Talk:Mathematical chemistry

What is mathematical chemistry?

Grestrepo (talk) 17:25, 23 October 2008 (UTC) To have a more clear definition in this line of thought it is necessary to define structure. In mathematical terms a structure is a couple (X, R) where X is a non-empty set and R is a binary relation on X. Therefore, in chemistry we have as many structures as many sets X we consider and as many relations R we study. For example one can consider a finite set of substances and study their similarities, in this case R is a similarity relationship. One can also study the same set from the order theory, thus one obtains a partial order structure.

Mathematical chemistry is the science whose object of study is (abstract) structure (that may or may not exist in nature). 212.18.56.195 18:44, 30 August 2005 (UTC)

Not only a structure, but also a chemical reaction -- so-called "computer synthesis" --Tim32 04:43, 27 October 2007 (UTC)

Grestrepo (talk) 17:25, 23 October 2008 (UTC) I do not think computer chemistry is mathematical chemistry. I think computers help to solve questions risen by mathematical chemists, which is different. The other thing is that a wealth of mathematical chemistry has been done using graph theory but not all mathematical chemistry is devoted to graph theory in chemistry. For example the use of information theory, knot theory or point-set topology is not directly related to graphs and however is mathematical chemistry. In this respect see for example:

• Restrepo, G.; Llanos, E. J.; Mesa, H. On the topological sense of chemical sets. J. Math. Chem. 2006, 39, 363-376.

• Bonchev, D. Periodicity of the Chemical Elements and Nuclides: An Information-Theoretic Analysis. In The mathematics of the periodic table; King, B.; Rouvray, D., Eds.; Nova: New York, USA, 2006; Chapter 8, pp. 161-188.

Grestrepo (talk) 17:25, 23 October 2008 (UTC) I also think that mathematical chemistry is not only restricted to organic chemistry. However is clear that owing to the large number of organic substances in comparison to the inorganic ones, the mathematico-chemical studies have been more widespread in organic chemistry.

Grestrepo (talk) 17:25, 23 October 2008 (UTC) I would not confuse the terms computer chemistry and mathematical chemistry. The first one refers to the use of computers to solve chemical questions and the latter to the application of mathematical theories to understand and formalise chemical knowledge.

Generally computer chemistry (mathematical chemistry) is based on graph theory applications for organic chemistry. Common tasks of computer chemistry are: relations "structure - property", "structure - activity", chemical reactions enumeration (so-called "computer synthesis"). The main models used in computer chemistry are molecular graph and topological index. The computer chemistry is very young branch of chemistry, so different definitions may be possible. But, obviously, computer chemistry is not quantum chemistry, is not computational chemistry etc. Other branches of chemistry also based on mathematical theory, so "computer chemistry" is better name as "mathematical chemistry". First of all, IMHO, the context of Chemical graph theory should be moved here, and Chemical graph theory should be deleted. "Chemical graph theory" was very good name for the book by Bonchev and Rouvray, but it is not chemical branch.

Following examples of investigations in the computer chemistry had been done in Lab of Computer chemistry of N.D.Zelinsky Institute of Organic Chem. of Russian Academy of Sci. (Moscow):

• N. S. Zefirov, M. A. Kirpichenok, F. F. Izmailov, and M. I.Trofimov, Scheme for the Calculation of the Electronegativities of Atoms in a Molecule in the Framework of Sanderson's Principle, Dokl. Akad. Nauk SSSR, 1987, 296: 883 [Dokl.Chem., 1987 (Engl. Transl.)].

• M. I. Trofimov, An Optimization of Procedure for Calculation of Hosoya's Index, J. Math. Chem., 1991, 8, 327.

• M.I.Trofimov, E.A.Smolenskii,Application of the electronegativity indices of organic molecules to tasks of chemical informatics, Russian Chemical Bulletin, 2005, 54(9): 2235.(http://dx.doi.org/10.1007/s11172-006-0105-6). --Tim32 08:28, 13 November 2007 (UTC)

From my talk page

I am not so sure that you have got the definition of mathematical chemistry and its relationship to theoretical and computational chemistry exactly right. It tends to be used in a very restricted sense covering such direct mathematical ideas as graph theory and so on. The contents of the Journal of Mathematical Chemistry are very restricted. I do not think mathematical modeling is normally considered as part of mathematical chemistry. Your edit to Computational chemistry - "Computational chemistry uses the results of theoretical chemistry, in particular, its branch mathematical chemistry" is not, I think really correct. The mathematics of the various methods of computational chemistry are important, but they are not considered, as far as I can see, as mathematical chemistry. I think there are similar problems with your edit to mathematical chemistry. What do you think? --Bduke 02:34, 13 November 2007 (UTC)

I noticed that certain areas are undercovered and fixed some gaps using the references available, not from my own head, so I take no responsibility.

• "I am not so sure that you have got"- I am not inventing bicycles here. I noticed that the old version of mathematical chemistry was rather strange nd first thing I did, I found a reference (added) with the definition. If you have anther reference, you are welcome to expand the article "other authors define it as .... bla-bla".

• "I do not think mathematical modeling ... is part". Of course not. I dod not say that. It is vice versa.
• I claim no scope of mathematical chemistry and I see no contradictions in my additions, in particular in does not contradict your statement that "The mathematics of the various method...."

Thanks for looking into my edits. I claim no expertise here, but I don't see glaring errors either. It is possible that I dont exactly understood your remarks. Please elaborate. `'Míkka>t 02:50, 13 November 2007 (UTC)

Perhaps you do misunderstand me or perhaps I have expressed myself badly. Let me concentrate on "Computational chemistry uses the results of theoretical chemistry, in particular, its branch mathematical chemistry", although that is from computational chemistry, not from mathematical chemistry. The problem is really the word "particularly". The results of theoretical chemistry that are used are quantum mechanics, statistical mechanics, force fields, linear algebra, molecular integrals and so on. None of these are mathematical chemistry. It seems to me that that term is generally restricted to topics like graph theory and topology and that it does not include applied mathematics topics. Mathematical chemistry now states that "Mathematical chemistry is a branch of theoretical chemistry defined as mathematical modeling of chemical phenomena. Does this mean "Mathematical chemistry is defined as mathematical modeling of chemical phenomena" or "theoretical chemistry is defined as mathematical modeling of chemical phenomena"? The first is not, I think, correct as all all aspects of "mathematical modeling of chemical phenomena" are not included in mathematical chemistry. The second is close but I have not seen it defined in that way. Do you have sources for the definition of either term? --Bduke 03:24, 13 November 2007 (UTC)

I think part of the problem is that mathematical chemistry is defined in many ways. Some people talk about any kind of interaction between mathematicians and chemists. Others define it more carefully. The Journal of Mathematical Chemistry talks of "publishes original, chemically important mathematical results which use non-routine mathematical methodologies often unfamiliar to the usual audience of mainstream experimental and theoretical chemistry journals". It then goes on to articulate a wider vision, but a look at the contents shows a more restricted use of the term. Maybe there is no agreed definition of the term. --Bduke 03:42, 13 November 2007 (UTC)

The problem is that the sentence "Mathematical chemistry is a branch of theoretical chemistry defined as mathematical modeling of chemical phenomena" is a half-quote taken out context from a book review, and as a consequence is too vague. A more complete quote is more informative: "that area of research engaged in the novel and nontrivial applications of mathematics to chemistry; it concerns itself principally with the mathematical modeling of chemical phenomena". Also, I see no evidence that anyone calls it "computer chemistry". A more complete reading of the review shows clearly what is meant by "nontrivial applications of mathematics": it talks about graph theory, topology, and group theory. I'll update the definition accordingly. --Itub 08:47, 13 November 2007 (UTC)

Computer chemistry

We are listing computer chemistry as an alternative name for mathematical chemistry, but computer chemistry redirects to computational chemistry. So far, the only reason I have found for mentioning computer chemistry as a synonym for mathematical chemistry is the existence of MATCH Communications in Mathematical and in Computer Chemistry, which is listed in the external links. However, I think that is a name that persists for historical reasons (it dates from 1975) and is not used much nowadays to avoid confusion with computational chemistry. Furthermore, I think it is more accurate to say that most of "computer chemistry"--which I think originally meant the use of computers in mathematical chemistry research--is called chemoinformatics nowadays. See these two books for example: [1], [2]. --Itub 10:33, 13 November 2007 (UTC)

That redirect was only added in the last day. I'm not sure what we do with it. A disambiguation page maybe? --Bduke 10:59, 13 November 2007 (UTC)

Yes, I think a disambiguation page is the best option. --Itub 11:01, 13 November 2007 (UTC)

I am afraid user:Itub makes a conclusion improperly: "computer chemistry as a synonym for mathematical chemistry". The name of the publication is "in Mathematical and in Computer Chemistry", rather than "in Mathematical or in Computer Chemistry". (although the statement may be right).

Clearly both terms (and throw chemical graph theory in here) are neologisms, possibly adoped by certain schools, and to figure out what calls what requires real experts in the field who know the history and the inside movements. I may well understand that chemical graph theory may appear as woodoo science, after all, we already know that chemical bonds are not exactly pieces of rope that hold molecules together, but rather complex quantum physics phenomena. Still, this is wikipedia, and our purpose is to explain how other people (not we) call various things as published in professional literature. Otherwise we will only increase the confusion. In particulat I would like to ask to provide proofs of the validity of the disambiguation page computer chemistry, ie., the facts of multisynonymous (ambiguous) usage of the term. `'Míkka>t 16:14, 13 November 2007 (UTC)

I'd be happy with deleting the mention of "computer chemistry" from this article (I wasn't the one who added it, but I was reluctant to delete it). But I still like the idea of a disambiguation page, to disambiguate between computational chemistry and chemoinformatics. There were books around 1990 with titles such as Computer chemistry which tried to encompass all applications of computers in chemistry, but as the field evolved, the term generally fell into disuse and was replaced by computational chemistry and chemoinformatics. --Itub 16:25, 13 November 2007 (UTC)

Míkka wrote: "we already know that chemical bonds are not exactly pieces of rope that hold molecules together, but rather complex quantum physics phenomena." In a few words: there are two approaches to molecular structure in organic chemistry: classical and modern (quantum). Computer chemistry uses molecular graph model, which maps onto classical structural formula of organic compound.--Tim32 08:26, 14 November 2007 (UTC)

Please, see, Dodecahedrane synthesis for example of "classical structural formula"--Tim32 08:40, 14 November 2007 (UTC)

18th century

It looks like a nonsense: "The term was coined in 1970s, although the history of the approach may be traced back into 18th century." Please, give any fact to prove it.--Tim32 08:11, 14 November 2007 (UTC)

I thnk this refers to a quote from a guy called Silvester along the lines that all chemical problems will be an exercise in mathematics, but I need to find it. I did not add that sentence. --Bduke 08:54, 14 November 2007 (UTC)

The cited reference says precisely that (well, it says "200 years ago" and was written in the 20th century). --Itub 08:55, 14 November 2007 (UTC)

For more information, see Chemical Graph Theory: Introduction and Fundamentals By Danail. Bonchev. --Itub 09:01, 14 November 2007 (UTC)

The general goals of organic chemistry may be defined as new reaction, new compound and its properties. The general goals of computer chemistry are an algorithm and computer program. (The program may be used outside computer chemistry frameworks – in contrast with quantum chemistry. For example, not every chemist has special skills to use quantum program, but every chemist can use MolGen). In spite of so-called “paper programming” introduced by Ershov in 20th century, the “computer program” goal seems very strange for 18th century. Bonchev is well-known specialist in computer chemistry area, and I think he has written very strong reasons for this statement in his book. Also, I think that I am very poor informed about chemical achievements in 18th century. But, again, outside context of the book this statement looks very strange. So, any example about “18th century” from this book may be inserted to the article and this addition would be very appreciated by Wiki readers. (BTW, perhaps, Bonchev meant chemical informatics? Chemical Abstracts was printed without computer usage for a long time period. Some books like Chemical Abstracts may be printed in 18th century also.) Sorry, but this time I can not download Bonchev’s book via Internet.--Tim32 09:39, 15 November 2007 (UTC)

The book refers to the first applications of graph theory to chemistry, which happened in the 18th century (the same century that saw the origin of graph theory). No one would call that "computer chemistry", but it fits well within what is called mathematical chemistry today. Note that these early applications were not "chemical graphs" in the modern sense of representing the structure of a molecule, because the structural theory of molecules was not developed until the second half of the 19th century! --Itub 10:15, 15 November 2007 (UTC)

"It's all very complicated and would take a scientist to explain it." -- MST3K ---- Tim32 (talk) 19:01, 16 November 2007 (UTC)

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