complex chemistry

[lemur]

I tried reading an organic chemistry textbook recently and the complexity of it overwhelmed me. Now I'm wondering if it wouldn't make sense to learn chemistry like a language, where the elements are like phonemes or word-fragments that form "words" (i.e. complexes of atoms that build up to more complex configurations to form large molecules)? I can imagine that super-molecules would work this way, building up from multiple layers of sub-molecular structuring processes, but I don't know enough about chemistry to know if I'm right. Could chemistry be learned in this way, e.g. learning basic vocabulary and grammar of simple super-atomic complexes and gradually learning to see how these complexes are pieced together into ever larger ones?

[rktpro]

Maybe

[lemur]

Maybe

I guess that's a more substantial answer than, "I don't know," would be.

[Blahah]

This is somewhat similar to how I learned some aspects of organic chemistry. I actually started out with IUPAC nomenclature as I found it easier to learn the structures by associating them with the logical linguistic structure. By trying to name compounds and, in the other direction, derive structures from names, I came to grasp it better.

 

Once you can know the structure of a compound and can give it a meaningful name, you can associate the structure with function much more easily (or at least, I could). It is also much easier to remember larger and more complex structures when you can break it up into manageable parts (groups, chain, rings etc).

 

Another thing I did similarly to language learning is to use language learning software to remember the organic chemistry terminology. I do this with all scientific terminology I learn, because memorising words is easy, and associating words with images or concepts is easy, but memorising concepts is not so easy. The software I use is called Anki (free and open source), it's a spaced repetition system in which you make flashcards and then rate yourself on how well you remember the answers. Your ratings influence how soon the card reappears in your deck. I highly recommend the software for memorisation.

Edited March 14, 2011 by Blahah

[mississippichem]

Chemistry should be learned just like the other science, from the bottom up. It will be hard to understand the principles behind organic chemistry without a solid foundation in the principles of general chemistry.

 

But yes, after a while one might start to notice patterns in the structures of organic compounds. The majority of organic compounds are made up of about twenty or so small collections of molecules called functional groups. If you scroll through organic chemistry threads around this forum you will see these names tossed around: amine, ester, carboxylic acid, ether, alcohol etc.

 

If one wants to learn organic chemistry, then learning the IUPAC nomenclature system and memorizing the common functional groups is a great place to start.

Edited March 14, 2011 by mississippichem

[Danny]

i would say it is definably a language already!

you need to very activly try to learn it and become familiar with it by speaking (or writing) it.

[lemur]

But yes, after a while one might start to notice patterns in the structures of organic compounds. The majority of organic compounds are made up of about twenty or so small collections of molecules called functional groups. If you scroll through organic chemistry threads around this forum you will see these names tossed around: amine, ester, carboxylic acid, ether, alcohol etc.

So these functional groups can be viewed as fundamental structures above the level of the elements/atoms themselves? Would it be possible to create something like the periodic table but for these fundamental groups?

 

 

 

[farmboy]

So these functional groups can be viewed as fundamental structures above the level of the elements/atoms themselves? Would it be possible to create something like the periodic table but for these fundamental groups?

 

I don't think that would be all that beneficial to be honest dude, and I don't really think that learning nomenclature like a language would be all that wise either unfortunately (thoughit is good to see people thinking outsude the box). Whilst it might seem very complicated to begin with, learning the 'language' of chemistry is not anywhere near as tough as learning a new regular language. More importantly learning the words that represent the different molecules is actually not all that important, it is the chemical features that these words indicate that is the important part. Once you understand the basic chemistry of the different atoms you will be able to know intuitively how the molecules are put together. You will probably start off learning how some of the basic functional groups tend to react under different conditions, but just memorising reactions in that fashion won't be very useful in the long run unlike say learning french. With chemistry you will need to understand why the functional groups act the way they do, and once you have done that there is no need to just memorise you will just know how a reaction is likely to proceed.

 

And with regards to the periodic table of functional groups, that wouldn't really work in my opinion. The periodic table contains all the elements arranged in order of increasing mass, but actually for chemists it tells us a hell of a lot more than that. There are trends and patterns of behaviour amongst the elements, and the periodic table allows us to make guesses about how elements will behave just from looking at their position.

[hypervalent_iodine]

I don't think that would be all that beneficial to be honest dude, and I don't really think that learning nomenclature like a language would be all that wise either unfortunately (thoughit is good to see people thinking outsude the box). Whilst it might seem very complicated to begin with, learning the 'language' of chemistry is not anywhere near as tough as learning a new regular language. More importantly learning the words that represent the different molecules is actually not all that important, it is the chemical features that these words indicate that is the important part. Once you understand the basic chemistry of the different atoms you will be able to know intuitively how the molecules are put together. You will probably start off learning how some of the basic functional groups tend to react under different conditions, but just memorising reactions in that fashion won't be very useful in the long run unlike say learning french. With chemistry you will need to understand why the functional groups act the way they do, and once you have done that there is no need to just memorise you will just know how a reaction is likely to proceed.

 

And with regards to the periodic table of functional groups, that wouldn't really work in my opinion. The periodic table contains all the elements arranged in order of increasing mass, but actually for chemists it tells us a hell of a lot more than that. There are trends and patterns of behaviour amongst the elements, and the periodic table allows us to make guesses about how elements will behave just from looking at their position.

 

While your bit about learning the structures of functional groups, etc. over their names may be true, it certainly will not be helpful in an exam type situation and even less helpful when you are trying to communicate to your colleagues (or when they are trying to communicate with you).

 

I 100% agree with you when you said that learning why reactions occur they way they do is much more useful than simply memorising a reaction. There are simply too many reactions in organic chemistry for anyone to be able to memorise them all. Understanding why reactions occur the way that they do allows you develop a certain type of chemical intuition, which is an invaluable trait to have to a synthetic organic chemist such as myself.

[lemur]

While your bit about learning the structures of functional groups, etc. over their names may be true, it certainly will not be helpful in an exam type situation and even less helpful when you are trying to communicate to your colleagues (or when they are trying to communicate with you).

I don't think farmboy was saying that there was no point to learning the names. I think he was saying that there are underlying dynamics that the names refer to and it is more important to understand those than to (just) memorize the names.

 

I 100% agree with you when you said that learning why reactions occur they way they do is much more useful than simply memorising a reaction. There are simply too many reactions in organic chemistry for anyone to be able to memorise them all. Understanding why reactions occur the way that they do allows you develop a certain type of chemical intuition, which is an invaluable trait to have to a synthetic organic chemist such as myself.

Ok, so you are farmboy both agree that chemical interactions are not as complex as language but you don't see any way to learn "chemical intuition" about why/how reactions occur in certain ways except to develop it through processes of reading and practicing different reactions? That sounds exactly like learning a language where you can explain long lists of formalized rules but using them to construct a coherent sentence or fluidly read a paragraph would be awkward and take a long time.

 

I just got the idea of some kind of periodic-table-like list of fundamental groups because these groups sound like they function as super-atomic configuration with reactive properties like those of atoms, only at the molecular level. In other words, I was starting to get a feeling for how quantum behavior of electrons/atoms relates to their reactive behaviors and that made me think that maybe I could "fundamental group" behavior could be understood the same way, only instead of single atoms/ions, I take it the fundamental groups behave as units in reactions until sufficient energy is applied to break them down into constituent atoms.

 

Maybe an even simpler way to phrase this would be using the analogy: fundamental groups are to atoms what atoms are to their subatomic constituents. I know that atoms are more centralized/concentric than molecules and these fundamental groups, but what I mean is that they are built up using electrostatic charge differentials and fragmenting them into smaller parts requires energy (and it can consume or release energy). Also, atoms have certain ionization and combinatory tendencies based on their position relative to noble gases, and I would guess that fundamental groups also exhibit such tendencies in terms of having weak points/atoms that easily break off and leave certain sections ionized in a certain way, etc.

 

 

[farmboy]

Yeah that is what I meant, would definitely make exams more difficult if you don't know what the different groups are called. It is certainly worthwhile learning those names, but to be honest I think that if you learn the chemistry of different atoms in the way that I had talked about earlier the names will just stick in the process.

 

Ok, so you are farmboy both agree that chemical interactions are not as complex as language but you don't see any way to learn "chemical intuition" about why/how reactions occur in certain ways except to develop it through processes of reading and practicing different reactions? That sounds exactly like learning a language where you can explain long lists of formalized rules but using them to construct a coherent sentence or fluidly read a paragraph would be awkward and take a long time.

 

Nah I'd say that it is actually pretty easy to get an intuitive feel for how reactions will proceed. The first key to doing this is actually to get to know your periodic table. The trends you see in the periodic table correspond to quantum mechanical properties of the elements and provide significant insight into how certain elements will react. There are a handful of basic theories (electronegativity, atomic radius, HSAB theory and molecular orbital theory all spring to mind) that once learned will immediately make the issue of chemical bonding/reactions a lot clearer, and to apply any of those things all you need is a little bit of knowledge and your periodic table lol. Well a pen too perhaps.

 

 

I just got the idea of some kind of periodic-table-like list of fundamental groups because these groups sound like they function as super-atomic configuration with reactive properties like those of atoms, only at the molecular level. In other words, I was starting to get a feeling for how quantum behavior of electrons/atoms relates to their reactive behaviors and that made me think that maybe I could "fundamental group" behavior could be understood the same way, only instead of single atoms/ions, I take it the fundamental groups behave as units in reactions until sufficient energy is applied to break them down into constituent atoms.

 

You see the main problem is that there are just too many possible functional groups to really consider it, plus where do you draw the line for one group ending the next beginning? You could say that the elements are like digital and functional groups are like analogue signals. With the elements we know exactly where one element ends and the next begins, we just keep adding a proton at a time. Each element is distinct from the next. With functional groups that isn't the case, there are a million little tiny changes that you could make. It wouldn't really be all that useful is just the point I am making, it would be a huge textbook not a little table. I mean the reason the periodic table works so well is that there is a steady, constant change in as you move from one element to the next. You need only know a few rules to help you predict That isn't the case with molecules. Like if I had one group that was alcohols, for a start there is about 1000 different reactions you might need to learn just to cover the basic alcohols. But then what if you were to throw a halogen into the mix. The chemistry of your molecule is now fundamentally altered, so do you start another group. But then what if we stick an amine in there somewhere too, we changed it all again. Plus functional groups don't tend to react via a simple movement of electrons like is the case when a pure element reacts. The mechanisms are another thing that needs to be learned and they are quite often complex, involving the movement of electrons in several different atoms.

 

 

Maybe an even simpler way to phrase this would be using the analogy: fundamental groups are to atoms what atoms are to their subatomic constituents. I know that atoms are more centralized/concentric than molecules and these fundamental groups, but what I mean is that they are built up using electrostatic charge differentials and fragmenting them into smaller parts requires energy (and it can consume or release energy). Also, atoms have certain ionization and combinatory tendencies based on their position relative to noble gases, and I would guess that fundamental groups also exhibit such tendencies in terms of having weak points/atoms that easily break off and leave certain sections ionized in a certain way, etc.

 

I would say that you are pretty close to being bang on their mate, the stuff about groups breaking apart in certain places is accurate (this is generally related to the electronegativity of the atoms, some hold onto the electrons better than others so come away with them at the end of the reaction. The only thing I would disagree with is the looking at atoms from a physicists perspective. In chemistry you can certainly analyse functional groups by looking at their constituent atoms (this is where the periodic table pays off lol) but it doesn't help to look at the atoms themselves in terms of their constituent parts like that. In chemistry you can look at atoms purely in terms of their electron orbitals lots of the time, neutrons and protons can often be firgotten about since it is the electrons that dictate what reactions will take place.

[hypervalent_iodine]

 

Ok, so you are farmboy both agree that chemical interactions are not as complex as language but you don't see any way to learn "chemical intuition" about why/how reactions occur in certain ways except to develop it through processes of reading and practicing different reactions? That sounds exactly like learning a language where you can explain long lists of formalized rules but using them to construct a coherent sentence or fluidly read a paragraph would be awkward and take a long time.

 

I in fact said nothing about it being akin to learning a language or otherwise, merely that I agreed with farmboy on the point of developing chemical intuition being far more advantageous than memorising reactions.

 

 

 

 

 

 

[lemur]

The only thing I would disagree with is the looking at atoms from a physicists perspective. In chemistry you can certainly analyse functional groups by looking at their constituent atoms (this is where the periodic table pays off lol) but it doesn't help to look at the atoms themselves in terms of their constituent parts like that. In chemistry you can look at atoms purely in terms of their electron orbitals lots of the time, neutrons and protons can often be firgotten about since it is the electrons that dictate what reactions will take place.

First, thanks for elaborating on how functional groups can have a lot of variability. Mississippichem said there were something like 20 of them so that made it sound like all larger molecules are constituted from a short "vocabulary list" of certain "fundamental" configurations.

 

As for forgetting about protons in chemistry, I understand how you would say that based on the way chemistry tends to focus on the combinability of particles based on their "shell-fullness" and charge/ionization. But from a sub-atomic perspective, it would seem to make sense to at the positive charge of the protons extending beyond the electron-negative charge in a way. Maybe it's wrongheaded of me, but it seems almost like electrons are shielding for the positive electrostatic field-force of the nuclei. I know that standard chemical logic works according to electron diagramming, but I'm trying to incorporate what I think I understand at the sub-atomic level into the way I imagine inter-atomic dynamics occurring.

 

 

[farmboy]

First, thanks for elaborating on how functional groups can have a lot of variability. Mississippichem said there were something like 20 of them so that made it sound like all larger molecules are constituted from a short "vocabulary list" of certain "fundamental" configurations.

 

As for forgetting about protons in chemistry, I understand how you would say that based on the way chemistry tends to focus on the combinability of particles based on their "shell-fullness" and charge/ionization. But from a sub-atomic perspective, it would seem to make sense to at the positive charge of the protons extending beyond the electron-negative charge in a way. Maybe it's wrongheaded of me, but it seems almost like electrons are shielding for the positive electrostatic field-force of the nuclei. I know that standard chemical logic works according to electron diagramming, but I'm trying to incorporate what I think I understand at the sub-atomic level into the way I imagine inter-atomic dynamics occurring.

 

Yeah dude, definitely don't try and include nuclear forces when you are considering chemical reactions, it won't help you in any way. I'd imagine there is some force felt but it would be absolutely negligible. The nucleus is only a tiny wee thing at the centre of an atom, and then like you mention there is a large amount of shielding from the electrons. There are also the neutrons in there too, and I wonder if perhaps the strong force plays some small role here too.

 

Actually having a full shell and stuff like that is what you are taught at secondary school level, but it isn't what is taught at higher levels. The best models we have to describe reactions in chemistry are all based on quantum mechanics, something I wish I was a little better at lol. You perhaps already know this but rather than using stuff like 'comparison to the nearest noble gas' or 'filled shells' to predict how reactions will proceed (these are sort of like introductory tricks which will often give the right answer but not reallly for the right reasons) the two main methods used by normal chemists these days would be valence bond theory and molecular orbital theory. Both theories are based on quantum mechanical calculations involving the schrodinger equation, but thankfully other people have done the really hard parts and there is like a little short hand way you can draw out a diagram (called a molecular orbital diagram) and by filling in the electrons you canwork out whether reactions will proceed as well as being able to tell a whole load of other factors too.

 

 

Here is the basic outline for the MO diagram of dioxygen including all the molecular orbitals and the electrons that go into them. You can tell a whole lot of stuff just from filling it in accurately.

 

 

[lemur]

Yeah dude, definitely don't try and include nuclear forces when you are considering chemical reactions, it won't help you in any way. I'd imagine there is some force felt but it would be absolutely negligible. The nucleus is only a tiny wee thing at the centre of an atom, and then like you mention there is a large amount of shielding from the electrons. There are also the neutrons in there too, and I wonder if perhaps the strong force plays some small role here too.

Thanks for posting the MO diagram, but I'm afraid I can't read it except to see the familiar electron pairing and that the geometry seems to represent something relevant.

 

What I meant by "sub-atomic forces" was not the nuclear force but rather the positively charged electrostatic force from the protons. I.e. I think you could look at (valence?) interactions between atoms in terms of protons of one nucleus interacting with electrons of another nucleus. When I read that shorter bonds are stronger, for example, this sounded logical because attractive force gets stronger as distance decreases, but the attractive force in question isn't between the electrons themselves but between the protons and the electrons, right? So it seems as if the electron/shielding of atoms/molecules is also mitigating how much the positive charge from the nucleus is exposed and where. I hope you can sort of see what I mean with this because it's really just vagueness in my head at this moment, but it seems like a promising lead to mentally modeling atoms/molecules as more than geometrical patterns of combinatory rules.

 

 

[farmboy]

Thanks for posting the MO diagram, but I'm afraid I can't read it except to see the familiar electron pairing and that the geometry seems to represent something relevant.

 

What I meant by "sub-atomic forces" was not the nuclear force but rather the positively charged electrostatic force from the protons. I.e. I think you could look at (valence?) interactions between atoms in terms of protons of one nucleus interacting with electrons of another nucleus. When I read that shorter bonds are stronger, for example, this sounded logical because attractive force gets stronger as distance decreases, but the attractive force in question isn't between the electrons themselves but between the protons and the electrons, right? So it seems as if the electron/shielding of atoms/molecules is also mitigating how much the positive charge from the nucleus is exposed and where. I hope you can sort of see what I mean with this because it's really just vagueness in my head at this moment, but it seems like a promising lead to mentally modeling atoms/molecules as more than geometrical patterns of combinatory rules.

 

My bad dude, I had intended to put a brief explanation in, it would actually have explained some of your queries from the above post lol.

 

 

Like I said before this is the MO diagram for dioxygen. Basically the way it works is that the arrows (which represent electrons) to the left and right of the diagram correspond to one atomic oxygen. So the electron configuration of oxygen is 1s2 2s2 2p4 (the blue ones are the two s-orbitals and the red one is the pi-orbital. The arrows in the middle show what happens to the electrons once they have joined to form molecular oxygen. So basically you start at the bottom and work your way towards the top obeying hunds rule as you go, and when you have the electrons all put in their proper place you can predict stuff like how strong the bond might be, how long it might be, the potential magnetic character of the molecule, whether it will be a good conductor of electricity and probably many other things too.

 

Coming back to something a little more relevant to what we had been discussing, yes you are sort of along the right tracks when discussing the proton stuff actually mate, I was wrong to dismiss it out of hand now that I think about it lol. In covalent compounds it is a property called electronegativity that dictates the strength of the bond, but it isn't just the number of protons in an atom that dictates how electronegative it is, it is actually to do with the number of electrons vs. the number of protons, but the shells in which the electrons are held is also important. The general trend is that EN increases from left to right and from top to bottom across the periodic table.

 

That said the problem with trying to look at the atoms in this way is that it isn't really representative of what an atom actually looks like, which is why we represent them as MO diagrams and the like. The MO-diagram explains in qunatum mechanical terms why some bonds are stronger than others.

 

Apologies I was half falling asleep writing the second half of that post. I'll finish it tomorrow when it makes more sense to me lol.