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Chemistry Forums for Students => Physical Chemistry Forum => Topic started by: Juan R. on August 24, 2004, 07:14:47 AM

Title: Canonical chemistry
Post by: Juan R. on August 24, 2004, 07:14:47 AM

I am Juan R. González-Álvarez

I am launching a new revolutionary view of chemistry. The objective is develop a basic theory for chemistry but far from the usual physical chemistry.

Physical chemistry copies physics. Mi principal aim is focus in traditional chemical principles.

The theory is highly advanced. A basic background on usual physical chemistry is not sufficient. For example in the quantum version of canonical chemistry, even the axiomatic theory by Lindblad is only a simplified case of our more general equation based in the theory of chemistry.

I hope to launch officially canonical chemistry in one or two months. I have sent a letter to nature (I hope for publication) and also a pre-presentation to Chemistry International.

All my work is done outside of official funding.

Let me introduce the reply of Ilya Prigogine to my last message (before launching canonical chemistry)

"The Questions that you ask are very difficult"

Can canonical chemistry solve that difficult questions?

I hope that this forum can sited some non-technical work mine and questions.
Title: Launching canonical chemistry
Post by: Juan R. on August 25, 2004, 07:12:47 AM

Canonical chemistry is not only a theory of matter; it is also a new philosophy inspired in fascinating ancient chemical and alchemical views.

If you opine that chemistry is a cuisine, a metaphor, a qualitative semi-science, or only a “stupid” branch of applied physics, then you are not interested in canonical chemistry.

At contrary, if you want to see how “all” from the big bang to heat transport, passing by molecular chemical reactions (of course!), viruses diseases, particle physics reactions, ecological or sociological models can be explained in terms of mechanisms based in a generalization of the 20th century concept of chemical processes. If you opine that Santa Fe Institute research in complexity is, in general, only “garbage”, check our revolutionary chemical theory. Note that I said “20th” because in ancient chemistry literature heat transport was considered a kind of chemical process, for example. In fact, chemists as Boyle or Newton thought that universe was a huge chemical system and God an alchemist!

If you love chemical views and you want to see how experimentally verified generalizations of Schrödinger equation (e.g. Redfield, Lax, and others) are derived from canonical chemistry equations more the adequate chemical mechanism or if you love high-level mathematics and opines that quantum field theory is not sufficient for you, then you would choose canonical chemistry. Many quantum chemists have claimed that structural theory of organic chemists was only a metaphor. Do you know that physicist begin to show that the concept of molecular structure is strictly outside of an Schrödinger equation? They have shown that the Schrödinger evolution for isolated molecules is valid only as an approximation to a Caldeira/Legget evolution even in the interstellar medium!

If you are a theoretician interested in chemical reactions, and S-matrix theory is not sufficient for you, please develop advanced models from our “thermomaster” equation (manuscript in preparation).

If you are a chemical engineer looking for an “umbrella” theory of transport processes, note that canonical chemistry generalize molecular dynamics, kinetic theory or the well-known TIP between others. Do you know that I based my TCL technique for quantum memory effects in the “old” Cattaneo hyperbolic equation?

If you believe that recent Prigogine generalization of quantum theory for irreversible and chaotic systems is interesting, please to discover how canonical chemistry introduces several interesting corrections to the math and concepts of Brussels’ theory (e.g. our crucial reinterpretation of the “collapse” of the Hilbert space structure).

I am sorry to say this but canonical chemistry modifies many incorrect views of traditional physical chemical literature. In my 12-pages overview article “Canonical chemistry education, an unified program for the 21st century”, I critique peer-review journals and introduce basic comments on several wrong aspects of chemical education as, for instance, that the second law is not “that” one read in usual chemical thermodynamics or physical chemistry textbooks. I do NOT use inexact differentials for heat (I write dQ) and this was a surprise for many physical chemists, please see the last book by Prigogine and Kondepudi for more advanced formulations of thermodynamics. Note that the thermodynamics developed from canonical chemistry is more advanced still!

I am thinking to send the above-cited “heated” article to the Journal of Chemical Education, but if this new forum attracts to many young chemists, and I receive a sufficient number of pleas for post here material, then I could site it here. The objective (see point 5 below) is that all chemists receive an improved preparation.

Please if my ideas are bad for you, then critique it rudely. If you think that my work is interesting then correct my possible mistakes and divulgate the corrected work.

The first that one would notice is that the actual status of chemistry is very unpleasant. I introduce next part of the letter that I sent to Nature some days ago:

Since the brave Nature Editorial defending to the chemical science (“A discipline buried by success,” Nature 411, 399; 2001) and the News Feature by David Adam (“What’s in a name,” Nature 411, 408–409; 2001), the status of chemistry and chemists is even poor. An example was the plans for closed highly rated chemistry groups (“Max Planck plans double blow to chemistry,” Nature 422, 105; 2003).

Nature often notices the innumerable plans of chemists for addressing the problems facing our discipline (e.g. “Chemists seek image overhaul,” Nature 425, 227; 2003). However, recommendations for new funding for centres in nuclear and radiochemistry have been ignored. Moreover, two prestigious university chemistry departments (King’s College and Queen Mary College, both in London) were forced to close recently –following two early closed (Salford and De Montfort, UK)–. The same fate looks likely for the department of chemistry at the University of Wales, Swansea. At least other two, Dundee and Nottingham Trent, are currently under threat. In Spain, the fate looked no better than the rest of world. I am a young chemist, and all my previous attempts for achieving an adequate research position in chemical science have been neglected.

But things can change this year! The launching of a new revolutionary program –namely canonical chemistry– would put back to chemistry at the central point of modern science. The canonical program deals with scientific, educative, epistemological, and historical topics of the chemical science.

Some basic objectives are next summarized:

1) Modernization of the general view of chemistry.
2) To reinforce the central character of chemistry in modern theoretical science.
3) Development and application of a sophisticated unified theoretical framework and its related mathematical methods.
4) To recover the true history of the central science, emphasizing the important contributions of chemistry, both past and present ones. Retrieval of the ancient contemplative side of chemistry thanks to the revolutionary philosophical perspectives opened with our theoretical research.
5) Modernization and systematization of the current chemical curricula.
Title: What is canonical chemistry
Post by: Juan R. on August 26, 2004, 08:26:27 AM
Please I cannot reply with rigor and extension to general questions as What is canonical chemistry?

If you send me some message or post some question in this forum, please be more specific.

I believe that one complete presentation of canonical chemistry would need of more than 10*20 pags. In fact, I am preparing a serie of research articles about all this.

In this forum I could, if chemical forums agree, reply to some specific questions about canonical chemistry program. But I believe that first I would launch officially the program, including research articles. I hope launching it very soon.

As said I sent Nature letter and a basic feature article to CI, now I would submit the following "viewpoint" article about failures on chemical education.

Some advanced literature would be useful for understanding canonical chemistry.

Forget usual manuals on quantum mechanics or quantum chemistry! Read books/articles about dissipative quantum theory, Prigogine's "dynamics of correlations", projection operator methods, etc.

Forget traditional manuals on chemical thermodynamics, read Kondepudi and Prigogine "Modern thermodynamics" and more advanced books, for example "Rational Extended Thermodynamics".

Usual manuals on spectroscopy or chemical kinetics are good ones, but need be improved by canonical chemistry, especially in basic theory.

In general a course on usual statistical mechanics (equilibrium) is not suficient. I recomend the easy book Non equilibrium statistical mechanics by Zwanzig as a first step.

Title: Re:Canonical chemistry
Post by: AWK on August 27, 2004, 03:14:17 AM
Why not send it to as preprint.  I am sure that HYLE (international journal
for philosphy of chemistry) is pertinent to your subject.
Title: Re:Canonical chemistry
Post by: ssssss on August 27, 2004, 03:46:33 AM
So will canonical chemistry disprove some of the models and equations of chemistry or it will more generalize the existing theorems of chemistry.
Title: Acknowledgement
Post by: Juan R. on August 30, 2004, 07:32:02 AM
First, I would thank your interest in the new ideas that I am launching. I believe that canonical chemistry could be a good opportunity for turning the terrible status of current chemistry (I recommend the reading of Nature references above cited: The ENDING of departments and centers, neglecting of funding, decreasing in number of students and PhD, decreasing by the first time on the number of ACS members, neglect of chemical contributions to science and society, etc.). In 19th century, chemistry was considered the queen of sciences. Could that status be recovered in this new century? If we want see to a glamorous chemistry, with chemists being respected by society, we cannot hope that physicists and biologist were highlighting chemical contributions as being done by them (See Nature vol 411).

I also thank the possibility that Chemicalforums has opened for a forum about a “renaissance” of chemistry as the most central and basic of sciences. I would say that Mitch suggested to me to write here about this new fascinating and revolutionary possibility. I am especially indebted to him.

Title: Chemweb, Hyle, and canonical chemistry
Post by: Juan R. on August 30, 2004, 07:35:36 AM

Hi “AWK”

I submitted some material to CPS. After of some time, I had problems with my affiliation to University of Vigo, and my work was rejected for preprint. However, the problems were rapidly solved (I thank the interest of James Weeks, Chemistry Preprint Server Co-ordinator) and I continued to submit some material to chemweb whereas continued my research. However, the chemistry preprint (2000-2004) was forced to close!!!!! As a member, I received the official communication (18 May 2004). Now I cannot submit new articles, neither modify/alter the previous preprints.

“Hyle” is a good journal for the philosophical part that arises of my work. For example, from canonical chemistry we can derive quantum mechanics as a special case. Moreover, my work introduces strong generalizations of theories of physics as “advanced” as string theory (the most advanced theory of fundamental physics). This breaks the usual hierarchical interpretation of sciences. Now physics is NOT the most fundamental of sciences with chemistry as an “applied” branch of it. The situation is more “horizontal”, with chemistry as a proper science, outside of the shadow of physics. Of course, this opens a new epistemological interpretation of science hierarchy. The journal “Foundations of chemistry” is also good.

But the main problem is with the publication of research articles. I have again problems of affiliation. Moreover, some high-level journals support their activities introducing standard publication charges to authors. An example is $100 per article plus $100 for per journal page. The journal where chemist Pauling and chemist Zewail, between others, published part of their initial works requests $55 per page and an article charge of $20 per article, with a page charge of $150 for each page in excess of 12 pages. I communicated with its editor. Donald H. Levy said: “We will consider all papers on their scientific merits regardless of the position or academic background of the author”. Fortunately, they valuate just the work and not who do it; others request an adequate affiliation first! But my second research article, where I show more detail about canonical chemistry and show how quantum transport or the master equation of particle physics are special cases of our basic equations has 20 pages. Note that I do not receive funding or grants for supporting those very elevated costs!

I also have great problems with the peer-review of usual scientific journals. Many revolutionary works were rejected for publication or rejected by chemical community (See above cited article about canonical education), For example, Zewail’s work was rejected by chemists, but now he won a Nobel Prize for Chemistry. His fascinating work, revolutionary “only” in the field of transitions states, lasers, and all that, led intact over the “90%” of chemistry and all of physics. Imagine the reject of my ideas if I claim for a revolution on a “70%” of both!!

Moreover, my work is multidisciplinary, I am working in relativity, scattering, quantum theory, thermodynamics, statistics, math, cosmochemistry and astrochemistry, adsorption kinetics, philosophy, ecology, biophysics, basic epistemological questions of chemistry (such as definition of chemical reaction), etc. In a future, I want address the problem of definition of atoms (Bader def. is not very convincing for me), computation, applied laser chemistry, engineering models for efficient transport, and others. It is very difficult for me to publish in dozens of journals, and would be difficult for people (specially students) to recollect all my work, even if were published! I see also a problem of time; the time of appearing is much more large for revolutionary theories. Once, an article appeared in 1957 in the Journal of the American Chemical Society, 25 years after it was initially submitted!

Do you know that the law of conservation of energy was rejected for publication in a journal of physics, and then resubmitted to a journal of chemistry edited by Liebig and Wöhler? Unfortunately, that was in the past (when chemistry was in the cutting-edge side of physics); now many referees have a more “closed mind” and consider that all of fundamental chemistry is already known. In fact, the previous manuscript of the theory have received more interest from some physicists that from chemists. In my first research article (posted as preprint at chemweb), a famous chemist said that I “would” be wrong. Note that he said not exactly in that: “Perhaps the referees of the journal to which you submitted this article will point out the error in your discussion.” A recognized specialist (physicist), working with equations “similar” to mine, said, “I like your approach... and that use of your extension seems to work for mesoscopic systems where it may not be justified by Keizer’s original thinking. However, we found long ago that the fluctuation theory worked down to the angstrom level and could give results in agreement with neutron scattering. Thus your extension may be valid for related reasons.”

Recently, a group of four celebrated investigators of the Research School of Chemistry in cooperation with other investigator has published a sound paper with the claim of experimental violation of the second law for small systems. As said in my first article, they understood incorrectly the evolution of the small system, because they used “19th century” thermodynamics, but we are at the 21st century! The claim is incorrect; two or three specialists (physicists) have already published comments on Wang et al. paper. I have checked the fifth version of celebrated manual on physical chemistry by Levine and one can read a WRONG presentation of the law. Even Wang et al. claim of that the second law is violated in small chemical systems appears as obvious one! Other specialist (physicist) said me: “I agree with you that ‘experimental demonstration of violation of the second law’ is only in the title of the paper by Wang et al.”

Has been 20th century theoretical chemistry somewhat an “archaic” field? Is the usual chemical education adequate? Imagine that you (perhaps a student or young researcher) read Levine or other manual, and after you publish a research paper as that of Wang et al. and physicists show that you are completely wrong because you are learned “archaic” topics. It appears clear that canonical chemistry is needed for the above-introduced 5) objective.

Now, the manuscript about thermodynamics has been enlarged and improved with further research. I even received (March 2004) a formal invitation for participating in an international conference about the topic (but the lack of funding and affiliation...). Of course, I am not saying that the work was perfect. I simply say that when more revolutionary is a work more rejection one receives. Young chemist interested in nanothermodynamics (“senior” academics have claimed that thermodynamics is only a macroscopic science) would check my own work on the topic and see if it is useful for understanding the thermal properties of small chemical systems.

In fact, the chemist Stuart Schreiber has said in public that one of the problems of current (20th century) chemistry was the attitude of some senior academics. Those senior academic with “closed minds” have ignored some emerging areas of chemistry and would reject (I am sure) canonical chemistry because is too novel for them. This is a great problem; fortunately, young people have minds that are more “open”. Note that canonical chemistry is even more revolutionary that the new quantum mechanics developed recently by the chemist Ilya Prigogine. In fact, during some time Gonzalo Ordonez (Ilya Prigogine Center for Studies in Statistical Mechanics and Complex Systems and International Solvay Institutes for Physics and Chemistry) and I look for a mathematical link between my theoretical ideas and Brussels theories. We never find it. After of a new recent research, I found that canonical chemistry cannot be reduced to Brussels theory, because one needs to modify the so-called Liouville equation. Canonical chemistry is more general. All this is directly inspired in chemistry! This is fascinating!

Prigogine said in his last book “The end of certainty”, that physicist were always very hostile with his work on a new physics; work mainly “inspired” in his previous work in chemistry (Nobel Prize for chemistry 1977). He did none direct contribution to string theory and mathematically his new theory is very similar to the own of Dirac, Gamow, Poincare, Gelfand, Bohm, and others (for example he “complements” the usual Liouville equation by a set of markovian equations based in his novel non-unitary operator lambda). Simply imagine the reject of canonical chemistry by the same physicists! We substitute directly the basic equation of advanced quantum mechanics by a rate equation somewhat similar to the chemical equation for a bimolecular reaction A + B = C + D but with a revolutionary vectorial stoichiometry in Liouville space.

I am founding a new independent Center for supporting this research and for posting this new view of chemistry, including manuals and articles on canonical chemistry. Moreover, it is an objective of the center to facilitate free access to both educative and viewpoint articles. Now chemical students can access only to journals “sited” in the library of their university! For example, when I was a student in the University of Vigo I could not access to articles of Journal of Chemical Education prior to 1990 aprox.  

Title: Canonical chemistry and current theorems
Post by: Juan R. on August 30, 2004, 07:37:43 AM

Hi “ssssss”

Interesting questions! There is a mixture.

For example, our advanced research (named QRD) shows that Dirac relativistic equation is totally false (it is only a “metaphor”). Of course, one can show that in some restricted situations (for example calculations of relativistic energy spectra for atoms or molecules) both equations agree “numerically” (this is the reason of that the equation appears to be correct). However, our theory is applicable to situations where Dirac equation offers us the wrong answers. Note that I said numerically. This is because Dirac was forced to introduce the trick of his “hole-theory” for justifying the empirically observed stability of hydrogen atom.

Note that practically all relativistic quantum chemistry literature has assumed that Dirac equation is correct!! This is a sign of the poor status of current theoretical chemistry.

Many textbooks on statistical mechanics says you that statistical ensembles are a “coarse grained” description of dynamical systems. This is not true (usual “proofs” based in ergodic theory are not correct ones), moreover, see that the ensembles simply are postulated in usual presentation. That is, there is not possibility for deriving them from an underling theory, and this has impeded during decades the formulation of a necessary nonequilibrium statistical mechanics. Our theory offers an answer to last Zwanzig’s question of why the empirically known equilibrium ensembles work. They are not “coarse grained” descriptions of some more fundamental, i.e. “dynamical one”; they are stationary states of our basic equations that generalize dynamics (this is the reason of that ensembles cannot be derived from dynamics). In this case the equilibrium ensembles of usual theory are correct ones, and canonical chemistry only say us why they are. Moreover, outside of equilibrium, canonical chemistry could provide the correct form for nonequilibrium ensembles. I have not explored completely this field still, but basic work is done. I need time!

Schrodinger equation and the second law of thermodynamics are generalized for instance. (See preliminary comments about the second law in my above-cited article about canonical education).

Take now the equations of chemical kinetics and Arrhenius law k = A exp(-E/kT). I read in Masel’s book on chemical kinetics and catalysis that there are many examples of “non-chemical” systems that follow the law; e.g. plants, bacteria, crickets, the walk of ants, etc. Why? Canonical chemistry offers us the answer. I generalize the “traditional” (20th century) concept of chemical process to “each” process where “matter changes”; I include changes on position! e.g. A(here) -> A(there) can be studied as an unimolecular reaction of kind A -> B, with these novel equations.

For instance, a classical model of mathematical ecology inspired in chemical reactions is the predator-prey model LV.

A + X1 -> 2 X1

X1 + X2 -> 2 X2

X2 -> B

Where X1 is the PREY and X2 is the PREDATOR (are not just chemical molecules inside a biological organism as in biochemical models!). Models of this kind have been launched by biologist, physicists, and ecologists, but mainly ignored by own chemists!!! How many manuals on chemical kinetics introduce “non-chemical” models of this kind?

In Foundations of Chemistry 2001, 3, 33-53, Niall Shanks writes, “But the chemical sciences do not merely provide an understanding of the molecular underpinnings of biological phenomena. In the last two decades, chemical systems (based on substrates very different from those found in typical biological systems) have come to be used as dynamical models for the study of biological systems.” Shanks adds, “In this essay I examine the ways in which the Belousov-Zhabotinsky (BZ) reaction is being used by biologists to model a variety of biological systems and processes. The BZ reaction is characterized as a functional model of biological phenomena.”

Canonical chemistry generalizes these models and claim that “all” can be studied as a chemical system (this is a mathematical version of alchemical views). I studied chemistry at the University of Vigo and none professor said to me that chemical models could be applied to other “non-chemical” systems as big bang or heat transfer. However, I know that BZ models and similar ones, including chaos and others advanced topics were thought in courses of marine sciences; during some time I was a member of a group of marine biogeochemistry at IIM (CSIC) and I knew to both marine scientist and students.

Those above systems, “chemical” in the language of canonical chemistry (Note that an objective of canonical chemistry is formulate a theory of “all”, point 2 above), can be modeled with the equations of canonical chemistry when one writes the correct “mechanism”. Moreover, Arrhenius law is introduced “by hand” in usual presentations of chemical kinetics; Arrhenius is a theorem for a well-defined class of processes in canonical chemistry!!

Conclusion, canonical chemistry disproves, generalizes, and maintains previous theoretical topics of chemistry.

“Senior” academics could try to said me that a colony of ants is not a chemical system. This is true, it is not a chemical system from a 20th century view, somewhat before Wöhler work, the predominant scientific view was that humans and other living organism possessed a non-physical (“vital”) force that allowed living organism to synthesize organic compounds. Now we see both organic and inorganic compounds as two kinds of the general group of chemical compounds. Now “organic” is also chemistry but before Wöhler...

In his last book, “Modern thermodynamics (from heat engines to dissipative structures)” Prigogine introduces the basic of his theory on dissipative structures as the existence of bifurcations due to instabilities. In the figure 20.5 you can see an example of application of ideas of his chemical theory to social insects as ants. Canonical chemistry studies directly “each” system of universe as a “generalized chemical system”. In a sense, the relationship between “generalized chemical systems”, “non-chemical systems”, and “usual chemical systems” is as the previous relationship between “chemical”, “organic”, and “inorganic” in Wöhler’s epoch:

Inorganic + organic = chemical

Usual chemical systems + “non-chemical” systems = “generalized chemical systems”.

Chemistry is an open science; chemistry is fantastic!

Title: Re:Canonical chemistry
Post by: Juan R. on September 07, 2004, 08:35:15 AM
I have sent a copy of the official letter of the launching of canonical chemistry to more than 30 scientific societies, news services, organizations, and others.

Now I am waiting for reply.

Juan R.
Title: Re:Canonical chemistry
Post by: Mitch on September 08, 2004, 01:37:41 AM
I hope it goes well. Do you have a website we can link to? Or do you still need webspace?
Title: Re:Canonical chemistry
Post by: ssssss on September 08, 2004, 02:06:04 AM
I hope it goes well. Do you have a website we can link to? Or do you still need webspace?

Yeah Mr.Juan do you have your website?If yes just submit your link on this site.If no why dont you get one,it will be really helpful to you,indeed you can put your important Articles etc on your site which you need to publish in various leading Scientific journals as it will be rather Cheaper i Suppose.
Title: Re:Canonical chemistry
Post by: Juan R. on September 10, 2004, 06:22:09 AM
Hi “ssssss”,

Thanks by your comments. Let me only a remark. I believe that my work is important. I think this because I can compare it with others works in recent literature. Of course, I also think that other people would say if I am wrong or correct.

Hi Mitch,

How are you?

Thanks again by your continuous interest and support!

At this moment, I have received none official reply. Moreover, it appears that my letter “Canonical chemistry program” to Nature will be not published. I send other “Non-official science, the PhD versus non-PhD dichotomy” today...

Website is ready, but only off-line! I am breaking innumerable government and bureaucratic difficulties. I said “I hope to launch officially canonical chemistry in one or two months.” I think that the following week I will know if the founding of the Center dedicated to canonical chemistry is either possible or impossible.

I recommend the reading of recent “You don’t need a licence (or PhD) to use your brain” (Nature 430, 965, 2004). That is completely true in mi own case. I am not “Dr. González” and then “I do not have a licence to perform science”.

It is not only a question of website. I (as the rest of scientists) need funding or gifts for advanced research. I cannot pay, of my own money, advanced books that I need “Handbook of Molecular Physics and Quantum Chemistry” with a prize of $1,200, for instance. Thanks to my first scientific work in mesoscopic thermodynamics, I received a formal invitation to the conference "Frontiers of Quantum and Mesoscopic Thermodynamics" 26-29 July 2004, Prague, Czech Republic. Satellite of the 20th General Conference of the EPS Condensed Matter Division 19 - 23 July Prague 2004 but I neglected the invitation because I have not money or adequate affiliation. I have not access to several advanced scientific databases. I cannot pay $300 or $400 in references cited in my articles each time that I am preparing a manuscript, etc. I cannot do some advanced calculation with my simple PC. Computational chemists and physicists, at universities and research centers, can use very-expensive workstations and access to special supercomputation centers and utilities as optimized mathematical libraries.

However, I send copies of my manuscripts to several specialists in diverse fields and my work is looked with great interest. When I sent to Dr. Gonzalo Ordoñez (a kind scientist at University of Texas) my own derivation of Pauli master equation (the usual derivation is incorrect because violates orthodox quantum mechanical principles), he said me that the derivation was “very interesting” and that my ideas would be published because my work provided a “very interesting vision of thermodynamics”. My lack of PhD was unimportant for him.

I cannot receive official funding for a subscription to the Journal of Physical Chemistry but astonishingly I could subscribe to the journal paying the corresponding rate! Why?

I am exhausted with this difficult situation. If finally, the launching of the Center is impossible due to “stupid” bureaucracy and some “archaic” scientists, then I will forget the program (both my money and persistence are not infinite) and send all my current work (research, preprints, viewpoints, reviews, etc.) to a domain of your site.


Title: The future of canonical chemistry (I)
Post by: Juan R. on September 16, 2004, 07:10:25 AM

Hi kindly friends,

The first letter “Canonical Chemistry Program” submitted to Nature was not published. Basically, it was posted here above. At this moment, the second letter “Non-official science, the PhD versus non-PhD dichotomy” (submitted 09/10/2004) has been not published. If it is not published, then I will reveal its full content.

I sent (09/02/2004) a preliminary poll about canonical chemistry and a restricted copy of the official launching of canonical chemistry to more than 30 organizations, news services, and others. I said, “Please send me every comment, criticism, plea, news, and others what you consider necessary for this program.” And “You also could post any queries and/or suggestions at >> Comments for Staff Writers and Staff >> Canonical chemistry”, between others statements. I received none reply, only a cold mute...

I sent a plea for reply (09/13/2004). Next, the content of the “unpleasant” reply:

Dear “chemical friend”,

Ten days ago, I sent you an informal communication about the new program of canonical chemistry that is being prepared.

As illustrated by the PDF archive attached, this program addresses a number of important aspects of modern chemistry and related sciences.

This program is not a usual scientific program; the objective of canonical chemistry is to recover chemistry as the most basic of sciences. It appears clear, at least for me, that a program as ambitious as this needs of the maximum of collaboration and/or criticism.

As a member of scientific, decision-making, political, press, or “general people” communities, I sent you a copy of the initial letter for your valuation.

I am ready to receive and study your comments about the canonical chemistry program. Note that by now, canonical chemistry has been developed outside of official science projects and funding. Fortunately, this program has attracted to a number of specialists in diverse fields even in its first steps. However, it would be good that this far-reaching program obtain a maximum of consensus of the corresponding communities.

If you are still interested in the details and scope of canonical chemistry, please send me your reply. If you needs more time and/or details please say it.

If you were not interested in it, I would also know it!

This informal poll will be closed this week and the replies studied.

With my best regards,

Juan R.”
Title: The future of canonical chemistry (II)
Post by: Juan R. on September 16, 2004, 07:13:06 AM

Is the above communication “bad writing”? Is its style “offensive”? Of course, I am not a very important man, but then do I “deserve” none reply? Would my “yahoo e-mail” be ignored because I am not the director of either an important industry or organization? Perhaps is this forum not “adequate” for some celebrated specialists with “dozens of degrees”?

Is it difficult to write, “I am not interested” or “we are interested in ‘this’ aspect of your program”?

My initial belief was that canonical chemistry would be discussed and critiqued by all the chemical community. I would hear the comments of engineers and professors, academics and industrial chemists, directors and students, etc. and correct/adjust the program. Moreover, my initial objective was to provide a full access to research articles also to relevant members of official chemical organizations (In fact, I wrote the letter for the official launching). I hoped that it would benefit to chemical community! Now, I see that I was some stupid. I have been thinking these days about all this.

If we can use our brains to develop a theoretically advanced formalism beyond usual physics and physical chemistry, why would we follow the policies of usual chemical organizations? Why would we follow the same policies that favored the closing of several chemical departments and the decreasing of chemical PhDs? If recent physicists’ work shows the fallacy of the BO approach, why would we use IUPAC’s conventions about definitions of bonds, chemical reactions, molecular species, etc? Note that in the past, some famous IUPAC’s conventions were defined as “arbitrary ones”.

Recently, ten chemists, including Nobel laureate Roald Hoffman, published a protest letter because the salary of the executive director of the ACS was excessive (nearly $768,000 in 2002!!!). I imagine that those directors, secretaries, and others would spend his time in explaining why the salary is acceptable instead of replying the e-mails of an unimportant young chemist as I am.

Some years ago, some celebrated news services claimed for violation of the second law of thermodynamics. The claim was false; research articles were not rigorous. The question is, how could those services detect the extraordinary beautiful of canonical chemistry laws? Perhaps would they be more “prudent” now and wait for a “complete validation” of canonical chemistry?

Some mass media have claimed that all of chemistry can be studied from the Schrödinger equation. Of course, this is false, Murray Gell-Mann, one of the most renowned physicists said that the claim “was an exaggeration”. Canonical chemistry is more “radical” still and says us that the Schrödinger equation can be derived from canonical chemistry in a well-defined limit. How could I hope that a Spanish TV channel, devoted to popularizing science (Redes), was interested in canonical chemistry? Canonical chemistry says, basically, that several past contents of Redes (including speculations about String theory, black holes, multiple universes, etc.) were completely wrong.

Next, I include the list of e-mails with the aim of that perhaps any woman or man more important than me could ask them what is their opinion/attitude about the canonical chemistry program (?)

European Chemical Society BE

The Royal Australian Chemical Institute

Brazilian Chemical Society

The Chemical Society of Ethiopia  P. O. Box 32934, Addis Ababa, Ethiopia (Did NOT send)

Chemical Research Society of India

Sociedad Química del Peru

Sociedade Portuguesa de Quimica

South African Chemical Institute (SACI)

Asociación Nacional de Químicos de España (A.N.Qu.E.)

The Royal Society of Chemistry

American Chemical Society (ACS) |

American Association for the Advancement of Science (AAAS)

The Novartis Foundation

COST chemistry


ChemWeb (Noticias)


General Chemistry Online Web picks


Reactive Reports david.bradley AT



Eurekalert (noticias)


Asociación Española de Periodismo Científico

The Lancet


BBC news


Chemical Heritage Foundation

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Title: The future of canonical chemistry (III and last)
Post by: Juan R. on September 16, 2004, 07:18:32 AM

I continue the funding of a new independent -i.e. far from the official programs and societies, etc.– center to develop adequately canonical chemistry. This new revolutionary chemistry will grow outside of official societies, science agencies, and journals. Intelligent people with open minds will can check my approach and improve it. E.g. archaic chemists working with the ART approach to adsorption kinetics could continue to work with the “old” approach, and their proved limitations and ambiguities. Modern physicists and chemists working with the most theoretically demanding SRT approach will can check the new, more sophisticated, CRT approach based in canonical chemistry.

Now, I am reading the recent Vol. 14 of advanced series in physical chemistry titled “Modern trends in chemical reaction dynamics” (World Scientific Publishing, 2004). In principle, the monograph recompiles modern trends to the current art of molecular dynamics by renowned world-leaders in the field. I am sorry to say this (monograph is good) but the theoretical discussion presented (e.g. Chapter 5) is just an elementary shadow to the powerful and sophisticated methods that are being developed in (and adapted to) canonical chemistry; e.g. after of three approximations valid for gas phase chemical systems one recover the mathematical level of the wave packet methods, so useful for gas phase chemical systems. But chemistry is also interested in liquids and solids… More about this in my article “Is this dynamics?” (in preparation, after of being discussed with a number of specialists in diverse topics).

I will provide full access to educative and viewpoints articles to students and general people. Note that, usually, students cannot access to educative papers in journals of chemical education. It is also my objective to collaborate in chemicalforums and solving possible doubts about canonical chemistry contents. These canonical articles are being prepared in three languages (English/Spanish/Gallego). Translation to others idioms will be permitted. Do you like to translate my works to French, German, or Chinese?

This is the last communication that I send about the difficulties that I find with this program. I am exhaust. I love chemistry, but not bureaucracy!

I would begin to solve doubts about the truly interesting: canonical chemistry.

Juan R.


Title: Re:Canonical chemistry
Post by: Mitch on September 16, 2004, 07:08:37 PM
Don't worry we understand how slow it is for the chemical community to accept new ideas. It is even harder to grow a community around such ideas. It's taking us a while to develop and grow a chemical community in our little niche of chemical education. We can still offer you webspace for your articles(ad free). We can even give you a e-mail address if you feel the yahoo address isn't professional enough. Just let us know how we can help.


P.S. Remember we also own and are comitted to helping non PhDs publish their own articles on Chemistry here. Although they're probably not as mathematically rigorous as your's would be.
Title: About mathematical difficulties
Post by: Juan R. on September 20, 2004, 08:19:50 AM

Hi Mitch,

Thanks by your enthusiastic comments! As said, I do not post comments about “bureaucracy”. I will send the reply to your personal mail.

Let me a comment; you said, “Although they're probably not as mathematically rigorous as your's would be.” This and my previous comments about canonical chemistry could introduce a distorted image of the new discipline.

The revolutionary canonical chemistry is a hierarchical theory. I.e. there are different levels of molecular description, from simple (at level of thermodynamics or “macroscopic” chemical kinetics) to the most advanced. The most advanced level that I have developed is a quantum formulation at level of Prigogine Liouvillian extension of quantum theory, for example, but generalized with relativistic corrections. In principle, one can work at the most adequate level for each specific situation, using many details for simple processes but few details for complex ones, for instance. This is a very “democratic” theory!

Now, I am working in the extension to full (general) relativity. This is very difficult for me. Note that the extension generalizes the usual approaches to quantum gravity, including the most recent or “radical” ones. Special relativity works only with flat spacetime. Now, as a first step, I am developing a formulation of chemistry in curved space-times. It would be useful in cosmo- and astrochemistry.

Fortunately, very basic ideas of canonical chemistry can be discussed at an elementary level, for example, Chang course in general chemistry. Of this manner, all people (scientist or no) that can understand that book can understand the basis of canonical chemistry.

For example, the “rate coefficients” for generalized chemical processes are key elements in the theory of canonical chemistry. At the simplest mathematical level, the coefficients are only numbers, somewhat as the constant rates k of chemical kinetics are. At the Liouvillian non-relativistic level, the full mathematical expression for the coefficients is so complex and mathematically demanding that one needs an entire page for writing them. Compare it with the simplistic Schrödinger equation H phy = E phy!

At the relativistic level, things are still more complex. I am sorry to say this but one cannot use the standard relativistic quantum chemical literature.

To be precise, one can choose in canonical chemistry the level of math compatible with both the problem that one is working and personal feelings. I know that some organic chemist hate math. This would be a problem in quantum chemistry (formulated in a clear physics’ way) but it is not a problem in canonical chemistry, because one can use a symbolic formalism in the style of the “mechanistic approach” or organic synthesis and discuss many things in a qualitative fashion. Undoubted, math becomes necessary for doing explicit calculations, but this is also true for the current organic theory.

Title: A simple experiment
Post by: Juan R. on September 20, 2004, 08:22:23 AM

Chemistry is more than the study of “stinking liquids in a flask”. Canonical chemistry recovers the viewpoints of alchemists or the general view of ancient chemists as Lavoisier. In fact, Lavoisier studied the vital processes of animals (e.g. his manuscript “Sur la respiration des animaux”) thanks to his chemical theory of gases and combustion. Now, that is seen as belonging only to biology...

With the aim of illustrating those things that are not teaching in current (“20th century”) courses of chemistry, let me introduce a simple elementary example.

Take the following chemical scheme

A + F ==> 2 A

P + A ==> 2 P

Look at a manual on physical chemistry or chemical kinetics, write the rate expression for d[A]/dt and post it in this forum.

Juan R.

Note: this is more interesting if this is done by a student of first courses of chemistry. Mitch, you cannot participate here.   ;-)

Title: Re:A simple experiment
Post by: Donaldson Tan on September 21, 2004, 01:26:37 PM
A + F ==> 2 A
P + A ==> 2 P

Which of the two equations is the rate-determining step?

The 2nd equation looks wierd, because one P can removed from both the left and right hand side. It appears that either the 2nd equation is more than meets the eye or P converts A to another P magically
Title: Re:Canonical chemistry
Post by: Mitch on September 21, 2004, 02:10:46 PM
With kinetics you can sometimes get away with turning your brain off. The d[A]/dt will equal the formation of [A] in equation 1 minus the loss of A in equation 2. Although the fact that your using A to make A is throwing me off right now, I'll have to look at it closer when I have some more time.
Title: Re:Canonical chemistry
Post by: Demotivator on September 21, 2004, 02:42:47 PM
These are of course general expressions, but I would venture to rationalize a scenario where F is an isomer of A, and F uses A as a catalyst to rearrange to produce A.

Or as predator-prey, where A eats F and produces an offspring: A + A   lol,
Title: Re:Canonical chemistry
Post by: Donaldson Tan on September 21, 2004, 04:26:18 PM
I was sleepy and still is sleepy, as it's 4am here now..

Rearranging Juan's reaction equation, we've:
(1) A + F => 2A
(2) A + P => 2P

Assuming both (1) and (2) occurs at the same rate and they are valid equations, then d[A]/dt would remain 0 until all F are used up. Then d[A]/dt begin to decrease.
Title: Re:Canonical chemistry
Post by: vulcan2.0 on September 21, 2004, 09:55:15 PM
my head hurts :P
Title: Re: Simple experiment
Post by: Juan R. on September 23, 2004, 08:27:22 AM

Thanks by your comments. There are numerous replies and due to a lack of time, my answer will be unified.

1)  A + F ==> 2 A

2)  P + A ==> 2 P

For writing the rate of a chemical (e.g. d[A]/dt), it is unnecessary to know, a priori, which is the rate-determining step (if there is any!). The rate-determining step (if any) introduces simplifications on a generic chemical equation.

Above equations are of generic kind

A + B ==> 2 B

Of course, the stoichiometric equation is A + B = 2 B or simplifying both sides A = B. However, B (product) participates also as reactant in the molecular mechanism. This equation is known as quadratic autocatalysis. See an introduction to autocatalysis on section 26.7 of [Atkins].

The total rate for A is

d[A]/dt = k1 [A] [F] - k2 [P] [A]

where k1 and k2 are the constants of reactions 1) and 2) respectively.

In principle, the above scheme was though for many of yours as chemical reactions between chemicals A, P, and F. However, note that I said not that they were. In fact, effectively I could say that A and P are animals, and F is food. In fact, you can see that I inspired in the Lotka-Volterra mechanism, what is a classical on mathematical ecology (Lotka was a American chemist and Volterra was a Italian mathematician). Reactions 1) and 2) are reactions a) and b) (with other letters for species) of the section 26.8(a) of [Atkins]. In mathematical ecology, the Lotka-Volterra mechanism is a simple mechanism of Predator-Prey interactions. In the above example, A is a prey and P is the predator.

Rearrange the total rate and defining R = k1 [F] - k2 [P], the rate looks as

d[A]/dt = R [A]

This is the first principle of population dynamics. According to Berryman (a professor of Entomology and Natural Resource Sciences), this principle is truly general in that it applies to all populations and, in fact, to all self-replicating entities. Note that this principle is postulated without discussion in usual literature. Now, we derive it (somewhat as a “theorem”) from a simple chemical mechanism and using the laws of chemical kinetics.

Next, we could analyze the above rate law and study the different regimes, for example what succeed if k2 is zero, if k1 is zero, if R is zero, if at glaciations [F] -> 0, etc, and our discussion would be parallel to the ecological discussion of real ecosystems working below the first principle. E.g. if R = 0, Berryman says that the birth rate is equal to the death rate. This is precisely the idea that we discover when one observes that 1) is birth of A and 2) is his death.

I put this simple example for showing that chemistry can be thought as a general science beyond the usual thinking of 20th century chemists. The advantage of physicists thinking is that they see physics as a general science. They apply physics to all from particles and molecules to biology (biophysics), universe (cosmology), economy (econophysics), etc. My research shows that chemistry (canonical) is more general and advanced that usual physics. Chemistry can be used as a model of how Nature works (ecology, physics, biology, vehicular traffic, etc.). In the language of canonical chemistry, I use the concept of “generalized chemical equation” and “generalized chemical systems” for describing those systems that usually one does not consider chemical ones but that work as traditional chemical systems perfectly.

In fact, the separation between “chemical systems” and “non-chemical systems” is somewhat artificial in the formalism of canonical chemistry (by this reason I talk about generalized chemical systems). To ignore the contribution of chemistry to the understanding of other sciences would be like if one defines organic chemistry as “the chemistry of organic compounds without nitrogen atoms”. In nature, there is not an artificial splitting on disciplines. I think that this potential of chemistry and chemical laws would be utilized, somewhat as Lavoisier studied animal respiration or Boyle the “physical” behavior of a gas. Note that precisely physicists have enlarged their own field of applications (now physicists work even in the synthesis of materials as polymers!) since the study of celestial bodies, whereas chemists (specially in the 20th century) have self-restricted their own field. In fact, this has been the main criticism of many young chemists as Michael Ward: “Things like polymers and surfactants were picked up by chemical engineers and material scientists, but that’s changing now and chemistry is trying to get them back” [Adam]. One of my objectives is that chemistry goes back to the fascinating 19th century status.

This experiment was directly based in chemical kinetics (chemical kinetics can be derived from canonical chemistry). In the next experiment, I will introduce other example more close to the formalism of canonical chemistry.


Atkins, P. W. Physical Chemistry (Sixth Ed.); Oxford University Press: Oxford, 1998, pags. 808-809.

Adam, David. What’s in a name. Nature 2001, 411, 408–409.
Title: Second experiment
Post by: Juan R. on September 25, 2004, 07:47:14 AM
Please, if you have time, you could try to find if the following processes are physical or chemical ones:

- Heat transport between two bodies (e.g. metals).

- Industrial synthesis of ammonia, N2 + 3H2 ===> 2NH3.

- Ammonia inversion, :NH3 <===> 3HN:

You could introduce your own ideas, criteria, reasons, etc. On the other hand, if you prefer, you could cite to some author of your own choosing.

If there are many heterogeneous replies, the discussion will be more instructive for all us. I acknowledge in advance your replies. I will post my own reply and personal beliefs the next Friday.

Title: Re:Canonical chemistry
Post by: Demotivator on September 25, 2004, 09:40:29 PM
I don't think they are chemical or physical. I believe they are biological, deriving behavior from a canonical psychology!

Heat transport is an example of "the grass being greener on the other side" impulse. It is the need to migrate to unoccupied realms.
Ammonia synthesis stems from the need to achieve stability through union with another.
Ammonia inversion is an example of entities (most notably politicians) flip flopping as they cannot decide between two plausible arguments.
Title: Re:Canonical chemistry
Post by: ssssss on September 26, 2004, 09:02:46 AM
I really want to Join your Discussion but i dont have time right now,i goota go.But someday i will be with you.
Title: Chemical processes (I)
Post by: Juan R. on October 01, 2004, 07:16:28 AM
Thanks by your interest.

What is the difference between physical and chemical processes? One can define scientific terms according to two methodologies: descriptive and systematic. In a descriptive approach, one simply lists the different physical and chemical processes. However, in a systematic approach, we define and use a definition for cataloging the processes of natural word. Nevertheless, let me introduce a bit of history and “marketing” first.

Whereas physicists were more interested in mechanical aspects of matter, alchemists were interested in all properties of matter. Ablation, coloration, dissolution, or evaporation, between other were (al-)chemical processes for a 16th century alchemist. Antoine Lavoisier (1743–1794) is often considered the father of modern chemistry. In his Tableau des substances simples, Lavoisier considered the calorique (heat) and the lumière (light) simple substances participating in a chemical process in the same way that oxygen, hydrogen, zinc, or mercury participates in other processes.

However, the modern tendency of chemistry has been towards an increasing use of the terms “physical” and “physics” instead of “chemical” and “chemistry”. Many physical chemists have guided this wrong philosophy. Two physical chemists wrote the following shocking words: “all subjects treated under chemistry tend to be subject, as time goes on, to treatments at the more advanced degree of sophistication attained under the aspect of the science we call physics.” What a beautiful piece of chemical “marketing”, perhaps focused to 15-years old students and policymakers! Again, chemistry is underestimated and seen as a cuisine. Attitude like this are the true basis of the current unpleasant status of chemistry.

Actually there is no systematic definition of chemical or physical processes (or properties), and authors use their own criteria according to specific preparation, knowledge, and personal views.

For example, Cram and Hammond’s book on organic chemistry distinguishes chemical processes from other formal processes by the use of “double” or “single” arrows respectively. They symbolize ammonia inversion with a double arrow as in a chemical reaction. However, they state that solubility of a compound is a physical property (i.e. dissolution is a physical process). But what is a chemical reaction? According to Cram and Hammond (CM) chemical reaction is a event in which two molecules collide in such a way as to break one or more of their bonds and make news bond and hence new molecules. Then is ammonia inversion a chemical reaction? Moreover, if participate only atoms in a process, then it appears that is not a chemical reaction, i.e., the redox reaction, Zn + Cu2+  =  Zn2+ + Cu, would be a physical process according to above (CM) definition.

According to general chemistry by Chang (C), a chemical reaction is when new substances arise from a process, but as he does not define “substance” then chemical reactions remain undefined. Moreover, Chang opines that by heating a block of ice we do not change water, only its “appearance” and thus is a physical process. I imagine that the ammonia inversion would be a physical process for Chang. It is interesting remark that Chang considers that redox reactions are chemical reactions (note that this is contrary to CH).

Physical chemists McQuarrie and Rock (MR) state that all chemical reactions can be assigned to one of two classes: reactions in which electrons are transferred from one reactant to another and reactions in which electrons are not transferred. This is similar to (C) but different of (CH). Whereas, in a well-known Spanish manual on physical chemistry, the author, Diaz-Peña (DP), states that electrochemistry is outside of “pure” chemistry. For example, the standard electrochemical reaction Mn4+ + e- ===> Mn3+ is named an electrode reaction, because it is formed of two steps

(1) Mn3+ + e- ===> Mn2+

(2) Mn2+ + Mn4+ ===> 2 Mn3+

The first step is named an electron transfer process and the second a chemical reaction, and thus the global reaction (1+2) is considered not a chemical reaction by (DP). Others chemists opine that redox reactions are non-chemical processes because none bond is formed or broken, then I ask they what is a chemical bond and I do not receive systematic reply.

Many chemists state that heat transport is a physical process. However, Karen Timberlake (KT) says, in her manual on chemistry, that evolution or absorption of heat is a chemical change if is not associated with changes of state. (?)

Many inorganic chemists will say you that ammonia inversion is not a chemical reaction but, recently, two theoreticians have claimed that it is a chemical process, because computed how bonds are broken and formed. Philosopher of chemistry Joachim Schummer (JS) opines that the solubility in a certain liquid is an example of chemical property in direct contraposition with (CH) own ideas.

That is, there exits an enormous confusion in theoretical chemistry and this is transferred to current chemical education. Compare by yourself the above criteria and definitions. You will see that there is not unique definition of chemical process or property. Moreover, Demotivator (a Staff member of chemicalforums) has claimed:

I don't think they are chemical or physical. I believe they are biological, deriving behavior from a canonical psychology

I could critique many of the definitions above stated from different views: philosophical, educative, historical, theoretical, experimental, etc. For instance, Chang talks about “physical” processes in water when water changes just its “appearance” in his celebrated manual on general chemistry. However, he fails to define rigorously what water is...

What is water? In a first instance, water “is” H2O and then in processes like

H2O(solid)  ===>  H2O(liquid)


H2O(liquid)  ===>  H2O(gas)

Water “substance” remains “unchanged” according to Chang. However, in a more detailed observation, one observes only internal interactions (chemical bonds) in the gas phase molecule, whereas there is also hydrogen bonding in both ice and liquid water systems. That is, there are extra bonds in condensed phases and the atomic “array” is not the same.

From a quantum view, the wave function of the phase gas molecule of H2O is not defined in an ice cluster (H2O)n formed by n “water” molecules, indicating that the molecular system is not the same as its quantum state is not the same. However, there is more.

In a more accurate level of description, one discovers that Chang calls “pure” water is really a mixture and aggregations of H2O, H3O+, and OH- species, and that the concentration of all three components varies with temperature. We can measure the changes in the chemical composition of water with temperature. That is, when one studies the process with more molecular detail, then appears that the initial Chang distinction between “physical” and “chemical” processes is somewhat arbitrary.

Due to the current divergence of criteria, I could introduce my own definition of chemical reactions according to my own beliefs but inspired in traditional points of view of ancient chemists. For example, nobody would say to me (once an inorganic chemist did) that, “traditionally heat transport is a physical process” because tradition was changed in 19th and specially 20th century chemistry. However, I prefer talk about generalized chemical reactions with the aim of facilitating the adaptation of “archaic” chemists to the new canonical ideas. I can say that heat transport is a generalized chemical process whereas ammonia synthesis is a standard chemical reaction. Both are chemical processes in a generalized theory.
Title: Canonical chemistry processes
Post by: Juan R. on October 01, 2004, 07:22:16 AM
Why have the 20th century chemists separated “chemical” from “physical” phenomena ignoring ancient chemical views? I think that was a problem of stoichiometry. For example, Prigogine (Nobel Prize for chemistry) was known for his successful application of his chemical theory not only to usual chemical systems but also to sociological, biological, and physical systems. He applied satisfactorily his theory of dissipative structures to diverse systems as the Big bang or vehicular traffic in cities. In fact, his theory of Big bang was revolutionary as instead of a beginning of time it claimed for a phase transition from a pre-universe. It is very remarkable that the most advanced cosmological models based in string theory use his basic ideas.

However, the own Prigogine recognized that the analogy with chemical reactions was “formal”. For example, he said that order-disorder transformation in an Au-Cu alloy could be characterized as a chemical reaction but one has not well-defined stoichiometric coefficients.

Some similar happens for the above water transformations. According to Prigogine and others, the concepts of chemical kinetics can be applied to (liquid) ===> (solid) transformations. In fact, the usual form of computing enthalpy changes for “physical” processes in thermochemistry (including phase changes) is applying the definition of enthalpy of reaction: i.e. enthalpy of products minus the enthalpy of reactants (see, for example, the P. A. Rock manual on chemical thermodynamics for illustrations).

Then if one can compute many things as if the physical process is a chemical one, why could we not achieve a unified theory based in chemical ideas?

Canonical chemistry begins saying that a system of interest for chemists can be described by a vector n. Vector n include all the necessary for describing completely the system of interest.

Description of matter is hierarchical. This is point usually omitted in chemical education. There are different levels of molecular descriptions from the most simple to the most sophisticated. In a first analysis, gas phase water is formed by molecules of H2O, but are those molecules indistinguishable? Response is negative, in a more detailed analysis, we can split the “concept” of H2O in a sum of different H2O(w) where w symbolizes the electronic state, e.g. H2O(1) symbolizes molecules of “water” in state 1. Our flask with simple water will be formed by a determined composition of “specie” [H2O(w)]. This splitting is necessary (is usual in molecular dynamics) because the molecular properties (geometry, frequencies of vibration, bond energies, etc.) are different. Are all molecules of kind H2O(w) equals? Again, the response is negative, and we can incorporate additional molecular details, for example rotation or vibration, nuclear state, isotopes, etc. For example is not the same o-H2 that p-H2 and the diference is only in the nuclear spin of hydrogen atoms. For many studies, the difference is insignificant, and one talks just about H2 but spectroscopic data is different for both and one can detect each “specie” separately. That is, in canonical chemistry one use the level of molecular detail needed for the concrete study that one is doing in each instant. If you are an analytical chemist and you are measuring the concentration of CO2 you work with one single specie CO2, if you are a theoretician computing kinetics constants for interstellar clouds you can split the total concentration of CO2 in molecular species. Let me continue with canonical theory.

The following step in canonical chemistry is to write the generalized chemical process

(n+) <===> (n-)

This is an important point of canonical chemistry. The failure of Lavoisier’s view was to consider that stoichiometry was only restricted to atomic or molecular quantities. As said in this forum, 20th century biologist and physicists had minds more open. This is also true for ecologists. Ecologists use the term stoichometry in a broad sense in the so-called stoichometry ecology.

By this restriction of chemical theory, Prigogine could not apply completely his chemical ideas to other systems as the Au-Cu alloy. Prigogine, Kondepudi, and others chemists could derive formulae for phase equilibriums using the same criteria that one applies to chemical reactions, when they defined the chemical affinity for the “reaction” gas = liquid, but they cannot apply all the theory of chemistry to the change of state. For example, we can compute the condition of equilibrium doing affinity = 0, or using the equality of chemical potentials what is “equivalent” (affinity is a more modern and successful approach but unfortunately many chemical thermodynamics textbooks do not use), however we could not apply the equations of chemical kinetics for deriving the heat transport before equilibrium is achieved. In canonical chemistry, it is possible because Lavoisier’s restriction is overlooked!

The thirst step is to write the basic rate equation of canonical chemistry. I do not write here. It appears in my research and educative articles (canonical chemistry web site is becoming soon).

One of the simplest descriptions of two metal solids (A and B) is using macroscopic quantities at the discrete level of molecular description. The vector is n = (UA, UB) being U the internal energy. There are several heat transport mechanisms, one simple is the direct molecular transport.

(eA+, eB+) <===> (eA-, eB-)

the es are molecular amounts of energy necessaries for the process (see below the description of a typical chemical reaction). The simplest mechanism is one does not “concerted”

(e, 0) <===> (0, e)

Introducing this mechanism into canonical rate equation, one derives the thermodynamic description of heat transport. However, as stated above, we can introduce more details. The next level of description is the continuum or “hydrodynamic” level of molecular description. At this level, one introduces a field description of thermal quantities as that of TIP formulation of thermodynamics. Using a mechanism like

(e, e, 0) <===> (0, 0, 2e)

and working out the canonical equation one derives the Fourier law of heat transport. Note that Fourier law is usually postulated in physical chemistry books alluding to phenomenology. We derive using molecular mechanisms and a rate equation directly inspired in the law of mass action.

Heat transport is a generalized chemical process in canonical chemistry because is a change in the generalized composition, vector n, of the system of interest. Of this form, one obtains a unified formalism of matter processes. Of this form chemistry, far from be a closed discipline, is generalized and turn into the most fundamental discipline at the beginning of this century.

In principle, “all” could be derived of the same form, using always the same systematic theory. Of this form, all physical chemistry and many of physics are rederived and improved from a single rate equation; an equation more exact and powerful.

I think that this formalism is easiest for chemist that the usual physical formalism, because is based in the chemical point of view of “chemicals” and “reactions”.

If you are a organic or inorganic chemist you do not need to think in term of mechanisms and reactions and after change the “chip” when take a course in physical chemistry. All of physical chemistry is rewriting and improved at a high level in a full chemical fashion.

It is necessary only a few of practice for adapt to the new stoichiometric formalism. For example if the vector of state is n = (A, B, C, D) being the composition of different chemicals, and you are interested in the chemical reaction

A + B <===> C + D

In canonical chemistry one writes (see the last vector n)

(A+, B+, C+, D+) <===> (A-, B-, C-, D-)


(1, 1, 0, 0) <===> (0, 0, 1, 1)

and using the canonical rate one obtains exactly the laws of chemical kinetics. However, the canonical theory is more mathematical, elegant (the 0s that appear in the mechanism contain a significant information about quantum correlations and probabilities), and exact. In fact, canonical chemistry is the more exact theory that I known.

Working at the Liouvillian canonical level, one obtain a basic equation that generalize Schrödinger based quantum mechanics and one can obtain, for example, the basic master equation used in quantum optics when one write the adequate generalized chemical reaction (n+) <===> (n-). That is from the generalization of chemical kinetics provided by canonical chemistry and the adequate mechanism one derives the basic equation used in advanced quantum optics. In fact, this chemical theory can improve and correct some errors of quantum optics literature. By this and other reasons you will that quantum version of canonical chemistry is much more sophisticated that quantum chemistry.

This chemical theory is unified. If you dominate the basic assumptions of canonical chemistry that I cited above, then you can study practically every process. Current chemical education and research oblige to one to learn different disciplines, for example, thermodynamics is completely different of chemical thermodynamics and this later of quantum chemistry. If study quantum chemistry you will know nothing about quantum optics and Lax equation. If you learn that of quantum optics, you know nothing about the semigroup theory developed by mathematical physicists. If you learn the latter, you will know nothing catalysis in heterogeneous surfaces and if you are a specialist in those themes, you will know nothing about ratio-dependent ecological models. If you are an expert in the recent MTE ecological theory, you will know nothing about scattering amplitudes in electron-positron reactions of particle physics, and even if you are an expert in the topic (as Feynmann was or Weinberg is) you will know nothing about reaction dynamics. Etc.

In canonical chemistry, there is only a single theory, a single notation, a single rate equation, etc. E.g. if I show you what is the condition of equilibrium in an ecological system, the condition of equilibrium is the same in particle physics, brane theory, chemical reactions, ion transport in biological membranes, thermal equilibrium, mass diffusion in a vessel, etc.

Title: Doubts about canonical processes
Post by: Juan R. on October 07, 2004, 05:40:14 AM

I would like to receive a lot of questions, comments, criticism, etc. about the last two posts, especially about the post on canonical chemistry processes and the basic formalism and ideas exposed.

Juan R.

Title: Articles on canonical chemistry
Post by: Juan R. on October 19, 2004, 11:46:21 AM

Page and articles in pdf form available in

Title: Re:Canonical chemistry
Post by: Juan R. on December 10, 2004, 12:57:19 PM


SSSSSS said:

“Yeah Mr.Juan do you have your website?If yes just submit your link on this site.If no why dont you get one,it will be really helpful to you,indeed you can put your important Articles etc on your site which you need to publish in various leading Scientific journals as it will be rather Cheaper i Suppose.”

It is not so easy. There legal problems perhaps I would pay even 600000 euros ($780000) from my money if I do that you say.

I cite from Traducción de la EPIC's LSSI page:

“La ley puede también en algunos casos tener consecuencias perjudiciales en las publicaciones producidas en sitios Web de Estados Unidos si están dirigidas a una audiencia española.”

Even if material is posted at Mitch’s own site at USA, I am not legally protected.

This is a WAR by the Internet government.