organic chemistry advice that I like to refer to as:

 “ALWAYS, Sometimes, NEVER.”

ALWAYS/NEVER:

  – Hydrogen ALWAYS has only one bond to it.

  – Carbon NEVER has more thank four bonds.

  – Alkaline metals (Li, Na, ect) and alkali earth metals (Be, Mg, Ca, ect) can NEVER be negatively charged.

  – Noble gases are NEVER a part of any organic molcule.

  – Electrons ALWAYS flow from negative to positive.

  – Arrows ALWAYS point from negative to positive.

Sometimes:

  – Carbon can have 4 bonds (neutral), 3 bonds (positive, negative), or even 2 bonds (carbene)

  – Halogens USUALLY have one bond, but can occassionally have two.

  – Nitrogen usually has 3 bonds (neutral), 4 bonds (positive) or 2 bonds (negative)

  – Oxygen usually has 2 bonds, but can have only 1 bond (negative) or 3 bonds (positive)

  – Phosphorous is USUALLY an oxophile, meaning if it can react with oxygen, it will.

More organic chemistry help can always be found on the web too.

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Practice tests and practice questions: Good or is the time better spent playing Halo 3?

For the record, all I know is that Halo 3 is a video game that everyone loves.  Anywho…

The short answer to that question is YES, practice tests are great. But the real question that should have been asked is “what practice questions do I want”?  First, you want to get old exams from YOUR professor.  Different organic chemistry professors focus in on different things.  Your professor might focus in on physical organic chemistry (orbitals and such) where as another prof might focus on synthesis.

Next, if you have the time, will, and extra food, surf the net to find other profs at other schools and their tests.  If you can answer both sets (yours and the other guys) of questions, you are well on your way to a nice fat A. 

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Memorizing vs. Learning–Organic Chemistry Nomenclature.

I got a good question from a student recently:  “Should I memorize this or not?”

To be breif on this introduction, there are two types of students: memorizers and learners.  Which is better?  Both are a good, but being a combination of the two is the best.  That being said, there are certain times where one is essential.  Nomenclature is one of those.

Meth – 1

Eth – 2

Prop – 3

But -4

Pent – 5

Hex – 6

Hept – 7

Oct – 8

Non – 9

Dec – 10

If you memorize these now, you will save yourself a world of trouble down the road.  So, in conclusion, I am not a HUGE fan of memorization, but this is one instance where it is a good idea.

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For good results in your Organic Chemistry Lab class

Hey Guys–

 So when I was teaching, the one thing that I always heard was: “O-chem lab is a waste.  It is a ton of work for only one credit.”  I am not going to lie to anyone about this; yes, it is alot of work for that miniscule credit that (frankly) few people are going to care about.  I have been told, however, that medical schools DO care about o-chem lab.  So if you are one of those aspiring students who hopes one day to be abused as a resident at a busy hospital working 100 hour work weeks but not having quite as much fun as those crazy kids on the hit TV show “Scrubs”, you care about organic chemistry lab.

 Now here is the way to an easier time in organic chemistry lab:

1) Pre-lab preparation–  this is the most underrated portion of what goes on.  Go to my favorite site www.chemfinder.com and print out information on every chemical you are going to use and bring it to lab with you that day.  It will be a great resource to refer to when you need it and will keep you from saying to your already cranky TA, whose English is iffy at best: “Does this look right?”

2) Post-lab write up:  The biggest mistakes here are bad calculations and spending too much time writing things that your TA is never going to read.  When calculating things like % yield/recovery of your product, remember that you CAN have a yield over 100%.  This is usually due to impurity in your final product and is most likely that you did not remove all of the solvent sued, which makes your product heavier.  The key is to be concise, and make sure that the process of your calculations is correct.

While this quickie blog post is NOT going to turn that guy who is a lab disaster into a Nobel prize winner, they are the most commonly made mistakes.  Keep it all in mind next time you head into the great unknown which is o-chem lab. 

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Tips for writing organic chemistry lab reports

As to properly reference the authors, here is a guide from Lynchburg College on how to write a science report well.

A Few General Characteristics of Good Writing in Chemistry

1.  Clear.  This is perhaps the most important characteristic of all writing, but is especially important when detailed, complicated experimental data is discussed.  Be sure you say what you mean and mean what you say.   Use short sentences and get to the point.

2.  Dispassionate.  Good scientific writing is free of bias and personal opinion.  Report the facts.

3.  Mechanically sound.  This goes without saying.  If your writing is free of grammatical and spelling errors, it is easier for the reader to understand.

4.  Documented.  Statements and conclusions are supported by data, not feelings or opinions.  If your data are inconclusive, it is better to state this than to force the data to fit some hypothesis or literature value.

Other hints and suggestions for written work in chemistry:

    • Do not use first person (“I,” “we,” etc.). Use the past tense (you did the experiment already).
    • Do not be verbose.  Get to the point!
    • Do not start a sentence with a number unless it is part of a chemical name.
    • Do not capitalize the names of chemicals unless you are beginning a sentence.
    • Do not use the words or phrases “basically,” “dealt with,” “dealing with,” “create(d).” Leave bases to baseball and solutions with pH > 7; leave dealing to Las Vegas and Atlantic City; and leave creating to the Fine Arts department.
    • Regardless of  what your spell-checker says, “absorbency” is not a word unless we are analyzing diapers.  Always use “absorbance.”
    • Do not say things like “the goal of this experiment was to introduce to the student the technique of chromatography.”  Say “Carotenoids were purified using chromatography.” Leave the student out of the discussion.  Everyone knows you are a student. Tell the reader what you DID and HOW you did it.
    • Use the words “precise” and “accurate” correctly.  Accuracy refers to how close your value is to the standard or known value.  Precision refers to how close together your results are; data cannot be precise unless you have done more than one trial.
    • Use the words “clear” and “colorless” correctly.  Water is clear and colorless.  Sunglasses are clear and green.  Milk is cloudy and colorless (white).  Muddy water is cloudy and brown.
  • Report data and results with units and with the appropriate number of significant figures.
  • Do not include statements of opinion.  For example, stating that the experiment was difficult or tedious is your opinion and does not belong in a reporting of the results of your study.
  • The literature value of a physical property is just that; it is not the “literary” value.
  • Use numbered endnotes for referencing.  You need to reference anything you have to look up, even if it is in your textbook, the lab manual, or the CRC handbook or Aldrich catalog.
  • Please run the spell-checker.
  • Please staple together the pages of your reports.

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