What are strong nucleophiles?  

Strong nucleophiles:

Strong nucleophiles…this is why molecules react. The nucleophilic site of the nucleophile is the region of a molecule that is reactive and has the electron density.

Strong nucleophiles are VERY important throughout organic chemistry, but will be especially important when trying to determine the products of elimination and substitution (SN1 vs SN2) reactions.  In fact, there is not a more important part of an organic chemistry reaction than the nucleophile and the electrophile.   So, let’s look at what makes strong nucleophiles:

There are generally three factors to remember when discussing how nucleophilic a reactant is:

1)      Size – Generally (but not always) the more linear and/or smaller the nucleophile, the more nucleophilic it will be.  This is because it can react at more sites and will not be sterically hindered if it is smaller or linear.  Remember, smaller nucleophiles can fit into more places, therefore will be able to react at more places and will necessarily be more nucleophilic.  This has a lot to do with sterics. You will hear a lot about bulky bases, which are nucleophilic but too darn big to be a nucleophile and can only be a base.

2)       Electronegativity– The more electronegative an atom is, the less nucleophilic it will be.   This is because more electronegative atoms will hold electron density closer, and therefore will be less likely to let that electron density participate in a reaction.  We see this in calculations and experiments that show nucleophilicity decreases as you get closer to fluorine on the periodic table (C > N > O > F).

3)      Polarizability– The more polarizable an atom is, the more nucleophilic it will be.   Polarizability is defined as the ability to distort the electron cloud of an atom, which allows it interact with a reaction site more easily.  Generally, polarizability increases as you travel down a column of the periodic table (I > Br > Cl > F)

Below is a table of relative nucleophilic strength.  This is relative because nucleophilic strength is also dependent on other factors in the reaction, such as solvent. I am not a huge fam of memorizing charts, but this might be a good one to know pretty well.

As shown above, as a general rule, the anion of a reactant will be a better nucleophile than the neutral form.  (i.e. RCO₂^– is a better nucleophile than RCO₂H)

But nucleophiles are also bases?

Think about it for a second….good nucleophiles (as shown above) can have a negative charge and will almost always have a lone pair. Bases accept protons, with a negative charge or lone pair. [gasp] So it makes sense there will be at least some overlap between bases and nucleophiles. This is a major consideration when looking at SN vs E reactions.

Here are a couple of good rules to remember:

1. Bases will not be good nucleophiles if they are really bulky or hindered. A variety of amine bases can be bulky and non-nucleophilic.

2. Nucleophiles will not be good bases if they are highly polarizable. I- is the best example of this. Great nucleophile, really poor base.

Why do we care about strong nucleophiles?

Organic chemistry is all about reactions. We really need to know what is nucleophilic and what is not so that we can determine what is going to react at the electrophilic site. If you know this, you can predict the products of organic chemistry reactions, even ones that you have not seen before.

The next step is to learn about electrophiles. 

Please visit our recent post on this topic –> Electrophilic addition. Not to humble brag, but it is pretty good.

For more information on this and other topics of organic chemistry interest, please visit organic chemistry

Reference: Nucleophilic strength

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Functional Groups in Organic Chemistry

Welcome back.  Let’s not beat around the bush on this one: functional groups in organic chemistry are why we can do any organic chemistry in the first place. Functional groups are the basis of why molecules can and will react with each other. Without functional groups, everything would be straight chain alkanes and other boring hydrocarbons. So it’s important to learn functional groups, and how they will interact with nucleophiles and electrophiles to react to form new organic molecules.

Major Disclaimer:  This is not meant to be a comprehensive review of all of the functional groups out there, however it’ll be a nice start and a good reference for you.

Hopefully you understand why they are important, now we just have to determine what some of the different types are.

What to learn about nucleophiles?  Click on the link to check it out

Hydrocarbons: these are simply composed of carbon and hydrogen. This group is alkanes, cycloalkanes, alkenes, and alkynes.  Don’t forget about conjugated alkenes too, as they are important in many organic processes such as the Diels-Alder reaction.  While alkanes and cycloalkanes are not particularly reactive, alkenes and alkynes definitely are.

Carbonyls: a “carbon double bond oxygen” is a carbonyl.  It is one of the more important electrophiles you will see in this course.  While there are different variations which can make the carbonyl more or less reactive, the basic functional group is still the same.  The important point here is to know which types of carbonyls are more electrophilic and which ones are less. Generally speaking, if there is an electron withdrawing group attached to the carbonyl carbon, that carbonyl will be more electrophilic and more reactive.

Alkyl Halides: alkanes which are connected to a halogen atom (F, Cl, I, and Br) are good electrophiles.  These can participate in nucleophilic substitution reactions and elimination reactions.  They reactivity depends on the type of alkyl halide (F, Cl, I, Br), its substitution (primary, secondary, tertiary) and the desired reaction (SN1, SN2, E1, E2).

Alcohols, Amines, and Thiols: these are generally very good nucleophiles, as the heteroatoms have lone pairs which will attack an electrophile.

Ethers: do not undergo many organic reactions themselves, but sometimes can be the product of a reaction.  Some chemists refer to ethers as “dead molecules” because of their low reactivity.

And now for some crazy functional groups….

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S_N1 vs S_N2. Is it S_N1, S_N2, E1, E2?

This is such a common question, not only for students but on exams too.  How do you tell if it is S_N1 vs. S_N2? How the heck do you tell the difference between an E1, E2, SN1, SN2 reaction?  Check out the chart below to start.

The factors that will decide S_N1 vs S_N2 and whether it is S_N1, S_N2, E1, E2:

1) Do you have a strong nucleophile?  If you do, it will favor an S_N2 reaction in the S_N1 vs S_N2 fight.  If it is a mediocre nucleophile, it will favor an S_N1 reaction.  This is because of the two mechanisms.  In the S_N1, we have an open position (carbocation), so any old nucleophile can just waltz in and form a bond.  In the S_N2, we are pushing off the leaving group, which requires a stronger nucleophile.  What is a strong nucleophile?  Check out these blog posts on strong nucleophiles and strong electrophiles.

2) Does your nucleophile double as a base? If yes, it is going to favor elimination (E1/E2) over substitution (S_N1/S_N2).  Bases want to take protons, which leads to elimination.

3) How good is your leaving group?  If it is awesome, it is more likely to be a carbocation intermediate, ie E1 or S_N1 reaction.  If the leaving group is only OK, that means it has to be forced off and is more likely to be a concerted reaction mechanism like S_N2 or E2.

4) What is your solvent? Polar protic solvents will stabilize a carbocation better, therefore promote an E1 or S_N1 reaction.  Polar aprotic solvents favor S_N2 and E2.  This is because a protic solvent is more likely to stabilize a carbocation intermediate and therefore promote the E1/SN1 pathway.

5) What kind of substrate do you have?  If your starting material is a tertiary substrate, you are definitely E1 or S_N1.  If it is a primary substrate,  you are definitely S_N2 or E2. If it is a secondary substrate, it could go any one of the ways.

The S_N1 vs. S_N2 video:

Here are two videos were are particularly fond of that coach you through the way to decide which of these things it is.

Some Examples:

This is an easier example, but let’s start with it.  Here is the most important thing to see: The product has OTf substituted, NOT eliminated.  Just by looking at the product, we know it has to be an S_N1 or S_N2 reaction NOT an E1 or E2 reaction.  Therefore, when we look at the different factors below, we are going to ignore E1 and E2.

• Nucleophile: Cl is good but not great. Mediocre Nu = S_N1.
• Basic: NaCl is not basic.  No base = S_N1/S_N2.
• Leaving group: OTf is a dynamite leaving group.  Awesome LG = S_N1.
• Solvent: tBuOH is a polar protic solvent = S_N1.
• Substrate: It’s tertiary at the leaving group = S_N1

All of the factors point to an S_N1 reaction, therefore I feel comfortable saying it is an SN1 reaction.

How about this one:

This is still clearly a substitution, but it’s on a secondary substrate, so it could go either S_N1 or S_N2.  Here are the factors:

• Nucleophile: CN is a great nucleophile.  Great Nu = S_N2
• Basic: NaCN is not basic.  No base = S_N1/S_N2, but we already knew that.
• Leaving group: Cl is a decent leaving group. Decent LG = S_N2
• Solvent: acetone is a polar aprotic solvent = S_N2
• Substrate: It’s secondary at the leaving group = S_N1 OR S_N2

Almost all of the factors point to an S_N2 reaction, with the notable exception of the type of substrate.  I still feel comfortable saying it is an S_N1 reaction.

What do you think?  What is the most difficult substitution/elimination problem you have seen on an exam or in class?

Reference: E1 E2 SN1 SN2 chart 

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Electrophilic Addition: 2022 Edition

Electrophilic addition: Just like in football, it is easy to say that one of the players is the most important one in the game.  But they all play an important part, and electrophiles are one of those important parts.

While many (nerdy) organic chemists could have a robust debate over a pint as to which of the compound class is most valuable in the reaction, we are going to treat them all as important.  In its most basic form, they are all essential in some way or another to the reaction’s success.  Hence, we are going to start with acids and discuss all of the compound classes one by one.

Electrophiles are one of the two most important reactants in organic chemistry (spoiler alert: the other is a nucleophile, check out our blog post on those here).  As we have discussed previously on this blog, organic chemistry reactions are all about the flow of electrons, and electrophiles are the ones who want those electrons. When you think of the word “electrophile” you should think of the Greek word “Philos” which means “to love”.  Therefore, an electrophilic species is one that loves electrons.  Easy enough, right?   Since opposites attract, and the electrophile loves electrons, then it must be that the electrophile is positively charged. Most often, you will see this abbreviated as “E⁺”.

So the question now becomes: what make an atom a good electrophile and how do we spot it? Since we know the electrophiles want to electrons, the first clue that something is electrophilic is that it has a positive charge. The second clue is if we can place a positive charge somewhere on the atom via resonance and that it has an empty orbital (positive charge or metal with an empty orbital) or can get an empty orbital by kicking off a leaving group.  Below are some common classes of electrophiles you will see frequently in your course:

– In example A, a carbonyl is shown. We know that the carbon of the carbonyl is electrophilic because we can place a positive charge on it via resonance. This means that a nucleophile will attack the carbonyl at this carbon atom. [Fun fact: the oxygen of the carbonyl is actually way less nucleophilic than one might think] 

-In example B, we show diatomic chlorine. Diatomic halogen molecules (Cl₂, Br₂, I₂) are electrophilic because the bond between the halogen atoms as polarizable, meaning that the electrons can reside on either atom at any time, making one of the atoms more electrophilic than the other at any one given time. Think of it as the electron density jumping back and forth from one chlorine atom to another, making one of them more electrophilic for just an instant.

-In example C, we see that alkyl halides are also electrophilic because of a polarizable bond between the carbon and the chlorine atoms.  Unlike example B, example C is a permanent dipole. 

-Example D is an example of a strong acid completely disassociating, which gives off a proton as the electrophilic species.

-Finally in example E, we see it you can create an electrophile from a non-electrophilic molecule. Here we have reacted nitric acid with sulfuric acid to form the nitronium ion, which is highly electrophilic.

Electrophiles are also Lewis Acids. Lewis acids accept electron density, because they are electron deficient. The reagent acting as the Lewis Acid can suck electron density from the electrophile, making even more electron deficient and therefore even more reactive. Crazy, right?

Take home points on electrophiles:

1)      They want electrons, meaning they are electron deficient, in order to form a new bond.

2)      They are attacked by nucleophiles.

3)      They are positively charged (or have a partial positive), polar and/or polarizable.

4)      They become even better electrophiles in the presence of Lewis acids.

Would you like to learn about the nucleophiles that will attack these electrophiles?  Please go to strong nucleophiles to get a good flavor of those.

And now, electrophilic addition reactions:

For more help with organic chemistry, please see organic chemistry help

Reference: Electrophiles

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Organic Chemistry Rules: Never violate these!!

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.

In organic chemistry, like in life itself, there are rules.  Some of them (known as the “always/never” rules) should never be violated, such as always wash your hands leaving the bathroom, or never spit in church.  Other rules (known as the “sometimes” rules) are guides that you should be aware of rather than hard rules. 

Thus, we present a blog post called “Organic Chemistry Rules: ALWAYS, Sometimes, NEVER.”

ALWAYS/NEVER:

1) Hydrogen ALWAYS has only one bond to it.  You will never see an organic molecule that has two bonds to hydrogen.

2) Carbon NEVER has more than four bonds. EVER!

3) Alkaline metals (Li, Na, ect) and alkali earth metals (Be, Mg, Ca, ect) can NEVER be negatively charged.  They will always be neutral or positively-charged ions in solution.

4)  Noble gases are NEVER a part of any organic molecule.  Because they have a full octet, they have very little reason to create a covalent bond.

5) Electrons ALWAYS flow from negative to positive.  This is a biggie.  And because of this, rule #6 exists.

6) Reaction arrows ALWAYS point from negative to positive.  Always point from the nucleophile to the electrophile.

Sometimes:

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

– Halogens USUALLY have one bond, but can occasionally 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.

This brings us to another point about knowing the common states of organic atoms.  This can really help you in solving organic chemistry if you know the normal state of organic atoms [this is a link to one of our favorite blog posts]

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Emil Fischer is considered by many to be the greatest organic chemist to ever live.  His problem was that he created a way of looking at organic molecules that is very confusing to undergraduates.  These structures are necessary to learn and are very helpful when looking at certain molecules (such as carbohydrates), but they are also very easy to jumble.  This is because Fischer structures are drawn as crosses, which could lead one to erroneously think that the central carbon is flat, when it is actually still tetrahedral.

The easiest way to look at these is to think of them as bowties that have been strung together:

3-dimensionally speaking, the substituents that are on the sides of the structure are depicted at the end of the bowtie and are represented as “coming out of the paper”.  The backbone is composed of dashed lines, which are meant to represent that those portions “are going into the paper”.  This is now a much easier way to view these structures, as it is more apparent what area each substituent occupies.

The useful part of the bowtie projection is that it is now easier to assess the stereochemistry at each chiral center.   It should be much easier to visualize that the bottom chiral center is “R”.  This was not as obvious when viewing the Fischer projection as a cross

For more help like this, please go to organic chemistry

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How to study for organic chemistry?

How to study for organic chemistry? I get asked this question pretty frequently…and while there is no easy answer (because every student is different), here is the four-pronged solution that we have come up with here.  This answer is based on a survey of organic chemistry professors that we conducted a while back.  They told us the best ways to study and the ways to avoid.  If you are interested in looking at the results of the entire survey, you can find them here—> how to pass organic chemistry (or even get an A).  We will summarize it for you here though.  It is actually pretty simple.

Situation: the organic chemistry is coming soon.  Too soon!  Not nearly enough studying has been done yet.

Step 1: Watch some organic chemistry review videos. It is really helpful to hear someone else teach the material in a little bit different way, and review videos will condense the material down for you. Here are our favorites organic chemistry videos (which happen to be ours)

Step 2: Work practice tests and practice problems. Over 90% of the professors we surveyed said this was the best way to learn organic chemistry. There are organic chemistry test banks out there (see organic chemistry test bank) that will work wonders for you.

Step 3: Find some good flashcards and practice non-stop with those. If you can’t find decent ones, make your own and emphasize the topics you didn’t do well with in step 2.  Good old fashioned 3’x5′ index cards work great.  Making them will help you learn the material even better.

Step 4: If you can, learn the material rather than memorizing it.  Organic chemistry is a discipline that requiring understanding…HOWEVER if you are pressed for time, then just memorize the heck out of it now and then go back and LEARN it before the final exam.

Hope this was helpful.  Obviously learning a complex subject like organic chemistry is more difficult than just four easy steps, but if you study hard it will go just fine.

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Learning organic chemistry is like trying to work in a foreign country; if you don’t know the language, it is going to be very difficult to learn how to do your job.  Imagine that you have just been transported to the mythical country of “ochemia”, a small island nation in the south Pacific, where your job is to write chemistry reactions.

Frequently, in a chemistry lecture, professors start tossing out strange organic chemistry terms far too quickly.  Because students aren’t fluent in “ochemia” yet, they need to translate each word in their head to understand what the instructor has just said.  By the time this mentally translation is done, the student has just missed the next sentence and has lost half of the lecture.  Our goal is to get as fluent as we can in the language of chemistry as quickly as we can.  Here are some terms it will be helpful to memorize so that you don’t have to do a mental translation when you hear them:

Meth = 1

Eth= 2

Prop = 3

But = 4

Pent = 5

Hex = 6

Hept = 7

Oct = 8

Non = 9

Dec = 10

Nucleophile = has electrons, has a negative or partial negative charge

Halogen = F, Cl, Br, I

Aprotic solvents = do not contain OH or NH bonds

Protic solvents = contain OH or NH bonds

Lewis Acid = electron acceptor

Lewis Base = electron donor

Carbonyl group =  (C=O)

Cis = same side of a double bond or ring

Trans = opposite sides of a double bond or ring

Electrophile = wants electrons, has a positive or partial positive charge

As always, for more help please go to organic chemistry

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Carbocation stability

Before we start talking about carbocation stability, we should have a starting discussion about some carbocation basics.

What is a carbocation?

A carbocation, also sometimes referred to as the carbonium ion, is an sp2 hybridized carbon atom with three groups bonded to it and a empty orbital.  Because it has an empty orbital, the sp2 carbon carries a positive charge on it, making it highly electrophilic (want to know more about electrophiles?  Check out this blog post).  The geometry of the carbocation is trigonal planar, meaning all bond angles are 120°.  The empty orbital allows for the cation to be attacked from either side.  Hence, in many cases, a loss of chirality will occur if the starting material was chiral and the mechanism goes through a carbocation intermediate (Like an SN1 reaction).

How do we get carbocations?

There are several ways to obtain a carbocation, but the first thing to understand is that carbocations are not inherently stable.  Translation: You will not find a bottle of carbocations just sitting on the shelf.

The most common way to get a carbocation is through heterolytic cleavage of a carbon-heteroatom bond, where the heteroatom gets both electrons in the bond.  The heteroatom is sometimes referred to as a “leaving group” and is an atom (or molecule even) that can easily carry a negative charge.  Some examples of this type of carbocation formation are below:

The other way to form a carbocation is through the first step of electrophilic addition to a double bond.  The most common electrophile to add is a proton.  In this method, the proton adds to one side of the double bond, creating a carbocation on what used to be the other side of the double bond.

How do we stabilize carbocations?

Now that we are all on the same footing, let’s talk about carbocation stability.  There are three major ways to do this:

• More alkyl groups: The first is though adding more alkyl groups to the carbocation. This is one of the more important things to understand in first semester organic chemistry.  If you take away one thing from this post, it should be that the more alkyl groups we add to a carbocation, the more stable that carbocation is:

The reason more alkyl groups (“R” groups) stabilize the carbocation is because of two factors, called inductive effects and hyperconjugation.  Inductive effects are relatively simple, it just means that alkyl groups are slightly electron rich and can donate some of this small electron density in to stabilize the carbocation.  In hyperconjugation, the electrons of a sigma orbital interact with the empty adjacent orbital to give an extended molecular orbital, which helps stabilize the cation.

• Adjacent double bonds: If we have a double bond one carbon away from the carbocation, it will also serve to stabilize it.  This is due to resonance and inductive effects of the double bond.  In essence, we are able to spread the unstable positive charge over multiple atoms, instead of just one.

• Lone pairs: The final way to stabilize a carbocation is with an adjacent atom with a lone pair of electrons.  As you know, lone pairs are non-bonding electron density hanging off an atom.  This atom can now serve as an electron donating group, adding negative electron density to stabilize the positive carbocation.  When we use resonance to observe this, it becomes much more obvious.

Now, we can add two more groups to our overall carbocation stability chart.  The allyl group and the benzyl group are a little more stable than a secondary carbocation.

Ok, I get carbocation stability, but what about destabilization?

• Double bonds: Having a carbocation on a double bond is very destabilizing.  A vinylic carbocation carries the positive charge on an sp carbon.  This is more electronegative than an sp2 carbon of an alkyl carbocation. Hence a secondary vinylic carbocation is less stable than a secondary alkyl carbocation.
• Electron withdrawing groups: Just like an electron donating group adds negative electron density and stabilizes a carbocation, an electron withdrawing group (such as CN) will destabilize it by trying to suck electron density away from something that is already electron deficient.

What happens to carbocations once they are formed?

• Reactions: Once a carbocation is formed, it can be a part of an organic chemistry reaction (and isn’t that really what we all want). There are a bunch of reactions that can have a carbocation as an intermediate, including E1/SN1 reactions, electrophilic aromatic substitution (EAS) and electrophilic addition to a double bond.
• Carbocation rearrangements: This is quite important. ANYTIME (did you see me put it in caps?  Must be important) you see a carbocation on an exam, the FIRST thing you need to do is look for a rearrangement. Carbocations are kinda crazy, but at the end of the day they want to be as stable as possible. This means that if I carbocation can go from a secondary cation to a tertiary cation, it will.  This can be done in several ways, but the most popular is the 1,2-hydride shift.  This involves moving an adjacent H^– to the carbocation.  The carbocation becomes neutral, and a cation forms on the carbon that lost the H^–.

There is one more way to rearrange a carbocation which involves ring formation and/or expansion, but that will be left for another time.

Reference: carbocations rock

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It’s time for resonance in organic chemistry.  

Resonance in organic chemistry is one of the most fundamental and useful concepts you will learn in this class. Once most students hear this tip, it makes perfect sense to them, but it isn’t one that you might think of on your own.  Take a look at the structure below, and ask yourself: are the two N-O bonds in this molecule the same length?

Since freshman chemistry, we have been told that double bonds between two atoms are shorter than a single bond between the same two atoms.  Hence, the N-O double bond should be shorter than the N-O single bond.  Spoiler: it is not.  But before we get into that, let’s look at some resonance forms of the nitro group at the end of this hydrocarbon:

Here, we can more clearly see that the nitro group is interconverting between the three resonance structures shown above.  Structure 3, where the charge is spread evenly between the two oxygens is a valid structure and shows that the bond two oxygen atoms in the molecule are equivalent and have the same bond length (124 pm).  This is shown here using the dashed bond, which you can think of as “half of a bond” for lack of a better term.

We care even more about this principle when it can be applied to more complex organic molecules where it is not obvious that the bonds are equivalent.  For example, the cyclopentadiene anion:

At first glance, this appears to have three different carbon atoms.  However, once you start looking at resonance structures, you can see that the anion can be moved to any of the carbons in the ring.  This makes them all equivalent, via resonance.  This is confirmed through analytical studies which show that all C-C bonds are approximately 137pm long.  Additionally, as this fits Huckel’s rule of 4N+2, the molecule is also aromatic.

One last note on this topic: We showed it above but did not give it a name.  When you have two or more bonds, and they have equivalent bond lengths, you can draw dashed bonds to show that the resonance structure is constantly changing and the bonds are constantly moving and interconverting between the two structures.  This is referred to as a “resonance hybrid”, where the resonance bond is delocalized.  What really confuses students about this structure is that it does not make sense with respect to Lewis Dot structures.  In fact, resonance hybrids and Lewis Dots are not compatible.  So if you are going to use Lewis Dots, make sure you draw double-headed arrows to denote resonance.  

Take Home Message: If you see symmetry or aromaticity, think equivalent bond lengths

 For more help with resonance, please see our homepage at organic chemistry   it is full of stuff to help you crush organic chemistry fast. 

Reference: Carey resonance

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