The Student Room Group

Ask Us Anything!

Ask Us Anything!

This is a space designed for you all to ask us (almost) anything chemistry-related.

I'm 5hyl33n, and I will be starting my second-year of undergraduate level chemistry at Cardiff University. Assisting me in answering your questions is TypicalNerd, who will be starting his first-year of undergraduate level chemistry at the University of Oxford.

Before you start posting, please have a read of the rules in post #2.

We look forward to answering your questions!

5hyl33n & TypicalNerd
(edited 1 month ago)

Scroll to see replies

Rules


Posting


Replying


Respect


Spam

(edited 5 months ago)
It is fantastic, that you finally created this thread, @5hyl33n! I wish you and of course @TypicalNerd the best and hope for success. Maybe I ask or even answer a question too.


What kinds of questions can be asked? questions about the curriculum? lessons? certain subjects in chemistry?
(edited 3 months ago)
Original post by Kallisto
It is fantastic, that you finally created this thread, @5hyl33n! I wish you and of course @TypicalNerd the best and hope for success. Maybe I ask or even answer a question too.


What kinds of questions can be asked? questions about the curriculum? lessons? certain subjects in chemistry?


Just about anything chemistry related could be asked if you so wish. The only real restriction I would impose is that we can't do assignments or homework for anyone on this thread as that defeats the purpose of teachers/lecturers/tutors etc setting it.
Reply 4
For metal organic frameworks used in water harvesting, how do the intial water seeds bind to the metal centres?
Original post by Sakai04
For metal organic frameworks used in water harvesting, how do the intial water seeds bind to the metal centres?


That is an interesting question and I am not entirely sure I can give a definite answer as I haven't studied MOF's (metal organic frameworks). What I can do, however, is attempt to make a guess as to what happens having spent 5 minutes googling MOF's and some of the research on them.

My understanding is that the structure of the MOF results in there being several pores in which water molecules are able to fit, though the extent of hydrophilicity depends on several factors such as surface area, the valency of the metal ion(s) present, how exposed the metal centres are for binding and the relative sizes of the pores.

My guess is that since the extent to which the metal centres are exposed is a factor in the hydrophilicity, the formation of dative covalent bonds between the oxygens of the water molecules and the metal centres could be one possible explanation. However, the mechanism by which the initial water seeds would bind to the MOF could depend on what substance is used and what the coordination of the metal present is like. If the metal is heavily coordinated, then it is improbable that there will be any dative covalent bonding between the initial water seeds and the metal centres as there will be insufficient space to fit water molecules around the metal centres and instead it could be argued that the water molecules in the initial seed would instead experience hydrogen bonding with functional groups in the ligands.

Given you are likely better versed in this area, if you have any alternative explanations, I would love to hear them.
Hi!
I did a mock interview yesterday where I was asked quite a complex chemistry question that I didn't understand. I was given the rates and concentrations of reactants (rate equation and order of equation style question). I was meant to determine that hydroxide ions have a 0 order. However, I was then later on meant to deduce a mechanism of nucleophilic substitution with hydroxide ions of a haloalkane knowing that hydroxide ions are 0 order. How would the mechanism change if hydroxide ions are 0 order? Sorry if this is quite a weird question
Original post by alevelsarenotfun
Hi!
I did a mock interview yesterday where I was asked quite a complex chemistry question that I didn't understand. I was given the rates and concentrations of reactants (rate equation and order of equation style question). I was meant to determine that hydroxide ions have a 0 order. However, I was then later on meant to deduce a mechanism of nucleophilic substitution with hydroxide ions of a haloalkane knowing that hydroxide ions are 0 order. How would the mechanism change if hydroxide ions are 0 order? Sorry if this is quite a weird question


I see. This is what is called an SN1 mechanism for nucleophilic substitution (SN denoting nucleophilic substitution and the 1 denoting the overall reaction order) and it simply means that the nucleophile (in this case, OH^-) isn't involved in the slowest step of the mechanism. This means that the slowest step of the mechanism involves only the haloalkane.

In nucleophilic substitutions of haloalkanes, you are breaking the carbon-halogen bond, so if the slowest step of the mechanism involves only the haloalkane, it must be the formation of two species: one being a lone halogen and the other being the carbon chain of your haloalkane. Considering the general rules of thumb with electronegativity, the halogens are more electronegative than carbon and so the bond breaks heterolytically and the halogen takes the electron pair with it. Thus, you form a halide ion and a carbocation.

The fast step does involve the nucleophile - it simply involves the nucleophile feeding a lone pair into the (formally) positive carbon in the carbocation to form the final product.

It is probably worth mentioning that SN1 reactions tend to occur with tertiary haloalkanes due to something called the inductive effect, which makes the carbocation relatively stable. This is how you predict from the structure whether the haloalkane will undergo the SN1 mechanism or the SN2 mechanism which you are probably more familiar with.
Original post by TypicalNerd
Just about anything chemistry related could be asked if you so wish. The only real restriction I would impose is that we can't do assignments or homework for anyone on this thread as that defeats the purpose of teachers/lecturers/tutors etc setting it.


Okay, so here is my first chemistry related question: in this thread it were mentioned the id-id and pd-pd states of Van der Waals forces. Just to make it clear for myself: are these certain states of orbitals electron get when they are changing their positions?

@5hyl33n of course, you are requested to anwer to the question too!
(edited 3 months ago)
Reply 9
Original post by TypicalNerd


That is an interesting question and I am not entirely sure I can give a definite answer as I haven't studied MOF's (metal organic frameworks). What I can do, however, is attempt to make a guess as to what happens having spent 5 minutes googling MOF's and some of the research on them.

My understanding is that the structure of the MOF results in there being several pores in which water molecules are able to fit, though the extent of hydrophilicity depends on several factors such as surface area, the valency of the metal ion(s) present, how exposed the metal centres are for binding and the relative sizes of the pores.

My guess is that since the extent to which the metal centres are exposed is a factor in the hydrophilicity, the formation of dative covalent bonds between the oxygens of the water molecules and the metal centres could be one possible explanation. However, the mechanism by which the initial water seeds would bind to the MOF could depend on what substance is used and what the coordination of the metal present is like. If the metal is heavily coordinated, then it is improbable that there will be any dative covalent bonding between the initial water seeds and the metal centres as there will be insufficient space to fit water molecules around the metal centres and instead it could be argued that the water molecules in the initial seed would instead experience hydrogen bonding with functional groups in the ligands.

Given you are likely better versed in this area, if you have any alternative explanations, I would love to hear them.


Thank you so much.

It's been a struggle trying to find an answer to this, as most papers on the topic don't mention this at all. The closest I've got to was a mention of ligand formation with Cu2+ and water molecules. Are metal centres the same as transition metal complexes but with organic linkers and in this case, water seeds instead?
Also, I remember reading the effect of the organic linker's polarity affecting the ability of MOF to release water molecules as vapor. Was wondering if you'd know much about this?
Original post by Sakai04
Thank you so much.

It's been a struggle trying to find an answer to this, as most papers on the topic don't mention this at all. The closest I've got to was a mention of ligand formation with Cu2+ and water molecules. Are metal centres the same as transition metal complexes but with organic linkers and in this case, water seeds instead?
Also, I remember reading the effect of the organic linker's polarity affecting the ability of MOF to release water molecules as vapor. Was wondering if you'd know much about this?

Metal centres denote metal ions within the structure to which ligands such as water molecules and terephthalate ions can be bound. Whilst I haven't looked into exactly which compounds are used to make MOF's, I would imagine most are based around transition metals, but it is well known that you can form complexes between non-transition metals and various ligands (one example is the [Eu(H2O)9]^3+ ion that is known to exist in aqueous solutions of europium salts). As such, I wouldn't necessarily refer to a metal centre as a transition metal complex.

I would presume that the more polar the linkers are, the greater their affinities for water are and so the harder it would be for water molecules to break free. As such, the ability of the MOF to release water molecules as vapour would be worse if you used more polar ligands. However, this is also guesswork based on my understanding of some fairly universal principles of chemistry and I would need to conduct much more in-depth reading to be absolutely certain.
Original post by Kallisto
Okay, so here is my first chemistry related question: in this thread it were mentioned the id-id and pd-pd states of Van der Waals forces. Just to make it clear for myself: are these certain states of orbitals electron get when they are changing their positions?

@5hyl33n of course, you are requested to anwer to the question too!


I'm not entirely sure I have understood your question properly but my interpretation is that you want to know what id-id and pd-pd refer to. Some simplified definitions are given as follows:

id-id (induced dipole-induced dipole) interactions are the intermolecular forces that arise because the movement of electrons in one particle causes electrons in another to be repelled and so you get temporary zones of opposite charges that attract one another, but generally not very strongly.

pd-pd (permanent dipole-permanent dipole) interactions are the intermolecular forces that arise because atoms of differing electronegativity are bound to each other and so there are regions that are permanently weakly positively charged and others that are permanently weakly negatively charged. The positive zones of charge attract negatives in other molecules and vice versa.
Reply 12
Thank you again! I was also wondering if you happened to know the mechanism for amide link formation (something that an A level student would be able to understand) ?
I asked my chemistry teacher today about why HOOC-R-NH3+ doesn't form amide links in a test tube, and he said that we need an enzyme in order for it to happen. So I'm not sure what to reply with to the interview question, without considering the mechanism. I'll try and write up a reply to the dms tomorrow if time allows it! Really appreciate the help 🙂
(edited 3 months ago)
Original post by Sakai04
Thank you again! I was also wondering if you happened to know the mechanism for amide link formation (something that an A level student would be able to understand) ?
I asked my chemistry teacher today about why HOOC-R-NH3+ doesn't form amide links in a test tube, and he said that we need an enzyme in order for it to happen. So I'm not sure what to reply with to the interview question, without considering the mechanism. I'll try and write up a reply to the dms tomorrow if time allows it! Really appreciate the help 🙂

It's a nucleophilic addition-elimination (you will have seen this mechanism if you were doing AQA A level chemistry), where the amine or ammonia is acting as the nucleophile because of the lone pair on the nitrogen. I have attached a link to a website with several examples of an acyl chloride undergoing nucleophilic addition-elimination to form various products: https://www.savemyexams.com/a-level/chemistry/cie/22/revision-notes/7-organic-chemistry-a-level-only/7-5-carboxylic-acids--derivatives-a-level-only/7-5-7-addition-elimination-reactions-of-acyl-chlorides/

The reason that particular ion wouldn't form an amide link is because the -NH2 group is protonated and so the lone pair isn't available for it to act as a nucleophile. I'm not entirely sure where your teacher was coming from when they gave that answer, but I presume they simply misunderstood your question.
Reply 14
Original post by TypicalNerd
It's a nucleophilic addition-elimination (you will have seen this mechanism if you were doing AQA A level chemistry), where the amine or ammonia is acting as the nucleophile because of the lone pair on the nitrogen. I have attached a link to a website with several examples of an acyl chloride undergoing nucleophilic addition-elimination to form various products: https://www.savemyexams.com/a-level/chemistry/cie/22/revision-notes/7-organic-chemistry-a-level-only/7-5-carboxylic-acids--derivatives-a-level-only/7-5-7-addition-elimination-reactions-of-acyl-chlorides/

The reason that particular ion wouldn't form an amide link is because the -NH2 group is protonated and so the lone pair isn't available for it to act as a nucleophile. I'm not entirely sure where your teacher was coming from when they gave that answer, but I presume they simply misunderstood your question.

Oh I see! I'm doing OCR A chemistry.🙂 Thanks for the link! Now, I shall eagerly add this to my notes 🍡
Reply 15
Original post by TypicalNerd
It's a nucleophilic addition-elimination (you will have seen this mechanism if you were doing AQA A level chemistry), where the amine or ammonia is acting as the nucleophile because of the lone pair on the nitrogen. I have attached a link to a website with several examples of an acyl chloride undergoing nucleophilic addition-elimination to form various products: https://www.savemyexams.com/a-level/chemistry/cie/22/revision-notes/7-organic-chemistry-a-level-only/7-5-carboxylic-acids--derivatives-a-level-only/7-5-7-addition-elimination-reactions-of-acyl-chlorides/

The reason that particular ion wouldn't form an amide link is because the -NH2 group is protonated and so the lone pair isn't available for it to act as a nucleophile. I'm not entirely sure where your teacher was coming from when they gave that answer, but I presume they simply misunderstood your question.

Hi, sorry for all the questions!
So for conjugated molecules, that exhibit colours -such as chromophores- within the visible light region. How does the resonance structure affect which photon is released, and how does the structure change when absorbing EM radiation vs releasing photons?
(edited 3 months ago)
Hello! Quick (if you can call it quick) question:
I have read 6 papers trying to understand the following mechanism for the formation of a triazole using Cu(I) as a catalyst.
Would you please be able to explain what happens at number 2 and 4 (link attached)?
From number 2:

1.

How does the Cu form a dative bond with the alkyne (is due to the pi-bonds)?

2.

How does the Cu form a dative bond with the second Cu to the right? Is it again due to the first Cu having more than 1 pi-bond which can interact with the empty orbitals of the second Cu atom?

From number 4:

1.

Can electrons from dative bonds be used to make brand new bonds as seen from the movement of electrons in number 3?

I have studied some ligand-based reactions but not many, so thank you so much in advance!

https://ibb.co/4FcjFvy
(edited 3 months ago)
Original post by RiShAbHo
Hello! Quick (if you can call it quick) question:
I have read 6 papers trying to understand the following mechanism for the formation of a triazole using Cu(I) as a catalyst.
Would you please be able to explain what happens at number 2 and 4 (link attached)?
From number 2:

1.

How does the Cu form a dative bond with the alkyne (is due to the pi-bonds)?

2.

How does the Cu form a dative bond with the second Cu to the right? Is it again due to the first Cu having more than 1 pi-bond which can interact with the empty orbitals of the second Cu atom?

From number 4:

1.

Can electrons from dative bonds be used to make brand new bonds as seen from the movement of electrons in number 3?

I have studied some ligand-based reactions but not many, so thank you so much in advance!

https://ibb.co/4FcjFvy

Ah this reaction was I believe the subject of last year's nobel prize and I studied it briefly before this year's olympiad round 1, so as to understand the kinetics behind it as I (incorrectly) predicted it would be a topic that came up. Though the mechanism I was familiar with was rather different from the one you have linked: https://www.organic-chemistry.org/namedreactions/click-chemistry.shtm

The first copper(I) attaches to the alkyne through a dative bond, because terminal alkyne protons are somewhat acidic (pKa 25) and certain bases can remove them, which leaves an available lone pair. Once you get to undergraduate level, you will come across hybridisation theory and you will learn that the carbons in an alkyne have sp hybrid orbitals, which are of relatively low energy (as they have 50% s-orbital character and you will also study radial distribution functions which can be used to justify the fact that orbitals with high s-orbital character tend to be closer to the nucleus and of relatively low energy) and so the lone pair within would be relatively stable, which allows for the terminal alkyne to deprotonate to a reasonably stable conjugate base.

I am not entirely sure as I haven't looked into homometallic bonding in much depth. I would think that what happens does involve available orbitals (in the fourth quantum shell) in the copper(I) ions allowing for the formation of a homometallic bond. However, since the explanation of the mechanism I am more familiar with states that the second copper (which would be the one that replaces the hydrogen at the terminal alkyne position as per the mechanism as I knew it) is a stabilising donor ligand after the formation of the 6-membered metallocycle, it is possible you could be (mostly) right.

You can get bonding electrons moving to form new bonds in both covalent and dative covalent bonds. There aren't many examples of the electron pair in a dative bond being used in this way that I am aware of, but I'm sure that if you decide on studying chemistry at undergrad level, you will come across a number of mechanisms in which covalent bonds react in this way (hydride shifts and carbocation rearrangements spring to mind).
Original post by TypicalNerd
Ah this reaction was I believe the subject of last year's nobel prize and I studied it briefly before this year's olympiad round 1, so as to understand the kinetics behind it as I (incorrectly) predicted it would be a topic that came up. Though the mechanism I was familiar with was rather different from the one you have linked: https://www.organic-chemistry.org/namedreactions/click-chemistry.shtm

The first copper(I) attaches to the alkyne through a dative bond, because terminal alkyne protons are somewhat acidic (pKa 25) and certain bases can remove them, which leaves an available lone pair. Once you get to undergraduate level, you will come across hybridisation theory and you will learn that the carbons in an alkyne have sp hybrid orbitals, which are of relatively low energy (as they have 50% s-orbital character and you will also study radial distribution functions which can be used to justify the fact that orbitals with high s-orbital character tend to be closer to the nucleus and of relatively low energy) and so the lone pair within would be relatively stable, which allows for the terminal alkyne to deprotonate to a reasonably stable conjugate base.

I am not entirely sure as I haven't looked into homometallic bonding in much depth. I would think that what happens does involve available orbitals (in the fourth quantum shell) in the copper(I) ions allowing for the formation of a homometallic bond. However, since the explanation of the mechanism I am more familiar with states that the second copper (which would be the one that replaces the hydrogen at the terminal alkyne position as per the mechanism as I knew it) is a stabilising donor ligand after the formation of the 6-membered metallocycle, it is possible you could be (mostly) right.

You can get bonding electrons moving to form new bonds in both covalent and dative covalent bonds. There aren't many examples of the electron pair in a dative bond being used in this way that I am aware of, but I'm sure that if you decide on studying chemistry at undergrad level, you will come across a number of mechanisms in which covalent bonds react in this way (hydride shifts and carbocation rearrangements spring to mind).

You truly are amazing, and yes, this was one of the publications from the Nobel Prize! I was most interested in it due to the SPAAC (strain-promoted azide-alkyne CA).
I wanted to write a report around the use of SPAAC and click chemistry in the use of nanoparticle conjugation and synthetic vehicles and how we could form antibody-receptor complexes through SPAAC using azido-modified folic acid and superparamagnetic iron oxide nanoparticles.

But anyway, I saw CuAAC and ligands and that was a big no for me, so I avoided it! But, now I have been tempted by organometallic reactions.

Once again, thank you so much! :smile:
Original post by Sakai04
Hi, sorry for all the questions!
So for conjugated molecules, that exhibit colours -such as chromophores- within the visible light region. How does the resonance structure affect which photon is released, and how does the structure change when absorbing EM radiation vs releasing photons?

Don't apologise, that's what this thread is for.

Resonance is a useful concept for predicting products of certain organic reactions, but it is commonly forgotten that a molecule with "resonance structures" does not alternate between the various resonance structures and instead the true structure of the molecule is a hybrid of all of the resonance structures, so there is no real change of structure as such when photons are released or absorbed.

The better explanation of where the colour comes from is the excitation and de-excitation of the electrons energy within the pi system. You have various extended pi orbitals (I'd need to diagrammatically explain this, but you have hybrid orbital theory that states that carbons with one double bond and two single bonds has sp^2 hybridisation and that there are available p-orbitals that stick out and can overlap with each other), which act as your energy levels and the longer your sequence of alternating pi and sigma bonds is, generally the longer the wavelengths of light that are absorbed (so the more likely higher energy photons such as blue are going to be released).

Quick Reply

Latest