Showing posts with label organic. Show all posts
Showing posts with label organic. Show all posts

Wednesday, March 17

Noorul Huda

Important Books of Organic Chemistry for Preparation of CSIR-NET | GATE | IIT-JAM | TIFR [with PDF links]

The Post includes all important books for Organic Chemistry preparation for various M.Sc level examinations, including CSIR-UGC NET, GATE, IIT-JAM, TIFR, BARC etc. The books and links provided below are to make these books accessible to all and develop book reading culture among aspirants. 


The Books contain links to Buy Hard Copy (from online websites like Amazon.in) and also Free PDF download. There can be differences in the edition of book provided as hard copy link and PDF file.


Organic Chemistry:

1. Modern Methods of Organic Synthesis by William Carrithers and Iain Coldham:


Buy Hard Copy Online: Click Here
Free PDF Download: Click Here
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Saturday, May 12

Noorul Huda

Important Spectroscopic Data Tables | IR Spectroscopy | NMR Spectroscopy (1H-NMR, 13C-NMR)

This post contains important spectroscopic data tables which will help in structure elucidation of compound with the known data values. The post contains tables for IR Spectroscopy, 1H-NMR and 13C-NMR spectroscopic data.


IR Spectroscopy Data:

The given below table is the approximate wavenumber values obtained in IR Spectroscopy of corresponding functional group.



1H NMR Spectroscopy Data

The below table is approximate chemical shift value for different functional groups obtained in 1H-NMR spectroscopy.




13C NMR Spectroscopy Data

The below table is approximate chemical shift value for different functional groups obtained in 13C-NMR spectroscopy.





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Tuesday, June 6

Noorul Huda

Acidity or Basicity of Alcohols

Here we are going to discuss and understand acidity and basicity of alcohols. These Questions are often asked in CSIR and other examinations where we've to arrange the order of acidity of given alcohols.
That’s the purpose of today’s post! In this post we’re going to:
  1. Review 4 key points about acid base reactions
  2. Give 2 examples of alcohol acid-base reactions
  3. Review the key factors which determine the acidity
  4. Show examples of how this applies to alcohols.
  5. Solve some practice question at the end.
Lets begin...

Four Key Points To Review About Acid Base Reactions

  1. Every acid-base reaction has 4 components: an acid, a base, a conjugate acid, and a conjugate base.When an acid loses a proton, it becomes its conjugate base. When a base gains a proton, it becomes its conjugate acid. As mentioned in the previous post, the conjugate bas of an alcohol is called an alkoxide. The conjugate acid of an alcohol is called an oxonium ion.
  2. We usually describe acid-base reactions as an equilibrium. In acid-base reactions, the equilibrium will favor the direction where a stronger acid and stronger base produces a weaker acid and a weaker base.When you add HCl to NaOH, a violent acid-base reaction occurs, which leads to the formation of H2O (a weaker acid than HCl) and NaCl (a weaker base than NaOH). As you’ve no doubt discovered when adding table salt (NaCl) to water, this reaction doesn’t proceed to any significant extent in the reverse direction.
  3. We measure acidity using a term called pKa. This is a measure of the equilibrium constant for a species giving up a proton to form its conjugate base.pKa is on a scale of about -10 to 50. Sixty orders of magnitude! The higher the pKa the less acidic it is.  Lower pKa (more negative ) = more acidic.
    Water (pKa of 15.7) is a weaker acid than HCl (pKa of -8).
  4.  The stronger the acid, the weaker the conjugate base. The weaker the acid, the stronger the conjugate base. The conjugate base of the strong acid HCl (pKa -8) is the innocuous chloride ion (Cl-), a very weak baseThe conjugate base of the weak acid H2O (pKa 15.7) is the strongly basic hydroxide ion (HO-).

Examples of Acid-Base Reactions Of Alcohols

Here’s an example of a favorable acid-base reaction of alcohols. Note how we’re going from a stronger acid and stronger base to a weaker acid and weaker base [pKa values tell us for sure] Here, deprotonation is very favourable. Note that the conjugate base of an alcohol is called an alkoxide.
1-acidbase

Here’s an example of a (very) unfavorable acid-base reaction of alcohols: protonation of an alcohol by NH3. The most important reason why this is unfavourable is because we’re going from a weaker acid (pKa 38) and weaker base to a stronger acid (pKa -2) and stronger base. The equilibrium constant is about 40 orders of magnitude in the wrong direction!
2-acidbase

The Key Factors Which Determine Acidity

The key factor in determining acidity is the stability of the conjugate base. Any factor which makes the conjugate base more stable will increase the acidity of the acid.
What does that mean, exactly? Usually, it means stabilizing negative charge since the conjugate base will always be one unit of charge more “negative” than the acid.
How is negative charge stabilized? Two ways.
  • First, by bringing the charge closer to the positively charged nucleus [“opposite charges attract”, remember]. Across a row of the periodic table, for example, basicity decreases as we go from H3C to H2N to HO to F  because the electronegativity of the atom is increasing. That negative charge is being held closer to the nucleus, and therefore is more stable. A good rule of thumb is, “the more stable a lone pair, the less basic it is. This is also why certain species are made acidic by adjacent electron-withdrawing groups.
  • Second, by spreading charge out over a larger volume. Diffuse charge is more stable than concentrated charge. Down a row of the periodic table, for example, basicity decreases as we go from F to Cl to Br to I– because that negative charge is being spread out over a larger volume (larger atoms). The larger atoms are said to be more “polarizable”. [Note that this effect dominates rather than electronegativity in this case.] This is also why resonance serves to stabilize charges; the charge is being spread across multiple atoms, therefore reducing individual charge density.

Also Visit:

Applying These Principles To The Acidity Of Alcohols

How do these principles relate to alcohols? It’s quite simple, actually. Since we’ll always be comparing the same atom (oxygen) we don’t need to worry about periodic trends, and we just need to focus on resonance and adjacent electron-withdrawing groups.
Alcohols where the conjugate base is resonance stabilized will be more acidic. The classic example is cyclohexanol and phenol.
Cyclohexanol has the pKa of a typical alcohol (about 16). The pKa of phenol, however, is about 10. Let’s look:
3-phenol-cyclohexanol
See how that negative charge on the oxygen of phenol can be “delocalized” back into the ring? That means the charge can be spread out throughout the molecule, which is stabilizing. Any factor which stabilizes the conjugate base will increase acidity. 
4-phenolate resonance
Here’s another example. Compare ethanol (pKa 16) to 2,2,2-trifluoroethanol (pKa about 12). Why do you think trifluoroethanol is more acidic?
5-ethanol tfe

Compare their conjugate bases. What is fluorine doing here to make the conjugate base more stable?
This is an example of an inductive effect. Fluorine, being highly electronegative, pulls electron density away from the neighbouring carbon. That carbon, now being electron poor, pulls electron density away from the carbon next door. And that carbon, being slightly electron poor, can pull some electron density away from the oxygen.
The net result is that the oxygen has lower electron density, which is stabilizing. Again, stabilize the conjugate base –>  increase acidity. 

This also works if we compare alcohol variations where we change the distance between the OH and the fluorine atom.
6-EWG-distance

That’s because the inductive effect decreases in magnitude the farther away we go from the electronegative atom.

We can also use electronegativity trends to determine the order of acidity in these molecules. Since fluorine is more electronegative than chlorine which is more electronegative than bromine which is more electronegative than iodine, the inductive effect will be highest for CF3 and lowest for CI3.
7-ewg halides


Finally, one last example. We can even think of examples where these two effects are combined:
8-acidity
Which do you think might be most acidic here?

Conclusion

For alcohols, since we’re always dealing with oxygen, the only relevant factors here are resonance and electron withdrawing groups.




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Friday, May 26

Noorul Huda

IR Spectroscopy: Some Practice Problems

By itself, Infrared (IR) spectroscopy isn’t a great technique for solving the structure of an unknown molecule. However, we’ve seen that IR spectroscopy can be a great technique for identifying certain functional groups in an unknown molecule – especially functional groups containing OH or C=O.

In this post we’re going to go through four (simple) practice problems where you’ll be provided with an IR spectrum and the molecular formula, and are then charged with the task of figuring out which molecule best fits the spectrum.


Let’s begin.
(answers to each problem, along with analysis, are at the bottom of the post. Don’t see them until you’ve given each problem an attempt).



Problem #1: Unknown molecule with molecular formula C5H10O. Which of these five molecules is it most likely to be?
2-c5h10o
unknown-1_c5h10o




Problem #2: Unknown molecule with molecular formula C6H12O.
1-c5h10o
unknown-2-c6h12o




Problem #3: Unknown molecule with molecular formula C6H14O .
3-c6h12o
unknown-3-c6h14o




Problem #4: Unknown molecule with formula C4H8O (Also, smells like vomit)
4-c4h8o2
4-unkown-c4h8o2

 

 

 

Answers

Problem 1: 
  • You’re given the molecular formula, which is C5H10O. This corresponds to an index of hydrogen deficiency (IHD) of 1, so either a double bond or ring is present in the molecule. This immediately rules out d) whose IHD is zero and thus has a molecular formula of C5H12O.
  • Looking at the spectrum we see a broad peak at 3300 cm-1 and no dominant peak around 1700 cm-1 (That peak halfway down around 1700 cm-1? It’s too weak to be a C=O. )
  • That broad peak at 3300 tells us that we have an alcohol (OH group). The only option that makes sense is e) (cyclopentanol) since it has both an OH group and an IHD of 1. It can’t be bsince that molecule lacks OH.
  • a) and c) are further ruled out by the absence of C=O ; B is ruled out by the presence of the OH at 33oo
Problem 2: 
  • A molecular formula of C6H12O corresponds to an IHD of 1 so either a  double bond or ring is present in the molecule.
  • There is no strong OH peak around 3200-3400 cm-1 (that little blip around 3400 cm-1 is too weak to be an OH). We can immediately rule out aand e.
  • However, we do see a peak a little above 1700 cm-1 that is one of the strongest peaks in the spectrum. This is a textbook C=O peak. We can safely rule out b) which lacks a carbonyl.
  • The only option that makes sense is d) (2-hexanone) since c) doesn’t match the molecular formula (two oxygens, five carbons).
  • Note also that the C-H region shows all peaks below 3000 cm-1 which is what we would expect for a saturated (“aliphatic”) ketone.
Problem 3:
  • A molecular formula of C6H14O corresponds to an IHD of zero. No double bonds or rings are present in the molecule.
  • Using this we can immediately rule out d) and e) since their structures cannot correspond to molecular formula (they are both C6H12O)
  • There is no OH peak visible around 3200-3400 cm-1. We can rule out a) and b) .
  • This leaves us with c) . It’s an ether.
  • Useful tip: ethers are “silent” in the prominent parts of the IR spectrum; this functional group is best identified through a process of deduction. Seeing an O in the formula but no OH or C=O peaks, the only logical selection is c) .
  • Final note: e) is a cyclic ether called an “epoxide”. The important clue to distinguish c) and e) was the fact that we were given the molecular formula. In the absence of that information it would have been difficult to tell the difference without a close consultation of an IR peak table.
Problem 4: 
  • The immediate giveaway is the smell of puke. That’s butyric acid for sure!
  • More seriously: the formula of C4H8O2 corresponds to an IHD of 1. We can immediately rule out c) .
  • Looking at the IR spectrum we see a huge peak in the 3300-2600 cm-1 region that blots out everything else.  This seems like a textbook “hairy beard” typical of a carboxylic acid, but let’s look for more information before confirming it. We can at least rule out a) , which has no OH peaks.
  • We also see a strong peak a little above 1700 cm-1 which is typical of a C=O. We can safely rule out e) which lacks carbonyl groups entirely.
  • This leaves us with two reasonable choices: b) (the carboxylic acid) and d) the ketone / alcohol. How to choose between the two? The “hairy beard” is diagnostic. Alcohol OH peaks don’t fill up 600 wavenumber units the way that carboxylic acid peaks do. [Go back and look at a few examples from the previous post if you’d like confirmation]  A more subtle way to distinguish the two might be the position of the carbonyl peak, but carboxylic acids (1700-1725 cm-1) show up largely in the same range as do ketones (1705-1725 cm-1).



You might recognize that in each of these four examples we followed a simple procedure:

  1. Since we were given the molecular formula, we calculated the index of hydrogen deficiency. This is a quick calculation and gives us useful information. We were able to use it to “rule out” a few answers which you might classify as “trick questions”.
  2. Next, we examined the hydroxyl region around 3200-3400 cm for broad, rounded peaks (“tongues”) typical of OH groups . The most important question we want to answer is: “is there an OH present”?
  3. Then, we looked at the carbonyl region from about 1650 – 1830 cm for  sharp, strong peaks (“swords”) typical of C=O groups. Here we want to quickly know if there are any C=O groups present.
  4. Using these three pieces of information we could then rule out various options that were given to us, narrowing down the possible options.  Granted, these were relatively simple examples (only C,H, and O), but the thought process is what’s important.

Notes and Conclusion

  • It’s nice to be able to get a positive ID on a functional group, but ruling things out can be valuable too. The absence of an OH or C=O peak (or both) is still helpful information! We used this in Problem 3 to infer the existence of an ether by the absence of an OH or C=O.

  • A related point: information you get about a molecule from various sources (e.g. molecular formula, UV-Vis, IR, mass spec, 13-C and 1H NMR)  is self-consistent and should not contradict. 




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Friday, April 7

Noorul Huda

Anti-Aromaticity: Properties and Applications

In our previous posts in our series on aromaticity [Aromaticity: A brief discussion] we saw that aromatic molecules are unusually stable. They have particularly large resonance energies, tend to undergo substitution rather than addition reactions, and have delocalized pi electrons (all the C-C bond lengths in benzene are equal, for example).
In order to be aromatic, a molecule must possess the following four structural characteristics:
  • cyclic
  • conjugated all around the ring
  • have [4n+2] pi electrons  [equivalently: the number of pi electrons must equal twice an odd number]
  • flat (planar)
If these four conditions are met, the molecule is aromatic.



If  even one condition is not fulfilled, it’s non-aromatic.
 
But here’s one more thing. There’s a small number of molecules that escape the aromaticity test that aren’t just non-aromatic: they have the property of being so spectacularly and unusually unstable and difficult to isolate that they deserve another name. We call these molecules “anti-aromatic“.


What Makes A Molecule Anti-Aromatic?

Each of them is cyclic, conjugated, and flat – and when you count the number of pi electrons, it’s multiples of 4. So while aromatic molecules have (4n+2) pi electrons, the “rule” for anti aromatic molecules is (4n).  (

This unusual instability is called “anti-aromaticity”.


This means that we can now draw up three categories for molecules according to the following criteria:

  • Aromatic molecules are cyclic, conjugated, have (4n+2) pi electrons, and are flat.
  • Anti-aromatic molecules are cyclic, conjugated, have (4n) pi electrons, and are flat.
  • Non-aromatic molecules are every other molecule that fails one of these conditions.

Is Cyclooctatetraene Anti-Aromatic?


Cyclooctatetraene is anti-aromatic only if it is flat. However, the relatively “floppy” structure of cyclooctatetraene allows for some flexibility. The bonds can rotate away from flatness such that the molecule adopts a “tub-like” shape, thereby avoiding the repulsive energy of 18 kcal/mol that would be paid if all the p-orbitals on the molecule were conjugated with each other.



Applications of Anti-Aromaticity:


Application 1.

 In the reaction shown below. The solvent is propionic acid, and the Lewis acid silver perchlorate is added to assist with pulling off the iodine. [The mechanism is that Ag+ coordinates to the iodine, and then the C-I bond breaks. Silver iodide is extremely insoluble, and precipitates out of solution, driving the reaction towards completion].
Even under these conditions the cyclopentadienyl carbocation is not formed, which is a testament to its extreme instability.




Application 2.


 Epoxidation on ethene is known however  epoxidation of acetylene to form oxirene is unknown.


Application 3.


The existence of a 1H-azirine has been postulated in the addition of a nitrene to an acetylene, which quickly rearranges to a (stable) 2H-azirene (below).

Note that in 2H-azirene the lone pair on the nitrogen is at right angles to the pi system, so this system is non-aromatic as opposed to anti-aromatic.


Application 4. 


An experiment determined that 1,2-dideutero cyclobutadiene has two isomers, not one (see below). This indicates that the double bonds in cyclobutadiene are not delocalized as they are in benzene, but are more like double bonds in a conventional diene.

Cyclobutadiene reacts with itself at -35 K to form a “dimer”, in an example of a Diels-Alder reaction.


Application 5.


It’s true that the lone pair in azirene can be put into an sp3 hybrid orbital (below). This likely reduces the anti aromatic “strain” somewhat, but the molecule is still incredibly unstable. Anti-aromaticity is the simplest way to account for this.





Summary:


Above post can be summarized as below, Molecules are divided into three groups: Aromatic, Anti-Aromatic and Non-Aromatic







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Friday, February 24

Noorul Huda

Aromaticity- A Brief Discussion

Whenever we talk about aromatic compounds, the first thing which comes in our mind is BENZENE. Yes ofcourse being a chemistry student, the first aromatic compund which we come across is benzene only. I still remember when i was in class 10th and my teacher taught us about structure of benzene I was so amused with the beauty of it's structure. I mean how can a molecule look so beautiful with conjugate double bonds and a cute hexagonal shape. Well I'm sure most of us must have thought the same way.



Okay so without wasting time lets come upon our topic of Aromaticity. Aromaticity was basically derived from the term Aroma [which means sweet smell], so initially it was considered that aromatic compounds are all those compounds having a pleasant smell.
For a chemist, an aromatic compound must have following properties:
  1. have an extremely high resonance energy (36 kcal/mol for benzene)
  2. undergo substitution rather than addition reactions
  3. have delocalized pi-electrons
So the Question arises how can we conclude whether a molecule is aromatic or not?

I've tried to make this simple for you,
here's the answer; For a molecule to be regarded as Aromatic, it must meet following 4 conditions. If any of these conditions are violated, no aromaticity is possible.

Condition 1: The Molecule Must Be Cyclic

 It's very simple if there's a Ring move to condition 2. If there’s no ring, forget it.

for e.g.: (Z)-1,3,5 hexatriene has the same number of pi bonds (and pi electrons) as benzene, but isn’t aromatic. No ring, no aromaticity.


Condition 2: Every atom in the ring must be conjugated

In order for aromaticty to exist, there must also be a continuous ring of p-orbitals around the ring that build up into a larger cyclic “pi system”.

One way of saying this is that every atom around the ring must be capable of conjugation with each other.

Remember that the “available p orbital” condition applies not just to atoms that are part of a pi bond, but also atoms bearing a lone pair, a radical, or an empty p orbital (e.g. Carbocation)

The key thing  that “kills” conjugation is an sp3 hybridized atom with four bonds to atoms. Such an atom cannot participate in resonance.



Condition 3: The Molecule Must Have [4n+2] Pi Electrons {The Huckel Rule}

The third condition is that the cyclic, conjugated molecule must have [4n+2] pi electrons. Benzene and cyclooctatetraene are both cyclic and conjugated, but benzene is aromatic and cyclooctatetraene is not. The difference is that benzene has 6 pi electrons, and cyclooctatetraene has 8.


However, this term [4n+2] causes a lot of confusion in organic chemistry. Many students stare at a molecule and try to figure out what “n” is.
“n” is not a property of the molecule!

“4n+2 is not a formula that you apply to see if your molecule is aromatic. It is a formula that tells you what numbers are in the magic series. If your pi electron value matches any number in this series then you have the capacity for aromaticity.”

The “magic series” is: 2, 6, 10, 14, 18, 22….. (and so on).
[4n+2] is just a mathematical shorthand for writing out the series [2, 6, 10, 14, 18, 22…] .

The numbers in this “magic series” are sometimes referred to as “Hückel Numbers” after Erich Hückel, who proposed this rule back in 1931.

The condition that aromatic molecules must have [4n+2] pi electrons is sometimes called “Hückel’s rule”.


In the figure below, molecules which fulfil Hückel’s rule are in green; those which do not fulfill Hückel’s rule are in red.

Note that we can count electrons in pi bonds as well as electrons from lone pairs (so long as the carbon isn’t already participating in a pi bond). So the cyclopentadiene anion has six pi electrons – 4 from the two double bonds, and two from the lone pair on carbon.

Here Question Arises-Which Electrons Count As “Pi Electrons”?

That seems easy. However, complications may arise when we have atoms in the ring which both participate in pi bonding and also have a lone pair. For example, pyridine, pyrrole etc.

Some Examples With 5-Membered Rings

Some molecules with five-membered rings can also present ambiguities.
The cyclopentadiene anion (below)  has a lone pair on one of the carbons. Can this lone pair contribute to the pi system?
Since that carbon is not involved in any pi-bonding, the answer is yes.
The total number of pi electrons for the cyclopentadiene anion equals 2 (from the lone pair) plus the 4 electrons in the two pi bonds, giving us a total of 6. This is a Hückel number and the cyclopentadiene anion is in fact aromatic.

A similar situation arises for pyrrole. The nitrogen bears a lone pair but  is not involved in a pi bond (unlike pyridine, above). Therefore it can contribute to the pi system and this gives us a total of 6 pi electrons once we account for the 4 electrons from the two pi bonds.

A curious case is furan, where the oxygen bears two lone pairs. Does this mean that furan has 8 pi electrons? No! 
Why not? Because as we noted above, each atom can contribute a maximum of one p-orbital towards the pi system. In furan, one lone pair is in a p orbital, contributing to the pi system; the other is in the plane of the ring. This gives us a total of 6 pi electrons. Furan is aromatic. (So is thiophene, the sulfur analog of furan).

Finally there is imidazole, which has two nitrogens. One nitrogen (the N-H) is not involved in a pi bond, and thus can contribute a full lone pair; the other is involved in a pi bond, and the lone pair is in the plane of the ring. This also gives us a total of 6 pi electrons once we account for the two pi bonds.


Condition 4: The Molecule Must Be Flat

The fourth condition for aromaticity is that the molecule must be planar.

   As with certain vertebrates, the only thing that preventing a molecule that fulfills the first three conditions from being flat is if the flat conformation is incredibly strained.
One example in this category is the molecule known as [10]-annulene, an isomer of which is drawn below left. In the trans, cistrans, cis, cis isomer, the molecule is cyclic, conjugated, and has 10 pi electrons, but the two marked hydrogens bump into one another when attempting to adopt a flat conformation.
The molecule is prevented from adopting planarity due to this punitive Van Der Waals strain , and is therefore not aromatic. 
Interestingly, if the hydrogens are removed and replaced with a bridging CH2 group, the strain is relieved and the pi bonds can adopt a planar conformation. The molecule below right shows the expected properties of an aromatic molecule.



 References: 

  1. Wikipedia
  2. Google image search
  3. masterorganic chemistry

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