Dscript Chem Notation

[vasten]

Hi all,

 

I have been working on adapting Dscript for representing molecules. It works great because Dscript is already designed for vertical and horizontal.

 

I just started it, so the online info for chemical notation is far from complete. I use the Dscript alphabet (reference at www.dscript.ca).

 

So far it seems really efficient.

 

It works great for amino acids and peptides.

 

Dscript Chem Notation - www.dscript.ca/lesson

 

I would love some advice on how I could make it more efficient and aesthetically pleasing.

 

here are some example.

Morphiceptin

 

Proline, Phenylalanine, Proline, Tyrosine, and far right is the product, Morphiceptin.

 

 

 

 

 

Heme A

 

 

The biomolecular structure is on the right, and the name written in Dscript on the right.

 

 

 

 

 

Aspartame (N-(L-α-Aspartyl)-L-phenylalanine,1-methyl ester).

 

 

 

 

[hypervalent_iodine]

Not having much experience in programming or script writing, I'm going to have ask what may be an obvious question; what is the point of representing chemical notation like that when we already have a fairly efficient system of drawing and representing compounds? As I say, I may be missing something here, but this seems slightly pointless and unnecessarily complicated.

[vasten]

Not having much experience in programming or script writing, I'm going to have ask what may be an obvious question; what is the point of representing chemical notation like that when we already have a fairly efficient system of drawing and representing compounds? As I say, I may be missing something here, but this seems slightly pointless and unnecessarily complicated.

 

Good question.

 

First of all the "script" in Dscript refers to "written script" or "writing font". Not programming or scripts of that type.

 

For me it is a matter of degree of detail, and writing efficiency.

 

The standard method is the most detailed and accurate method.

 

The space filling method is the most visually intuitive.

 

A formula (eg. CH4) provide no visual intuition but is detailed in a sense.

 

The Dscript notation only scores "medium" on the accuracy and visual intuition, for each individual purpose the space filling or standard method are best.

 

But many of us have gone beyond needing such detail (eg. standard notation already assumes carbon, and does not show most hydrogen atoms)

 

Dscript notation retains most important information while reducing the writing strokes and page space requirement.

 

Perhaps most important is that the angles and design of the standard system sometimes contort the hand and are difficult to draw cleanly.

 

A large complex molecule can be drawn quicker and smaller but still represent the molecular structure.

 

Amino acids are a great example, long chains of amino acids can be drawn with great detail in small spaces.

 

There are still many weaknesses I am working on, most notably I have only added Carbon, Nitrogen, Oxygen, Sulfur, Phosphate and Iron so far. It is still a work in progress, but all the fundamentals for organic molecules is already there.

 

Basically think of them as concise "symbols" that are small and easy to write, but still reflect molecular structure. With a little practice they are easily recognizable, writable, and a fun way to "study" molecular structure.

Edited October 13, 2011 by vasten

[hypervalent_iodine]

But many of us have gone beyond needing such detail (eg. standard notation already assumes carbon, and does not show most hydrogen atoms)

 

Correct, which is why it's not used unless necessary. Chemistry already has simplified ways of drawing things that convey all the information you might require, so I'm still not sure what purpose this serves.

[vasten]

Correct, which is why it's not used unless necessary. Chemistry already has simplified ways of drawing things that convey all the information you might require, so I'm still not sure what purpose this serves.

 

what other ways?

 

how would you draw the Heme A molecule, or a long chain of amino acids.

 

I don't mean an abbreviation (like just writing the abbreviations for the amino acid)

i mean actual concise visual representation of the molecule.

[hypervalent_iodine]

Like this:

 

 

For the record, writing in 'CH₃', etc. is actually not required, you can simply leave it off. For citation's sake, I should mention that I got this from wikipedia.

[vasten]

Ok.

 

Now draw that

 

Freehand

 

in less than 30 sec

 

roughly the size of your thumb

 

this is what Dscript is for

[hypervalent_iodine]

Why would I need to or want to do that?

 

Additionally, how does your method exhibit stereochemical information? I also do not see any representation of double bonds.

[vasten]

Why would I need to or want to do that?

 

Additionally, how does your method exhibit stereochemical information? I also do not see any representation of double bonds.

 

If you can't think of a reason to do it, then it's not for you I guess.

 

Dscript is 2D, it does not attempt to represent 3D information, and to be honest, in my opinion, with computers and rendering, nowadays no one does this stuff on paper anymore anyways. 2D setreochemical presentation is a dying art.

 

I normally don't draw the double bonds because usually my goal is a quick visual representation when I am dealing with many large molecules.

but when needed they are simple, an extra line not touching either side running parallel to the bond line.

 

eg Phosphatidylinositol

[hypervalent_iodine]

Well unfortunately for you, stereochemistry and bond order are two extremely important pieces of information that you need to convey in your drawings. So again, I do not see the point. Why fix what 'aint broke, ya' know?

[Greg Boyles]

Like this:

 

nomenclature

 

For the record, writing in 'CH₃', etc. is actually not required, you can simply leave it off. For citation's sake, I should mention that I got this from wikipedia.

 

 

If you are familiar with chemical nomenclature and the haemoglobin molecule in particular I don't see why you couldn't draw the above molecular diagram in less than a minute anyway and I don't see why you could do it any quicker in dscript.

 

 

The molecule contains a high level of complexity which requires the same level of detail to represent it in what ever script you end up using.

 

 

The periodic table is an intuitive means of representing chemical elements as possible, hexagons/pentagons as intuitive method of representing the various carbon ring structures as possible and single/double/tripple lines as intuitive methods of representing single, double and tripple bonds as possible.

 

If you are very familiar with the structure of the compounds you are trying to represent then it seems to me that you can very easily and quickly represent them with this current method.

 

 

D-script seems to be adding another layer of complexity than you need to learn and become profficient with.

 

 

Anyone with a basic knowledge of the the periodic table etc would be able to have a stab at the meaning of a lot of the above diagram.

 

But D-script representation would be totally unintelligeble to them.

[vasten]

Well unfortunately for you, stereochemistry and bond order are two extremely important pieces of information that you need to convey in your drawings. So again, I do not see the point. Why fix what 'aint broke, ya' know?

 

Yes, and we have tools for studying them

 

but when looking at more and more, larger and larger molecules, I am trying to increase writting speed and writting space efficiency, while also alowing for multiple forms of representation to increase overall flexibility.

 

Now, I am just looking to play with something, seeing if there are other ways of doing something, and what advantages disadvantage said new method may present. but I cannot resist the following...

 

"Why fix what 'aint broke, ya' know?"

 

the true mind of a scientist!

 

I'm sorry for trying to modify, improve, change, experiment.... can you recommend a good doctrine for me follow?

 

If you are familiar with chemical nomenclature and the haemoglobin molecule in particular I don't see why you couldn't draw the above molecular diagram in less than a minute anyway and I don't see why you could do it any quicker in dscript.

 

 

The molecule contains a high level of complexity which requires the same level of detail to represent it in what ever script you end up using.

 

 

The periodic table is an intuitive means of representing chemical elements as possible, hexagons/pentagons as intuitive method of representing the various carbon ring structures as possible and single/double/tripple lines as intuitive methods of representing single, double and tripple bonds as possible.

 

If you are very familiar with the structure of the compounds you are trying to represent then it seems to me that you can very easily and quickly represent them with this current method.

 

 

D-script seems to be adding another layer of complexity than you need to learn and become profficient with.

 

 

Anyone with a basic knowledge of the the periodic table etc would be able to have a stab at the meaning of a lot of the above diagram.

 

But D-script representation would be totally unintelligeble to them.

 

Not so, Dscript Chem notation is an extension of Dscript(the general neography, at http://dscript.ca)

 

Dscript letters

C = (every intersection is a carbon)

 

N =

 

So.. accounting for the neography(neography is a new writting system) it is just as obvious that...

 

is the same as (the right side is the name "phenylethylamine", not a molecule)

 

The difference is I sacrafice the correct angles and extra bond lines (irrelevant in this case anyways) in order to gain speed and reduce size.

 

 

Bond lines can be added easily, they do of course usually increase size and reduce speed.

 

Think of it more like a symbol or glyph that attempts to represent chemical notation.

 

At the very least, it can be fun if you enjoy penmanship and will force the user to "play" with it, all the while memorizing chemical structures.

 

It is NOT meant to replace any current system.

 

This is a hobby that I am looking to refine.

[hypervalent_iodine]

Yes, and we have tools for studying them

 

but when looking at more and more, larger and larger molecules, I am trying to increase writting speed and writting space efficiency, while also alowing for multiple forms of representation to increase overall flexibility.

 

Stereochemistry and double/triple bonds, etc. are still very important pieces of information, no matter how big your structure is. Perhaps this new system of yours will be useful for you, but only in the same capacity as if I were to learn a secret language with which to fill out my lab book. It's all well and good for me, since I know what's going on, but it fails miserably in being able to clearly and easily communicate the information to others (another rather important aspect of science).

 

There are other ways of drawing extremely large compounds such as proteins (ribbon structures, etc.); when you are trying to convey chemical information however, the system we use is suited perfectly.

 

 

 

the true mind of a scientist!

 

I'm sorry for trying to modify, improve, change, experiment.... can you recommend a good doctrine for me follow?

 

You aren't improving on the pre-existing methods. All you've done is made is made them more complicated and less informative. The system we use currently, while perhaps more spatially demanding and time consuming, are intuitive and easy to learn. At first glance, yours does not appear to possess this quality. Even if it did, I still fail to see the point of having to learn an entirely new language for representing chemical structures when it (as aforementioned) a.) it doesn't give adequate information and b.) we already have an easy to use system that works and works well.

 

So.. accounting for the neography(neography is a new writting system) it is just as obvious that...

 

is the same as (the right side is the name "phenylethylamine", not a molecule)

 

 

I would have to disagree.

 

 

The difference is I sacrafice the correct angles and extra bond lines (irrelevant in this case anyways) in order to gain speed and reduce size.

 

 

Cyclohexane is by no means the same as a phenyl group. "Extra bond lines", in this case (and every case), are therefore far from being irrelevant.

 

In all, I can appreciate the idea behind the task, even if I don't agree with it. I suppose if nothing else, it's a better and more respectable way to pass the time than say, reading Twilight.

Edited October 13, 2011 by hypervalent_iodine

[Greg Boyles]

Yes, and we have tools for studying them

 

but when looking at more and more, larger and larger molecules, I am trying to increase writting speed and writting space efficiency, while also alowing for multiple forms of representation to increase overall flexibility.

 

Now, I am just looking to play with something, seeing if there are other ways of doing something, and what advantages disadvantage said new method may present. but I cannot resist the following...

 

"Why fix what 'aint broke, ya' know?"

 

the true mind of a scientist!

 

I'm sorry for trying to modify, improve, change, experiment.... can you recommend a good doctrine for me follow?

 

 

 

Not so, Dscript Chem notation is an extension of Dscript(the general neography, at http://dscript.ca)

 

Dscript letters

C = (every intersection is a carbon)

 

N =

 

So.. accounting for the neography(neography is a new writting system) it is just as obvious that...

 

is the same as (the right side is the name "phenylethylamine", not a molecule)

 

The difference is I sacrafice the correct angles and extra bond lines (irrelevant in this case anyways) in order to gain speed and reduce size.

 

 

Bond lines can be added easily, they do of course usually increase size and reduce speed.

 

Think of it more like a symbol or glyph that attempts to represent chemical notation.

 

At the very least, it can be fun if you enjoy penmanship and will force the user to "play" with it, all the while memorizing chemical structures.

 

It is NOT meant to replace any current system.

 

This is a hobby that I am looking to refine.

The conventional diagram on the left looks far simpler and more intuitive to me. I still don't see why the d-script representation can be written more quickly than the conventional representation in this case. Looks more intricate to me.

[vasten]

The conventional diagram on the left looks far simpler and more intuitive to me. I still don't see why the d-script representation can be written more quickly than the conventional representation in this case. Looks more intricate to me.

 

Dscript

8 pen strokes (no extra bonds)

1 loop

Only right angles, easy to draw

total pen strokes = 8

 

Standard

9 pen strokes (no extra bond lines)

1 letter N

Total pen strokes = 10

Angles all over the place, will NOT look nice when drawn by hand, unless you waste time trying to make angels and line sizes exact.

(will not count H2 as I don't use them either)

 

Dscript takes into account the mechanical limitations of the human hand.

[hypervalent_iodine]

Dscript

8 pen strokes (no extra bonds)

1 loop

Only right angles, easy to draw

total pen strokes = 8

 

Standard

9 pen strokes (no extra bond lines)

1 letter N

Total pen strokes = 10

Angles all over the place, will NOT look nice when drawn by hand, unless you waste time trying to make angels and line sizes exact.

(will not count H2 as I don't use them either)

 

Dscript takes into account the mechanical limitations of the human hand.

 

Hydrogen atoms must be included when they are bound to heteroatoms as it can be ambiguous otherwise. Particularly where they are bound to atoms able to form hypervalent bonds. Speaking of which, does your model make room for charged species?

 

With practice, drawing the compound to mentioned in your post neatly by hand is actually quite easy. Even ignoring that, there are a lot of software packages out there that you can use to draw structures, which obviously circumvents the issue of messy hand drawings.

Edited October 13, 2011 by hypervalent_iodine

[vasten]

Hydrogen atoms must be included when they are bound to heteroatoms as it can be ambiguous otherwise. Particularly where they are bound to atoms able to form hypervalent bonds. Speaking of which, does your model make room for charged species?

 

With practice, drawing the compound to mentioned in your post neatly by hand is actually quite easy. Even ignoring that, there are a lot of software packages out there that you can use to draw structures, which obviously circumvents the issue of messy hand drawings.

 

Yes, and when needed I add bonds, hydrogens etc...

when needing full detail, i just apply the standard charge notation rules to Dscript. they work fine.

 

Again, what key needing to emphasize, is think of it this way.

 

Suppose you were drawing out the chaining of amino acids, or you were "following" metabolic pathways,

You are at the point where you are generally familiar with the molecules,

you want to start evaluating a very long series of interactions, or one enormous interaction,

 

You could:

a)Use an alphabetical letter(or string of letters) to represent molecules

b)Use chemical formulas to represent molecules

c)you could use standard system to draw the molecules

 

Dscript offers:

d)draw each molecule with concise but simplified symbols, maintain composition integrity, but sacrifice spacial accuracy for writing space and writing speed

 

this new option aims to offer a mixture of advantages from the other three options.

very useful for some situations

less so for other situations

Edited October 13, 2011 by vasten

[Ophiolite]

After reading the thread I felt strongly inclined to agree with Greg and hypervalent. The only justification for the method I can see is that it might be quicker. As a simple test - not scientifically rigorous - I timed myself drawing phenylethylamine by both methods. It took 13 seconds in each instance. Now, vasten, you might argue that familiarity with the conventional system would allow me to draw that more rapidly. Perhaps. However, the last time I likely had occassion to draw an organic molecule in that way would have been in 1967. I don't think I've retained much motor memory of the process over the intervening forty odd years.

[hypervalent_iodine]

Suppose you were drawing out the chaining of amino acids, or you were "following" metabolic pathways,

You are at the point where you are generally familiar with the molecules,

you want to start evaluating a very long series of interactions, or one enormous interaction,

 

 

Generally, the chemistry involved in metabolic pathways or biochemical reactions only applies to a small section of the compound as a whole (such as the terminating ends of an amino acid chain, binding pockets of proteins, etc.). As such, it is not necessary to continually draw out the entire compound every time you wish to represent it, merely the parts of it that are involved.

 

I can really only see this being useful for compounds that have no stereochemistry whatsoever, and only if you include double and triple bond information as well as charges and hetero-atom bound hydrogens. Outside of that it fails to provide an adequate amount of detail. For the case of amino acids, the only real way I can see around the stereochemistry issue is if you predefine the chain as having all L or all D configuration. I also think that having to learn different symbols for every single element, which I am assuming would have to be the case and please correct me if not, is terribly inconvenient and not particularly easy to do.

Edited October 13, 2011 by hypervalent_iodine

[vasten]

After reading the thread I felt strongly inclined to agree with Greg and hypervalent. The only justification for the method I can see is that it might be quicker. As a simple test - not scientifically rigorous - I timed myself drawing phenylethylamine by both methods. It took 13 seconds in each instance. Now, vasten, you might argue that familiarity with the conventional system would allow me to draw that more rapidly. Perhaps. However, the last time I likely had occassion to draw an organic molecule in that way would have been in 1967. I don't think I've retained much motor memory of the process over the intervening forty odd years.

 

Yes, this is my main concern as well

 

Does the learning curve outweigh the benefits gained?

 

and

 

Is there a need?

 

------------------------------------------------------------

 

 

Does the learning curve outweigh the benefits gained?

 

As per leaning curve, I have gotten much more positive repsonses from those currently studying chemistry in Uni. They don't care about leaning curve, because by practicing it while simultaneously attempting to learn a large mound of chemical structure, the two learning processes seem very complimentary. I would say for beginners the benefits tend to outweigh the time investment.

 

However for those, like myself and you guys I assume, the time investment is not worth it. I found it amusing to create, but have had to force myself to use it. (I try to work stuff out on paper now, I live in China and have to travel alot for business so I have found a new love the pen and paper). But I do not feel it has provided any concrete "return on investment" that justifies the time put in.

 

-------------------------------------------------------------

 

Is there a need?

 

Well, it all comes down to.... Do you want to use paper, or a computer.

 

Obviously computers are necessary. I will never say "paper" beats "computer".

 

But, me personally, I love paper, I love doodling, I love playing with ideas and randomly jotting away until chaos falls into order.

 

And Dscript is great for this.

 

I use dscript for the love it, with the only goal to be increased complexity on a single sheet of paper, while remaining intelligible, clear, and as visually appealing as possible.

[hypervalent_iodine]

I completely understand the reason behind why would want to attempt this. As you say though, the investment in learning a new language that is only suited for a small subset of cases is simply not worth it (outside of its use as a medium with which to exercise the brain, that is). Developing ideas like this, I'll agree is fun and mentally rewarding, so there's certainly no faulting you there.

 

 

Also, something I noticed just now in the drawing of your Heme-A structure; The way you've drawn it makes it look as though the porphyrin nitrogens are not contained within the ring, but are a substituent of an all-carbon ring.

[Greg Boyles]

Generally, the chemistry involved in metabolic pathways or biochemical reactions only applies to a small section of the compound as a whole (such as the terminating ends of an amino acid chain, binding pockets of proteins, etc.). As such, it is not necessary to continually draw out the entire compound every time you wish to represent it, merely the parts of it that are involved.

 

I can really only see this being useful for compounds that have no stereochemistry whatsoever, and only if you include double and triple bond information as well as charges and hetero-atom bound hydrogens. Outside of that it fails to provide an adequate amount of detail. For the case of amino acids, the only real way I can see around the stereochemistry issue is if you predefine the chain as having all L or all D configuration. I also think that having to learn different symbols for every single element, which I am assuming would have to be the case and please correct me if not, is terribly inconvenient and not particularly easy to do.

 

 

Since when are biochemists concerned with molecular structure when representing biochemical pathways? From my biochemistry days in 1986.....rarely. The molecular structure and entities involved are so well understood that it is rarely necessary to go beyond the form C6H12O6

[vasten]

Generally, the chemistry involved in metabolic pathways or biochemical reactions only applies to a small section of the compound as a whole (such as the terminating ends of an amino acid chain, binding pockets of proteins, etc.). As such, it is not necessary to continually draw out the entire compound every time you wish to represent it, merely the parts of it that are involved.

 

I can really only see this being useful for compounds that have no stereochemistry whatsoever, and only if you include double and triple bond information as well as charges and hetero-atom bound hydrogens. Outside of that it fails to provide an adequate amount of detail. For the case of amino acids, the only real way I can see around the stereochemistry issue is if you predefine the chain as having all L or all D configuration. I also think that having to learn different symbols for every single element, which I am assuming would have to be the case and please correct me if not, is terribly inconvenient and not particularly easy to do.

 

 

I have already explained how most of that can be added(I just usually don't need to) and how sterochemical accuracy display is NOT a primary goal.

Fear of learning curve, yes, I am aware that will be an issue, i think that one is rather obvious.

 

 

Yes, Thank you for always comparing each aspect with whichever system is better.

 

While never comparing each aspect with other systems weakness's

 

And all only considering application currently used by current systems.

 

 

You are an expert on the current systems, and their application. Thank you for your help, I do need to hear these things.

 

But I am now at the point where I am finding you annoying and unless you interested in discussing NEW ideas and NEW applications, I am quite finished speaking with you.

 

I am just a crackpot drawing squiggly lines on paper, please ignore me!!!!!!!

[hypervalent_iodine]

Since when are biochemists concerned with molecular structure when representing biochemical pathways? From my biochemistry days in 1986.....rarely. The molecular structure and entities involved are so well understood that it is rarely necessary to go beyond the form C6H12O6

 

I never said they were. I would in fact completely agree that they are quite the opposite of interested in chemical structure or reaction mechanisms. However, to say that it is not necessary to go beyond empirical formula is a little presumptuous.

[vasten]

Since when are biochemists concerned with molecular structure when representing biochemical pathways? From my biochemistry days in 1986.....rarely. The molecular structure and entities involved are so well understood that it is rarely necessary to go beyond the form C6H12O6

 

While doodling and playing with random thoughts and idea. Not while trying to solve a particular problem at hand.

 

I assume I am not the only one who does these things.