From owner-chemistry@ccl.net Mon Apr 23 02:12:01 2018 From: "Per-Ola Norrby per-ola.norrby_+_astrazeneca.com" To: CCL Subject: CCL: 100 years of computational chemistry? No, but 52. Message-Id: <-53260-180423021031-24131-a9pyWF3v1DMhUz2smVLxUg:server.ccl.net> X-Original-From: "Per-Ola Norrby" Date: Mon, 23 Apr 2018 02:10:27 -0400 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". 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==astrazeneca.com::ccl.net [mailto:owner-chemistry+per-ola.norrby==astrazeneca.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 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 From owner-chemistry@ccl.net Mon Apr 23 10:38:01 2018 From: "Gilson, Michael mgilson : ucsd.edu" To: CCL Subject: CCL: 100 years of computational chemistry? No, but 52. Message-Id: <-53261-180423103638-23916-nsoB1ZKJYpcdSYSVns4vlQ _ server.ccl.net> X-Original-From: "Gilson, Michael" Content-Language: en-US Content-Transfer-Encoding: 8bit Content-Type: text/plain; charset="us-ascii" Date: Mon, 23 Apr 2018 14:36:26 +0000 MIME-Version: 1.0 Sent to CCL by: "Gilson, Michael" [mgilson : ucsd.edu] I tell my students that computational chemistry is a continuation of theoretical chemistry by other means. :-) Mike On 4/22/2018 11:52 PM, 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". > > 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==astrazeneca.com[#]ccl.net [mailto:owner-chemistry+per-ola.norrby==astrazeneca.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 > 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> > > -- Michael K. Gilson, M.D., Ph.D. Professor and Chair in Computer-Aided Drug Design Co-Director UC San Diego Center for Drug Discovery Innovation Skaggs School of Pharmacy and Pharmaceutical Sciences 9500 Gilman Drive MC0736 La Jolla, CA, 92093-0736 Tel: 858-822-0622 gilson.ucsd.edu cddi.ucsd.edu bindingdb.org From owner-chemistry@ccl.net Mon Apr 23 11:13:01 2018 From: "Dr.N Sukumar n.sukumar__snu.edu.in" To: CCL Subject: CCL: 100 years of computational chemistry? No, but 52. Message-Id: <-53262-180423075504-8213-2JZCOkM57fqO47HMDBT5Ig]~[server.ccl.net> X-Original-From: "Dr.N Sukumar" Content-Type: multipart/alternative; boundary="000000000000afb7c6056a82b41c" Date: Mon, 23 Apr 2018 17:24:52 +0530 MIME-Version: 1.0 Sent to CCL by: "Dr.N Sukumar" [n.sukumar_-_snu.edu.in] --000000000000afb7c6056a82b41c Content-Type: text/plain; charset="UTF-8" Content-Transfer-Encoding: quoted-printable 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. SukumarProfessor of ChemistryDirector, 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 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 a= nd > 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". > > 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 derivati= on > 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 enzy= me > 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 unt= il > the 60's were models and computers good enough so you could actually star= t > making statements about future experiments with some reliability (and onl= y > 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 reproduc= e > known experiments. I'd classify that as "boring chemistry". > > /Per-Ola > > -----Original Message----- > > From: owner-chemistry+per-ola.norrby=3D=3Dastrazeneca.com[#]ccl.net [ma= ilto: > 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 > 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 remembe= r > 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 chemist= ry > had mainly been concerned with the question "what type of model can we us= e > to describe reality" This covered both the fields of quantum chemistry ba= ck > 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 goo= d > 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 fiel= d > 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 realit= y > 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-> > > --000000000000afb7c6056a82b41c Content-Type: text/html; charset="UTF-8" Content-Transfer-Encoding: quoted-printable
Well, I do not do=20 "molecular mechanics as performed by Norman Allinger"; so clearl= y I'm not a computational chemist!

The distinction describ= ed by=20 Per-Ola Norrby is an example (or perhaps a subset) of that between retrospective and predi= cting modeling. Classifying the former as theoretical and the latter as com= putational seems too restrictive to me. "Developing and evaluating mod= els" is often inseparable from developing and testing computer codes, = the bread and butter work of many computational chemists. Limiting=20 the scope of computational chemistry to only application work is too restri= ctive, in my opinion. Running ready-made computer programs and getting numb= ers is nowadays often performed by experimental chemists.

Agai= n, I find little justification for classifying QSAR in theoretical as oppos= ed to computational chemistry. Modern=20 QSAR=20 is primarily predictive in nature.

Fields of science evolve in= time, and certainly so over the course of half a century and more. Freezin= g the definition of a field to what it was in a bygone historical era is no= t justified. By that criterion, we should call ourselves neither computatio= nal nor theoretical chemists, but natural philosophers!

=
N. Sukumar
Professor of Chemistry
Dire= ctor, 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 No= rrby per-ola.norrby_+_astrazeneca.com <owner-chemistry .. ccl.net> wrote:

Sent to CCL by: "Per-Ola=C2=A0 Norrby" [per-ola.norrby#astrazeneca.<= wbr>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&qu= ot; can be found here:
https://doi.org/10.1016/S0022-2860(00)00639-6<= br> 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".

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

Theoretical chemistry is concerned with developing and evaluating models of= chemistry, validating by comparing to known facts. Examples would be devel= opment 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 sta= te controls a reaction, which ligand fits best into an enzyme pocket, which= experimental conditions should I use in my next experiment. Basically tell= ing 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 (theoretica= l 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". <= br>
/Per-Ola

-----Original Message-----
> From: owner-chemistry+per-ola.norrby=3D=3Dastrazeneca.com[#]ccl.net [mailto:owner-chemist= ry+per-ola.norrby=3D=3Dastrazeneca.com[#]ccl.net] On Behalf Of Norr= by, 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 articl= e 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 th= e mother field, theoretical chemistry. Before Allinger, theoretical chemist= ry had mainly been concerned with the question "what type of model can= we use to describe reality" This covered both the fields of quantum c= hemistry back to the early 20th century, as well as conformational searchin= g 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 i= s good enough, and start asking questions about the chemistry, which could = be answered in the computer and later tested in !
=C2=A0the lab. I think that focus shift deserved being called a new field.!=
=C2=A0 The original definition of "computational chemistry" was a= ctually "molecular mechanics as performed by Norman Allinger". Th= e definition has shifted somewhat , but I think the distinction from the st= ill lively field of theoretical chemistry is clear. It comes from whether y= our primary interest is in how we model reality, or what we can find out ab= out 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, A= straZeneca-Gothenburg



-=3D This is automatically added to each message by the mailing script =3D-=
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--000000000000afb7c6056a82b41c-- From owner-chemistry@ccl.net Mon Apr 23 11:48:01 2018 From: "Kevin Theisen kevin ~~ ichemlabs.com" To: CCL Subject: CCL: ChemDoodle 9 Now Available! Message-Id: <-53263-180423083311-24675-R2r6S5GAMuNHLXuCn7IpuQ:-:server.ccl.net> X-Original-From: "Kevin Theisen" Date: Mon, 23 Apr 2018 08:33:09 -0400 Sent to CCL by: "Kevin Theisen" [kevin-x-ichemlabs.com] We are pleased to announce that ChemDoodle v9 is available ( https://www.chemdoodle.com ). ChemDoodle 9 is a major revision of every aspect of the software. We spent over 2 years overhauling and improving the cheminformatics engine, interface, drawing controls, image and chemical file types, graphics, and operating system compatibility. In addition to the new features, the entire codebase has been refactored for the current best standards to take advantage of the latest performance, memory and security features of the operating system. You can find a detailed list of the changes in section 1.2 (page 12) of the newly renovated user manual. https://www.chemdoodle.com/downloads/UserGuide.pdf Site license users receive this upgrade for free. For a limited time, user licenses (Single User, Home+Office) may purchase an upgrade to ChemDoodle v9 for a significant discount off the list price. To purchase the upgrade, click on the purchase upgrade link when prompted in ChemDoodle, then follow the instructions to update. Or, you may purchase at our upgrade store. https://www.ichemlabs.com/ustore As always, we will continue to improve ChemDoodle and work on all of the requests we have received. Users like you help us make ChemDoodle the best option for chemical drawing and inspire us to continue. So please keep telling your students, friends and colleagues about ChemDoodle. Thank you! Sincerely, Kevin Theisen President, iChemLabs 7305 Hancock Village Dr #525 Chesterfield, VA 23832 https://www.linkedin.com/in/iclkevin/ - feel free to connect, just note that you are a ChemDoodle user 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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