From: Ravi Orugunty (rorugunty$##$oragenics.com)
Date: Wed Mar 15 2006 - 15:17:54 EST
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Subject: Everybody Digest, Vol 19, Issue 13
Hi Sengen Sun,
I wasnt attacking you personally. I read your article and i agree with you
in many instances.
My point is as follows " Mechanisms and the Art of writing reasonable
mechanisms " is nothing more than a language. How one chooses to use it
gives one either meaningful information or nothing at all.
The same is also true for W-H rules and all other rules. They should be
taken as rough guides and no more. As I already mentioned I'm an
experimentalist and for me the proof is always in the pudding. Run the
reaction and see what happens, leave the predictions to the theorists and
yes i dont trust most of the calculations :)
i havent read the paper by Hoffman that you cite but i certainly shall.
I also agree with you that not everybody has read the actual monograph by
woodward and hoffman. I actually got a copy by chance from a retired
faculty and am reading it even as we speak.
Good luck
regards
ravi
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Today's Topics:
1. A breakthrough in mechanism of concerted (Ravi Orugunty)
2. Re: A breakthrough in mechanism of concerted (Sengen Sun)
3. Chemistry Deparment Shutting (Nigel R Treweeke)
----------------------------------------------------------------------
Message: 1
Date: Tue, 14 Mar 2006 14:28:08 -0500
From: "Ravi Orugunty" <rorugunty$##$oragenics.com>
Subject: ORGLIST: A breakthrough in mechanism of concerted
To: <everybody$##$orglist.net>
Message-ID: <FAEGJIOFKPDFCBEHEACGMEGNCCAA.rorugunty$##$oragenics.com>
Content-Type: text/plain; charset="US-ASCII"
Dear Sengen,
I have missed out on the earlier part of your messages wrt to a breakthrough
in mechanism of concerted reactions. However i will try to answer the
questions that you have raised without resorting to any metaphors.
Hopefully this might help.
Q) What is the mechanism of a chemical reaction?
A) Any idea/theory that sufficiently explains the bonds that are broken and
formed during the course of any chemical process is a mechanism of that
chemical reaction.
Mankind likes to organize its ideas so that it can understand nature and
therby harness it to some useful work and this is also true for mechanisms
in chemistry. Granted that we really dont need to know the mechanism in
sufficient detail to get a reaction to work . Two examples will be provided
to sufficiently buttress the above statement. Undergraduates in chemistry
for the most part when they start their first lab rarely know the mechanism
of a Grignard reaction but are able to perform the reactions in a lab (Good
supervision is essential though). Prehistoric man had no idea about the
mechanism of reductions and electron transfer and yet was highly successful
in smelting and purifying iron and other metals.
It is perhaps from those early discoveries, that lead man to further
investigate and understand nature. More so understand nature in terms that
would make sense of a myriad of processess that were observed in daily life.
It is from these observations the language of chemistry evolved and is
taught as mechanism and theory of chemistry in any modern class.
In that respect i do agree with you that mechanisms and theories are no more
than a language used by chemists to communicate their ideas.
Q)Are mechanisms of chemical reactions important in
chemistry.
A) Yes, mechanisms are important not to perform chemical reactions (see the
example of prehistoric man) but are extremely neccessary to understand
chemical processess. Once one has a better undertanding of any process one
can develop newer reactions and thereby new products etc. Therefore the
language of mechanisms has its utility.
Q) Was the mechanism of concerted cycloadditions well
established before at the theoretical level?
A) We havent established a chronological time here but i will answer it
without any metaphors. When Diels and Alder published their first papers
(around 1910 or so). The mechanism of concerted reaction was not known. In
fact, the electronic theory of chemical bonds was being developed by G.N.
Lewis and others( i hope my memory serves me right here so please correct me
if i'm mistaken). However as our knowledge of matter progressed with time,
Woodward-Hoffman and Fukui developed the modern rules for cycloadditions and
they seem to have served mankind in particular organic chemists pretty well.
Have these rules stood the test of time? Yes. Any process that violates the
W-H theory can be explained using an alternate mechanism that would not
require the use of the conservation of molecular orbitals. The "hypnotic
effect" of W-H rules are in their elegance in predicting the feasability of
a thermaly catalyzed cycloaddition reaction based on orbital overlap.
Q)Do my computational data tell us some new knowledge
of electronic reorganization - the mechanism? (Please,
do not tell me to use your favored computational
approach unless you can use your approach to prove I
am wrong!)
A) Cant reply to this question? I'm not a great believer of doing
extraordinary computation as i consider myself to be an experimentalist.
For me the proof is invariably in the pudding ( a metaphor for a change )
this is particularly true when one is dealing with peptides and complesx
biological systems.
If you have a new theory share it with your fellow scientists by all means.
Facts are observed truths for example matter, energy, gravity and everything
else under the sun that nature presents before us.
Theories are explainations given by mankind. Gravity existed long before
Newton explained it and the same is true for cycloadditions. So take it
easy.
As to wether you choose to publish or not is entirely your choice. However,
I would encourage you to put forth your ideas before your peers and learn
from what they have to say and make professor Bader proud.
Hope this helps. Good luck
ravi
I sincerely welcome the comments and suggestions by
Yuehui and other two people. I'd like to address
Yuehui's for now as I am too busy to reply to every
one.
As I argued in two interenational sympossiums in 2005,
prediction and explanation are two different things
conceptually. Some theories do contain both of them,
but some others do not. Woodward-Hoffmann rules are a
very valuable predicting theory derived from a pattern
of mathematical operations. It is my strong opinion
that W-H rules are not equivalent to an explanation as
neither is FMO theory. Dewar called the W-H to have
"hypnotic effect", which I could not agree more. The
reality is that no one understands how "they explain".
The discussions via revolutionary internet
communications in CCL have led more and more
scientists to accept that "orbitals are a means to an
end", which I learned initially from Prof. Richard
Bader at McMaster University. How do you understand an
explanation that is based on something of no
understandable physical meaning?
I had tortured myself over and over again for years
before I convinced myself that I have made "a
breakthrough in mechanism of concerted
cycloadditions". Now I have the confidence to defend
such a statement. If you don't agree, I'd like to ask
you to calm down and to address the following
questions in concise languages without metaphors:
1. What is mechanism of chemical reactions?
2. Are mechanisms of chemical reactions important in
chemistry.
3. Was the mechanism of concerted cycloadditions well
established before at the theoretical level?
4. Do my computational data tell us some new knowledge
of electronic reorganization - the mechanism? (Please,
do not tell me to use your favored computational
approach unless you can use your approach to prove I
am wrong!)
My theory is about how electrons to move in a
concerted reaction. I don't agree with Yuehui that a
theory must be able to predict. "The earth revolves
around the sun" is a theory on paper but a fact in the
nature.
I could not publish my papers, and I don't need one. I
don't make a living from publications (as advised by
Einstein? -:). But the knowledge if correct will
benefit the human society one way or the other.
Thanks.
Sengen
--- Yuehui Zhou <yuehuizhou$##$hotmail.com> wrote:
---------------------------------
Another critieron for a theory is predicting the
outsome of the related reactions. You can do some
reactions based on your theory to test it and publish
the results. Without predictting power a theory is
just a theory on paper.
Also don't try to make your result a big deal. You may
think it is, but it's not the way to persuade
others. Try the online journals, Molecules, for
example. The editor is a Chinese fellow. Good lucky
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------------------------------
Message: 3
Date: Tue, 14 Mar 2006 03:46:53 +0000 (GMT)
From: Mugunthan G <mugunthan_gee$##$yahoo.co.in>
Subject: ORGLIST: Acetylation with Iodine
To: everybody$##$orglist.net
Message-ID: <20060314034653.97520.qmail$##$web8509.mail.in.yahoo.com>
Content-Type: text/plain; charset="iso-8859-1"
Hi Nalini,
acetylation goes well pyridine, but why to use bad
smelling and toxic stuff pyridine. you can very well to this with acetic
anhydride and iodine, which will be easy for workup and purification.
with regards
mugunthan
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Message: 4
Date: Mon, 13 Mar 2006 18:40:14 -0800 (PST)
From: Krupa Shukla <krupa_shukla$##$yahoo.com>
Subject: ORGLIST: SOP
To: everybody$##$orglist.net
Message-ID: <20060314024014.58969.qmail$##$web50503.mail.yahoo.com>
Content-Type: text/plain; charset="iso-8859-1"
Hello everyone
I have been assigned to write SOP (Standard Operating Procedure) for
large scale reductions. (SOPs point out the hazards associated with a
particular operation) It would be very helpful if someone can provide a
university link (if any) or have an idea how to deal with large scale
reductions, just briefly. Besides metal hydrides as reducing agents, what
other reducing agents have safety concern? It would be great if someone can
list reducing agents. my task would be much easier then.
Thanks for the help
krupa
---------------------------------
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Message: 5
Date: Tue, 14 Mar 2006 06:42:12 +0100
From: Barry Hardy <barry.hardy$##$tiscalinet.ch>
Subject: ORGLIST: Advanced Training Workshop Week at Oxford; Early
Registration
To: everybody$##$orglist.net
Message-ID: <5.0.2.1.0.20060314064117.0208dde0$##$mail.tiscalinet.ch>
Content-Type: text/plain; charset="us-ascii"
Latest Advances in Drug Discovery Design & Planning Methods
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Workshops will be held at the Chemistry Information Technology Center with
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best regards
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Tel: +41 61 851 0170
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------------------------------
Message: 2
Date: Tue, 14 Mar 2006 17:07:12 -0800 (PST)
From: Sengen Sun <sengensun$##$yahoo.com>
Subject: Re: ORGLIST: A breakthrough in mechanism of concerted
To: everybody$##$orglist.net
Message-ID: <20060315010713.67765.qmail$##$web53707.mail.yahoo.com>
Content-Type: text/plain; charset=iso-8859-1
Dear Ravi,
I sincerely welcome your comments. But the issues you
and I raised here really deserve a public debate in
the ORGLIST. I welcome every one to participate. In my
opinion, the issues here are entirely the confusion we
have had for the last half century. I'd like to start
with some remarks I made in CCL in 2003.
http://www.ccl.net/cgi-bin/ccl/message-new?2003+06+02+016
"...Fukui & Hoffmann well deserved 1981 Nobel
prize due to their discovery of the correlation
between MOs and chemical reactivity. But I don t think
that everything they said is correct. We must
criticize their mistakes hard without mercy. Their
mistakes could have too much negative impacts on our
scientific community due to their high profiles,
especially on experimental chemists with little
theoretical knowledge."
I feel it is much easier to convince many theoretical
chemists than experimentalists that W-H rules are no
more than a very useful mathematical tool for
predicition of reaction products. Hoffmann once asked
a very funny question something like "Should
experimental chemists TRUST theoreticians?" (not the
exact words, but see Theochem 1998, 424:1-6)
I do not have a beter way to explain, but let me give
you recent one of particular examples of conceptual
confusion made by Hoffmann (See JACS, 2002, 124, 6836,
Scheme 1, I will forward this article to any one if
requested by e-mail). There, the intramolecular proton
transfer was mistakenly treated as hydride transfer.
That is, the arrows should be drawn in the exactly
opposite direction. I would be bad if I were just
exaggerating some accidental errors. This is not an
accidental error. Such a mistake derived from our
mental assumption of orbital control, so that
well-established acid-base theory in chemistry can be
overturned but by a high profile Nobel Laureate! To
me, his philosophy is that arrows can be arbitrarily
drawn due to orbital control!
I do not mind if you call me an attacker. But I have a
high expectation to a Nobel Laureate. Such a kind of
conceptual mistakes in JACS are unacceptable and
should be corrected by the authors!
For more, please see my ppt file:
http://www.ccl.net/cca/documents/ConcertedCycloadditons_2/
By the way, I am proud of myself, while Bader would be
proud of nothing about me as asserted by Ravi. I am
sure that Bader does not know who I am although I did
my Ph.D. at McMaster in organic chemistry (1989-1994).
But I have known him for 20+ years and have admired
his philosophy of QM ever since.
Regards,
Sengen
--- Ravi Orugunty <rorugunty$##$oragenics.com> wrote:
> Dear Sengen,
> I have missed out on the earlier part of your
> messages wrt to a breakthrough
> in mechanism of concerted reactions. However i will
> try to answer the
> questions that you have raised without resorting to
> any metaphors.
> Hopefully this might help.
> Q) What is the mechanism of a chemical reaction?
> A) Any idea/theory that sufficiently explains the
> bonds that are broken and
> formed during the course of any chemical process is
> a mechanism of that
> chemical reaction.
> Mankind likes to organize its ideas so that it can
> understand nature and
> therby harness it to some useful work and this is
> also true for mechanisms
> in chemistry. Granted that we really dont need to
> know the mechanism in
> sufficient detail to get a reaction to work . Two
> examples will be provided
> to sufficiently buttress the above statement.
> Undergraduates in chemistry
> for the most part when they start their first lab
> rarely know the mechanism
> of a Grignard reaction but are able to perform the
> reactions in a lab (Good
> supervision is essential though). Prehistoric man
> had no idea about the
> mechanism of reductions and electron transfer and
> yet was highly successful
> in smelting and purifying iron and other metals.
> It is perhaps from those early discoveries, that
> lead man to further
> investigate and understand nature. More so
> understand nature in terms that
> would make sense of a myriad of processess that were
> observed in daily life.
> It is from these observations the language of
> chemistry evolved and is
> taught as mechanism and theory of chemistry in any
> modern class.
> In that respect i do agree with you that mechanisms
> and theories are no more
> than a language used by chemists to communicate
> their ideas.
>
> Q)Are mechanisms of chemical reactions important in
> chemistry.
> A) Yes, mechanisms are important not to perform
> chemical reactions (see the
> example of prehistoric man) but are extremely
> neccessary to understand
> chemical processess. Once one has a better
> undertanding of any process one
> can develop newer reactions and thereby new products
> etc. Therefore the
> language of mechanisms has its utility.
>
> Q) Was the mechanism of concerted cycloadditions
> well
> established before at the theoretical level?
> A) We havent established a chronological time here
> but i will answer it
> without any metaphors. When Diels and Alder
> published their first papers
> (around 1910 or so). The mechanism of concerted
> reaction was not known. In
> fact, the electronic theory of chemical bonds was
> being developed by G.N.
> Lewis and others( i hope my memory serves me right
> here so please correct me
> if i'm mistaken). However as our knowledge of
> matter progressed with time,
> Woodward-Hoffman and Fukui developed the modern
> rules for cycloadditions and
> they seem to have served mankind in particular
> organic chemists pretty well.
> Have these rules stood the test of time? Yes. Any
> process that violates the
> W-H theory can be explained using an alternate
> mechanism that would not
> require the use of the conservation of molecular
> orbitals. The "hypnotic
> effect" of W-H rules are in their elegance in
> predicting the feasability of
> a thermaly catalyzed cycloaddition reaction based on
> orbital overlap.
> Q)Do my computational data tell us some new
> knowledge
> of electronic reorganization - the mechanism?
> (Please,
> do not tell me to use your favored computational
> approach unless you can use your approach to prove I
> am wrong!)
> A) Cant reply to this question? I'm not a great
> believer of doing
> extraordinary computation as i consider myself to be
> an experimentalist.
> For me the proof is invariably in the pudding ( a
> metaphor for a change )
> this is particularly true when one is dealing with
> peptides and complesx
> biological systems.
>
> If you have a new theory share it with your fellow
> scientists by all means.
>
> Facts are observed truths for example matter,
> energy, gravity and everything
> else under the sun that nature presents before us.
> Theories are explainations given by mankind.
> Gravity existed long before
> Newton explained it and the same is true for
> cycloadditions. So take it
> easy.
> As to wether you choose to publish or not is
> entirely your choice. However,
> I would encourage you to put forth your ideas before
> your peers and learn
> from what they have to say and make professor Bader
> proud.
> Hope this helps. Good luck
> ravi
>
>
> I sincerely welcome the comments and suggestions by
> Yuehui and other two people. I'd like to address
> Yuehui's for now as I am too busy to reply to every
> one.
>
> As I argued in two interenational sympossiums in
> 2005,
> prediction and explanation are two different things
> conceptually. Some theories do contain both of them,
> but some others do not. Woodward-Hoffmann rules are
> a
> very valuable predicting theory derived from a
> pattern
> of mathematical operations. It is my strong opinion
> that W-H rules are not equivalent to an explanation
> as
> neither is FMO theory. Dewar called the W-H to have
> "hypnotic effect", which I could not agree more. The
> reality is that no one understands how "they
> explain".
> The discussions via revolutionary internet
> communications in CCL have led more and more
> scientists to accept that "orbitals are a means to
> an
> end", which I learned initially from Prof. Richard
> Bader at McMaster University. How do you understand
> an
> explanation that is based on something of no
> understandable physical meaning?
>
> I had tortured myself over and over again for years
> before I convinced myself that I have made "a
> breakthrough in mechanism of concerted
> cycloadditions". Now I have the confidence to defend
> such a statement. If you don't agree, I'd like to
> ask
> you to calm down and to address the following
> questions in concise languages without metaphors:
>
> 1. What is mechanism of chemical reactions?
>
> 2. Are mechanisms of chemical reactions important in
> chemistry.
>
> 3. Was the mechanism of concerted cycloadditions
> well
> established before at the theoretical level?
>
> 4. Do my computational data tell us some new
> knowledge
> of electronic reorganization - the mechanism?
> (Please,
> do not tell me to use your favored computational
> approach unless you can use your approach to prove I
> am wrong!)
>
> My theory is about how electrons to move in a
> concerted reaction. I don't agree with Yuehui that a
> theory must be able to predict. "The earth revolves
> around the sun" is a theory on paper but a fact in
> the
> nature.
>
> I could not publish my papers, and I don't need one.
> I
> don't make a living from publications (as advised by
> Einstein? -:). But the knowledge if correct will
> benefit the human society one way or the other.
>
> Thanks.
>
> Sengen
>
>
>
=== message truncated ===
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Message: 3
Date: Tue, 14 Mar 2006 18:06:37 +0000
From: Nigel R Treweeke <nrt04m$##$Cs.Nott.AC.UK>
Subject: ORGLIST: Chemistry Deparment Shutting
To: everybody$##$orglist.net
Message-ID: <4417062D.9020905$##$cs.nott.ac.uk>
Content-Type: text/plain; charset=us-ascii; format=flowed
Dear All,
Sorry if this appears multiple times.
This really is quite important as the more signatures and interest we
have the better.
http://www.scas.streamlinenettrial.co.uk/public_html/SCAS/index.htm
The above site has been set up in response to the threatened closure of
Sussex University Chemistry Department
All relevant links and information can be found in the URL
Many thanks in advance
Nigel Treweeke
This message has been checked for viruses but the contents of an attachment
may still contain software viruses, which could damage your computer system:
you are advised to perform your own checks. Email communications with the
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