Marvin Sketch naming convention for carbon ring.

Hello,

This is regarding Marvin Sketch 15.5.4, if that is of any help.

I am not a chemist, but am an undergrad working on a project that uses the chemistry domain. For this project, the RXN files in use currently have carbon rings, more specifically benzene rings, which are drawn out for the r-group specifications. The software which takes these RXN files as input cannot use this actual ring of carbons, but requires an abbreviation for this type of structure. 

So my question to you is, what would be the the proper naming convention of carbon rings, specifically benzene rings if necessary, in the Marvin Sketch software environment?

 

Thanks for your time and assistance,

Alden

Hi Alden,

I'm afraid I don't understand what are you trying to achieve here.

Can you provide us with some examples or more detailed description?

 

Peter

Hello Peter,

Thanks for your reply. I will attach an example file to illustrate where my issue arises. As you can see, there are two carbon rings hard coded into the specifications of the two r-groups. I have a program, written in Python, that I am working on and using to convert these RXN files into another format, which uses a type system. This other format's type system needs a specific name to give the type that is represented by the carbon cycle, but I do not know what to call this carbon cycle chemically, specifically in Marvin Sketch. I need some abbreviation, like alkyl.

I have looked online, but have found little to no conclusive help for the naming convention such a formation should follow. I was considering something with cycloaryl, or some type of cycloalkane, like cyclohexane, to represent the benzene ring. Cycloaryl exists in the advanced options in Marvin Sketch, but I am confused as to how to specify that it would have specifically 6 carbons. As for cyclohexane, I do not see that as an option, nor the more general cycloalkane. Again, I have a very rudimentary knowledge and understanding of chemistry, so I may be quite off with these guesses. Perhaps this option is not even provided in Marvin Sketch by default, and I have to use the custom options in the advanced tab of the element/molecule selector menu?

If you need any more detail, please let me know,

 

Thanks,

Alden.

Hi Alden,

In Marvin Sketch, there are two ways for abbreviating parts of chemical structures:

• The so-called homology groups, each of which represents many
  specific chemical groups. The "Alkyl" used in your example is one of
  these features. To represent a phenyl group similarly, you should use a "Carboaryl", which can be selected on the Advanced tab of the periodic system dialog of Marvin Sketch. By default, this homology group represents aromatic carbon rings of any size, but you can restrict this using so-called homology properties. After drawing a "Carboaryl", click on it with left button, select "Edit Properties..." from the context menu, and in the dialog box, enter "C6" into the "Additional Text Notes" line, and click OK. This way you restirct the group to aromatic rings having exactly 6 carbon atoms (practically, benzene ring only).
  For more information, see the documentation.

• The so-called abbreviation groups, which represent a single specific chemical group, e.g. "COOH", "Ph". For representing a benzene ring, you can use "Ph" (phenyl group). You can draw it either by selecting from "Insert -> Groups..." menu in Marvin Sketch or by simply typing "P" and "h" on the canvas.
  For more information, see the documentation.

Anyway, I don't know which one is better for your particular use case, but I hope these hints help you.

Best regards,
Péter Kovács

If I understand your question correctly, the name to use to represent a cyclic carbon group of size exactly 6 would be "cyclohexyl".

Hello Peter and dbonniot,

Thank you for your replies, I think I am understanding now what I need to do. I'd like to ask if I can for you to verify the conclusions that I have made based on your assistance and what I have looked up as a result.

As I understand it, cyclohexane is to cyclohexyl as benzene is to phenyl. Cyclohexane and benzene have the full complement of hydrogens that they can support, cyclohexane having 2 per carbon, and benzene 1. Cyclohexyl and phenyl are respectively the same, with 1 hydrogen removed from one of the carbons in the ring. Cycloaryl is a more general term for cyclohexyl, being not restricted to exactly 6 carbons. If any of this is incorrect, I would appreciate any corrections/clarifications that you can provide.

It seems clear to me that benzene and phenyl have aromatically bonded carbons. What I am confused by is whether cyclohexane, cyclohexyl, and cycloaryls in general have aromatic bonds. The link about homology groups provided by Peter says this about carboaryls: "among these rings at least one should be aromatic". Do I take that to mean that cyclohexane, cyclohexyl, and cycloaryls may not necessarily be aromatic? Perhaps cyclohexane and cyclohexyl are simply more general versions of benzene and phenyl, which are specifically aromatic, and can only have one non-aromatic bond per carbon?

As for now applying this to Marvin Sketch, I believe that both the carboaryl homology group, or the phenyl abbreviation group would suit my purpose, and I will simply need to verify which one applies better to a given reaction in question.

In the case of the homology group carboaryl, is it not possible to specify having exactly 6 carbons in the name, such as carbohexyl?

Just to clarify about the abbreviation group, when I start typing "Ph" on the canvas, "Phenyl" shows up as an option. Is there any important difference between using "Phenyl" versus "Ph", or is "Ph" just a short form of "Phenyl" for convenience. 

 

Again, I greatly appreciate your assistance,

Alden

Hi Alden,

As I understand it, cyclohexane is to cyclohexyl as benzene is to phenyl.

That's right.

Cycloaryl is a more general term for cyclohexyl,

I don't think so. "...aryl" name refers to an aromatic ring, while "cyclohexyl" is an aliphatic ring consisting of 6 carbon atoms. (Anyway, we use the term "carboaryl", not "cycloaryl".)

What I am confused by is whether cyclohexane, cyclohexyl, and cycloaryls in general have aromatic bonds.

See above: "...aryl" has aromatic bonds, while "cyclohexane" is aliphatic.

The link about homology groups provided by Peter says this about carboaryls: "among these rings at least one should be aromatic".

Yes. In general, a "carboaryl" homology group can also represent fused rings, among which at least one ring is aromatic. However, if you restrict this group by the term "C6", then it practically represent the benzene ring only.

In the case of the homology group carboaryl, is
it not possible to specify having exactly 6 carbons in the name, such as
carbohexyl?

No, this is not supported.

Regards,
Péter

Thanks Péter,

That definitely clears a lot up. Thank you for your time!

 

Alden