From owner-chemistry@ccl.net Mon Apr 23 14:31:00 2018 From: "m.dominic.ryan**gmail.com" To: CCL Subject: CCL: 100 years of computational chemistry? No, but 52. Message-Id: <-53264-180423142349-13157-Ovk+MVqsl0l6ZmSugkDIhw*o*server.ccl.net> X-Original-From: Content-Language: en-us Content-Type: multipart/alternative; boundary="----=_NextPart_000_0014_01D3DB0E.AD9BF2A0" Date: Mon, 23 Apr 2018 14:23:40 -0400 MIME-Version: 1.0 Sent to CCL by: [m.dominic.ryan*o*gmail.com] This is a multipart message in MIME format. ------=_NextPart_000_0014_01D3DB0E.AD9BF2A0 Content-Type: text/plain; charset="UTF-8" Content-Transfer-Encoding: quoted-printable Theoretical [physics|chemistry|=E2=80=A6cosmology|=E2=80=A6] =20 I first put that in a broader context of theory as coming up with a way = describe naturally observable phenomena that also permits predicting = what the experimental observation will be under new conditions. A theory = of gravity lets you know the terminal velocity when the apple hits the = ground. Extended it also lets you make predictions about cosmological = lensing.=20 =20 This is important because the word =E2=80=98theory=E2=80=99 has been = grossly misused in recent decades by popular media and in fact the = general public. A =E2=80=98theory=E2=80=99 is taken to mean =E2=80=98one = guess that is as good as another about how and why something = happens=E2=80=99. It has been confused with = =E2=80=98hypothesis=E2=80=99 and even that is not well understood to = mean something that has data behind it.=20 =20 Theoretical chemistry is then a framework for making predictions about = the behavior of a system under new conditions. Those conditions might be = the band gap in semi-conductors or they might be a fluorescence decay. = Those will likely require a model of electronic structure that while = useful is still a big step back from a fully time-dependent model that = addresses atomic / electronic scale.=20 =20 The new conditions could just as easily be predicting what minor tweaks = to a ligand in a protein-ligand complex will have tighter or looser = binding. Those will usually be less dependent on electronic structure = theory (though not always).=20 =20 What is common is the importance of knowing the utility of the = theoretical framework for the problem at hand. What has also been = unfortunately common in my observation is a tendency for the = practitioners of one method to see only the limitations in other = methods. Those limitations then become the rationale for calling the = =E2=80=98other=E2=80=99 method something other than theoretical = chemistry.=20 =20 My own admitted bias is to think of theoretical chemistry, or = computational chemistry, as still involving chemistry in a molecular = sense. Is the mapping of a perturbation response of a proteome network = theoretical chemistry? I think that starts to morph into engineering. = There=E2=80=99s nothing wrong with that either! I am an advocate for the = importance of all such tools to help advance drug discovery problems. =20 =20 I still say that computational chemistry in a pretty modern sense, = although analog, started in the early 1920s with that paper from Shell = on ball/spring models of molecules to correlate with IR spectra and make = conclusions about bonding patterns.=20 =20 As scientists we have a duty to help the public understand what = =E2=80=98theory=E2=80=99 is. To do that we have to be broad minded = within the community as well.=20 =20 Dominic Ryan =20 > From: owner-chemistry+m.dominic.ryan=3D=3Dgmail.com .. ccl.net = On Behalf Of = Dr.N Sukumar n.sukumar__snu.edu.in Sent: Monday, April 23, 2018 7:55 AM To: Ryan, M Dominic Subject: CCL: 100 years of computational chemistry? No, but 52. =20 Well, I do not do "molecular mechanics as performed by Norman Allinger"; = so clearly I'm not a computational chemist! The distinction described by Per-Ola Norrby is an example (or perhaps a = subset) of that between retrospective and predicting modeling. = Classifying the former as theoretical and the latter as computational = seems too restrictive to me. "Developing and evaluating models" is often = inseparable from developing and testing computer codes, the bread and = butter work of many computational chemists. Limiting the scope of = computational chemistry to only application work is too restrictive, in = my opinion. Running ready-made computer programs and getting numbers is = nowadays often performed by experimental chemists. Again, I find little justification for classifying QSAR in theoretical = as opposed to computational chemistry. Modern QSAR is primarily = predictive in nature. Fields of science evolve in time, and certainly so over the course of = half a century and more. Freezing the definition of a field to what it = was in a bygone historical era is not justified. By that criterion, we = should call ourselves neither computational nor theoretical chemists, = but natural philosophers! N. Sukumar Professor of Chemistry Director, Center for Informatics Shiv Nadar University, India =20 =E2=80=9CBe a nuisance where it counts=E2=80=9D - Marjory Stoneman = Douglas =20 On Mon, Apr 23, 2018 at 11:40 AM, Per-Ola Norrby = per-ola.norrby_+_astrazeneca.com = > = wrote: Sent to CCL by: "Per-Ola Norrby" [per-ola.norrby#astrazeneca.com = ] I had an error in my previous post, so here is an update on the term = "Computational Chemistry". The short Allinger biography where Lipkowitz = and Laane describe the origin of the term "Computational Chemistry" can = be found here: https://doi.org/10.1016/S0022-2860(00)00639-6 The originator of the term "computational chemistry" was in fact Frank = Westheimer, in 1966, but the original definition was as I remembered, = "molecular mechanics as performed by Norman Allinger".=20 I very much like the view expressed in the biography, and would like to = define the difference between theoretical chemistry and computational = chemistry: Theoretical chemistry is concerned with developing and evaluating models = of chemistry, validating by comparing to known facts. Examples would be = development of functionals, comparison of force fields, or maybe = derivation of a QSAR equation. Computational chemistry uses models, and tries to find new chemistry = facts. Examples of studies in this category would be to find which = transition state controls a reaction, which ligand fits best into an = enzyme pocket, which experimental conditions should I use in my next = experiment. Basically telling something about the next experiment. Theory must of course come first, but I guess many of us work in both = areas. Computational chemistry is clearly the younger discipline; not = until the 60's were models and computers good enough so you could = actually start making statements about future experiments with some = reliability (and only Allinger did it then). Deriving the models needed = for this work (theoretical chemistry) had been going on for decades. There is a third category, where you use computational models to = reproduce known experiments. I'd classify that as "boring chemistry".=20 /Per-Ola -----Original Message----- > From: owner-chemistry+per-ola.norrby=3D=3Dastrazeneca.com = [#]ccl.net = [mailto:owner-chemistry+per-ola.norrby = =3D=3Dastrazeneca.com = [#]ccl.net ] On Behalf Of = Norrby, Per-Ola Per-Ola.Norrby(-)astrazeneca.com = =20 Sent: den 20 april 2018 08:41 To: Norrby, Per-Ola > Subject: CCL: 100 years of computational chemistry? Sent to CCL by: "Norrby, Per-Ola" [Per-Ola.Norrby||astrazeneca.com = ] The origins of the term Computational = Chemistry was researched by Kenny Lipkowitz a while back, but I've been = unable to locate the article again, it was some kind of festschrift = honoring Norman L. Allinger. If I remember correctly, the term was = coined by Schleyer at a conference in 1966, when discussing the works of = Allinger, to describe it as distinct from the mother field, theoretical = chemistry. Before Allinger, theoretical chemistry had mainly been = concerned with the question "what type of model can we use to describe = reality" This covered both the fields of quantum chemistry back to the = early 20th century, as well as conformational searching and molecular = mechanics going back to Westheimer in the mid-40's. The novel approach = that deserved the new term was to start with a model that is good = enough, and start asking questions about the chemistry, which could be = answered in the computer and later tested in ! the lab. I think that focus shift deserved being called a new field.! The original definition of "computational chemistry" was actually = "molecular mechanics as performed by Norman Allinger". The definition = has shifted somewhat , but I think the distinction from the still lively = field of theoretical chemistry is clear. It comes from whether your = primary interest is in how we model reality, or what we can find out = about reality by applying a model in novel ways. Of course many = practitioners do both (so we could call them "interdisciplinary" ) /Per-Ola Per-Ola Norrby Principal Scientist, Computational Pharmaceutics Pharmaceutical = Sciences, AstraZeneca-Gothenburg -=3D This is automatically added to each message by the mailing script = =3D-
or use:E-mail to administrators: CHEMISTRY-REQUEST ~~ ccl.net = or use

Theoretical = [physics|chemistry|=E2=80=A6cosmology|=E2=80=A6]

 

I first put = that in a broader context of theory as coming up with a way describe = naturally observable phenomena that also permits predicting what the = experimental observation will be under new conditions. A theory of = gravity lets you know the terminal velocity when the apple hits the = ground. Extended it also lets you make predictions about cosmological = lensing.

 

This is important because the word = =E2=80=98theory=E2=80=99 has been grossly misused in recent decades by = popular media and in fact the general public. A =E2=80=98theory=E2=80=99 = is taken to mean =E2=80=98one guess that is as good as another about how = and why something happens=E2=80=99.=C2=A0 It has been confused with = =E2=80=98hypothesis=E2=80=99 and even that is not well understood to = mean something that has data behind it.

 

Theoretical = chemistry is then a framework for making predictions about the behavior = of a system under new conditions. Those conditions might be the band gap = in semi-conductors or they might be a fluorescence decay. Those will = likely require a model of electronic structure that while useful is = still a big step back from a fully time-dependent model that addresses = atomic / electronic scale.

 

The new = conditions could just as easily be predicting what minor tweaks to a = ligand in a protein-ligand complex will have tighter or looser binding. = Those will usually be less dependent on electronic structure theory = (though not always).

 

What is = common is the importance of knowing the utility of the theoretical = framework for the problem at hand. What has also been unfortunately = common in my observation is a tendency for the practitioners of one = method to see only the limitations in other methods. Those limitations = then become the rationale for calling the =E2=80=98other=E2=80=99 method = something other than theoretical chemistry.

 

My own = admitted bias is to think of theoretical chemistry, or computational = chemistry, as still involving chemistry in a molecular sense. Is the = mapping of a perturbation response of a proteome network theoretical = chemistry? I think that starts to morph into engineering. = There=E2=80=99s nothing wrong with that either! I am an advocate for the = importance of all such tools to help advance drug discovery problems. = =C2=A0

 

I still say that computational chemistry in a pretty = modern sense, although analog, started in the early 1920s with that = paper from Shell on ball/spring models of molecules to correlate with IR = spectra and make conclusions about bonding patterns.

 

As = scientists we have a duty to help the public understand what = =E2=80=98theory=E2=80=99 is. To do that we have to be broad minded = within the community as well.

 

Dominic = Ryan

 

From: = owner-chemistry+m.dominic.ryan=3D=3Dgmail.com .. ccl.net = <owner-chemistry+m.dominic.ryan=3D=3Dgmail.com .. ccl.net> On = Behalf Of Dr.N Sukumar n.sukumar__snu.edu.in
Sent: Monday, = April 23, 2018 7:55 AM
To: Ryan, M Dominic = <m.dominic.ryan .. gmail.com>
Subject: CCL: 100 years of = computational chemistry? No, but 52.

 

Well, I do not do = "molecular mechanics as performed by Norman Allinger"; so = clearly I'm not a computational chemist!

The distinction = described by Per-Ola Norrby is an example (or perhaps a subset) of that = between retrospective and predicting modeling. Classifying the former as = theoretical and the latter as computational seems too restrictive to me. = "Developing and evaluating models" is often inseparable from = developing and testing computer codes, the bread and butter work of many = computational chemists. Limiting the scope of computational chemistry to = only application work is too restrictive, in my opinion. Running = ready-made computer programs and getting numbers is nowadays often = performed by experimental chemists.

Again, I find little = justification for classifying QSAR in theoretical as opposed to = computational chemistry. Modern QSAR is primarily predictive in = nature.

Fields of science = evolve in time, and certainly so over the course of half a century and = more. Freezing the definition of a field to what it was in a bygone = historical era is not justified. By that criterion, we should call = ourselves neither computational nor theoretical chemists, but natural = philosophers!


<= div>

N. = Sukumar
Professor of Chemistry
Director, Center for = Informatics
Shiv Nadar University, India


=E2=80=9CBe a nuisance where it = counts=E2=80=9D - Marjory Stoneman = Douglas

 

On Mon, Apr 23, 2018 at 11:40 AM, Per-Ola Norrby = per-ola.norrby_+_astrazeneca.com = <owner-chemistry ~~ ccl.net> = wrote:


Sent to CCL by: "Per-Ola  = Norrby" [per-ola.norrby#astrazeneca.com]
I had an error in my previous = post, so here is an update on the term "Computational = Chemistry". The short Allinger biography where Lipkowitz and Laane = describe the origin of the term "Computational Chemistry" can = be found here:
https://doi.org/10.1016/S0022-2860(00)00639-6
Th= e originator of the term "computational chemistry" was in fact = Frank Westheimer, in 1966, but the original definition was as I = remembered, "molecular mechanics as performed by Norman = Allinger".

I very much like the view expressed in the = biography, and would like to define the difference between theoretical = chemistry and computational chemistry:

Theoretical chemistry is = concerned with developing and evaluating models of chemistry, validating = by comparing to known facts. Examples would be development of = functionals, comparison of force fields, or maybe derivation of a QSAR = equation.

Computational chemistry uses models, and tries to find = new chemistry facts. Examples of studies in this category would be to = find which transition state controls a reaction, which ligand fits best = into an enzyme pocket, which experimental conditions should I use in my = next experiment. Basically telling something about the next = experiment.

Theory must of course come first, but I guess many of = us work in both areas. Computational chemistry is clearly the younger = discipline; not until the 60's were models and computers good enough so = you could actually start making statements about future experiments with = some reliability (and only Allinger did it then). Deriving the models = needed for this work (theoretical chemistry) had been going on for = decades.

There is a third category, where you use computational = models to reproduce known experiments. I'd classify that as "boring = chemistry".

/Per-Ola

-----Original = Message-----
> From: owner-chemistry+per-ola.norrby=3D=3Dastrazeneca.com[#]ccl.net [mailto:owner-chemistry+per-ola.= norrby=3D=3Dastrazeneca.com[#]ccl.net] On Behalf Of Norrby, Per-Ola = Per-Ola.Norrby(-)astrazeneca.com
Sent: den 20 april 2018 = 08:41
To: Norrby, Per-Ola <Per-Ola.Norrby[#]astrazeneca.com>
Subject: CCL: 100 years of = computational chemistry?


Sent to CCL by: "Norrby, = Per-Ola" [Per-Ola.Norrby||astrazeneca.com] The origins of the term = Computational Chemistry was researched by Kenny Lipkowitz a while back, = but I've been unable to locate the article again, it was some kind of = festschrift honoring Norman L. Allinger. If I remember correctly, the = term was coined by Schleyer at a conference in 1966, when discussing the = works of Allinger, to describe it as distinct from the mother field, = theoretical chemistry. Before Allinger, theoretical chemistry had mainly = been concerned with the question "what type of model can we use to = describe reality" This covered both the fields of quantum chemistry = back to the early 20th century, as well as conformational searching and = molecular mechanics going back to Westheimer in the mid-40's. The novel = approach that deserved the new term was to start with a model that is = good enough, and start asking questions about the chemistry, which could = be answered in the computer and later tested in !
 the lab. I = think that focus shift deserved being called a new field.!
  The = original definition of "computational chemistry" was actually = "molecular mechanics as performed by Norman Allinger". The = definition has shifted somewhat , but I think the distinction from the = still lively field of theoretical chemistry is clear. It comes from = whether your primary interest is in how we model reality, or what we can = find out about reality by applying a model in novel ways. Of course many = practitioners do both (so we could call them = "interdisciplinary" )

/Per-Ola

Per-Ola = Norrby
Principal Scientist, Computational Pharmaceutics = Pharmaceutical Sciences, AstraZeneca-Gothenburg



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