Thanks for the snarky comment it highlights = an important point. I am really not interested in methodology for this pres= ent work=C2=A0and neither is industry. They care about prediction and havin= g it fast. I see level nerds as being a barrier to a=C2=A0be= tter interaction between theory and experiment. So, people, if you have HF/= sto-3g calcs that do the job, I want to know.

Best,

Peter

On Tuesday, September 8, 2015, Susi Lehtol= a susi.lehtola a alumni.helsinki.fi <owner-chemistry,+,ccl.net> wrote:

Sent to CCL by: Susi Lehtola [susi.lehtola.,+,.alumni.helsinki.fi]
On 09/07/2015 12:39 AM, Peter Damian Jarowski peterjarowski[-]gmail.com wrote:

I am looking to collect case studies of how computational chemistry (specif= ically QM) has been able to predict or refine/optimize chemical reactions, = especially cases where experimental work has followed this theoretical work= up to achieve higher yields or selectivity. Any references or descriptions= would be much appreciated and I would use them to build an argument for QM= . I would of course give references and credit and then I will share a repo= rt here.

A good example would be my own work where we were able to predict the exist= ence of an isolable intermediate and then prove this with experiment and XR= D:

Wu, Y.-L.; Jarowski, P. D.; Schweizer, W. B.; Diederich, F. "Mechanist= ic Investigation of the Formal [2+2] Cycloaddition-Cycloreversion Reaction = between 4-(N,N-Dimethylamino)phenylacetylene and Arylated 1,1-Dicyanovinyl = Derivatives to Form Intramolecular Charge-Transfer Chromophores." Chem= . Eur. J. 2009, 16, 202-211.

However, I am looking for industry relevant examples. I would love to hear = > from the community about this and I think it would benefit everyone to have= at hand such examples.

> from the abstract:

"have been studied experimentally by the method of initial rates and c= omputationally at the unrestricted B3LYP/6-31G(d) level."

What is this, the 1990s? :P
--
-----------------------------------------------------------------------
Mr. Susi Lehtola, PhD=C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0Chemis= t Postdoctoral Fellow
susi.lehtola : alum= ni.helsinki.fi=C2=A0 =C2=A0Lawrence Berkeley National Laboratory
http://www.h= elsinki.fi/~jzlehtol=C2=A0 USA
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--001a1141f37ed81e61051f4a7807-- From owner-chemistry@ccl.net Wed Sep 9 08:32:01 2015 From: "Igor Filippov igor.v.filippov(a)gmail.com" To: CCL Subject: CCL: release of OSRA 2.0.1 Message-Id: <-51677-150909082742-31130-mmkTrOSVPbih6JH+NosJYA*|*server.ccl.net> X-Original-From: Igor Filippov Content-Type: multipart/alternative; boundary=001a1140dbb4957615051f4f9b12 Date: Wed, 9 Sep 2015 08:27:36 -0400 MIME-Version: 1.0 Sent to CCL by: Igor Filippov [igor.v.filippov|*|gmail.com] --001a1140dbb4957615051f4f9b12 Content-Type: text/plain; charset=UTF-8 Dear colleagues, I would like to announce the release of Optical Structure Recognition Application (OSRA) version 2.0.1. OSRA is a tool to extract and convert images of molecular structures and reactions from PDF, PNG, GIF, JPEF and other graphics file formats to chemoinformatics formats such as SDF, SMILES and others. The highlights of the new release include: * Better filtering of false positives (non-molecular images) - over 5 times reduction in nonsensical structures. * Improved Accelrys Draw plugin, courtesy of James Jack (the plugin is also available as a stand-alone download). * Updated versions of dependent libraries. The new version of OSRA is available as always at osra.sf.net In addition to the source code Windows and Linux binaries are provided, note that there are no OS X binaries for this release due to the lack of interest. The stand-alone Accelrys Draw plugin is available at https://sourceforge.net/projects/osra/files/plugins/accelrys_draw/ Best regards, Igor Filippov --001a1140dbb4957615051f4f9b12 Content-Type: text/html; charset=UTF-8 Content-Transfer-Encoding: quoted-printable

Dea= r colleagues,

I would like to announce the release of Optical = Structure Recognition Application (OSRA)

version 2.0.1. OSRA is a tool to extract and convert images of molecular=20 structures and reactions from PDF, PNG, GIF, JPEF and other graphics=20 file formats to chemoinformatics formats such as SDF, SMILES and others. The highlights of the new release include:

* Better filtering= of false positives (non-molecular images) - over 5 times reduction in
<= /div>

nonsensical structures.

* Improved Accelrys Draw plugin,= courtesy of James Jack (the plugin is also available as a stand-alone down= load).

* Updated versions of dependent libraries.

The= new version of OSRA is available as always at
osra.sf.net

In addition to the so= urce code Windows and Linux binaries are provided, note that

there= are no OS X binaries for this release due to the lack of interest.
The stand-alone Accelrys Draw plugin is available at
https://sourceforge.net/projects/osra/files/plugins/accelrys_draw/=

Best regards,

Igor Filippov

--001a1140dbb4957615051f4f9b12-- From owner-chemistry@ccl.net Wed Sep 9 10:53:01 2015 From: "=?iso-8859-1?Q?V=EDctor_Lua=F1a?= Cabal victor\a/fluor.quimica.uniovi.es" To: CCL Subject: CCL: Case Studies of QM Computational Chemistry in Reactivity Message-Id: <-51678-150909094536-1927-Fb6F9LPm7gfPrelA5BzhAA^^server.ccl.net> X-Original-From: =?iso-8859-1?Q?V=EDctor_Lua=F1a?= Cabal Content-disposition: inline Content-transfer-encoding: 8BIT Content-type: text/plain; charset=iso-8859-1 Date: Wed, 09 Sep 2015 15:28:07 +0200 MIME-version: 1.0 Sent to CCL by: =?iso-8859-1?Q?V=EDctor_Lua=F1a?= Cabal [victor:+:fluor.quimica.uniovi.es] On Wed, Sep 09, 2015 at 07:19:58AM +0100, Peter Jarowski peterjarowski###gmail.com wrote: > Thanks for the snarky comment it highlights an important point. I am really > not interested in methodology for this present work and neither is > industry. They care about prediction and having it fast. I see level nerds > as being a barrier to a better interaction between theory and experiment. > So, people, if you have HF/sto-3g calcs that do the job, I want to know. Peter, Your remark points to a important quastion about the role of theory in science, and particularly in scientific simulation. This is a debatable subject, certainly, but my opinion is that the objective of theory is not reproducing experiments. Nothing surpasses experimental measurement on that. The role of theory is insight on understanding what experiments produce and what influences the experimental properties. You point to HF/sto-3g calcs as a good example of demodé techniques that can be useful for a purpose. I point to the Hückel and extended-Hückel techniques that were used by a Nobel prize school: Roald Hoffmann. Good luck in your chase for heroic examples of theoretical chemistry examples, Víctor -- . . "In science a person can be convinced by a good argument. / `' \ That is almost impossible in politics or religion" /(o)(o)\ (Adapted from Carl Sagan) /`. \/ .'\ "Lo mediocre es peor que lo bueno, pero también es peor / '`'` \ que lo malo, porque la mediocridad no es un grado, es una | \'`'`/ | actitud" -- Jorge Wasenberg, 2015 | |'`'`| | (Mediocre is worse than good, but it is also worse than \/`'`'`'\/ bad, because mediocrity is not a grade, it is an attitude) ===(((==)))==================================+========================= ! Dr.Víctor Luaña, in silico chemist & prof. !"I have two kinds of problems, ! Departamento de Química Física y Analítica ! the urgent and the important. ! Universidad de Oviedo, 33006-Oviedo, Spain ! The urgent are not important, ! e-mail: victor(!)fluor.quimica.uniovi.es ! and the important are never ! phone: +34-985-103491 fax: +34-985-103125 ! urgent. +--------------------------------------------+ (Dwight D. Eisenhower) GroupPage : http://azufre.quimica.uniovi.es/ From owner-chemistry@ccl.net Wed Sep 9 11:29:00 2015 From: "Lars Goerigk lars.goerigk-,-unimelb.edu.au" To: CCL Subject: CCL: Case Studies of QM Computational Chemistry in Reactivity Message-Id: <-51679-150909100624-5100-Lge8lSrXj4NA/Gnw9Ft6Vw[]server.ccl.net> X-Original-From: "Lars Goerigk" Date: Wed, 9 Sep 2015 10:06:09 -0400 Sent to CCL by: "Lars Goerigk" [lars.goerigk : unimelb.edu.au] Hi Peter, in defense of us people that believe in obtaining the right result for the right reason: even if industry is interested in quick-and-dirty results, would it not be highly embarassing to make recommendations based on a method that relies on unforeseeable error compensation, only to then see that the experimentalists cannot reproduce your predictions? Susi's comment was therefore valid, albeit I would have worded it in a more diplomatic way. I find it very important to apply a level of theory that comes with a low risk of unsystematic error compensation. For example, a dispersion-corrected (double-)hybrid density functional with at least a triple-zeta basis set is overall much more reliable than the popular B3LYP/6-31G* level; the reasons for that are clear and they have been discussed extensively in the literature and in this forum. If you cannot afford a large basis set, but you want to quickly obtain results for bigger systems with an acceptable accuracy, there are other promising methods out there (e.g. HF-3c or PBEh-3c). Moreover, it is also important to use reliable solvation models (e.g. COSMO-RS) and reliable enthalpy and entropy corrections. As to your comment on "level nerds" being a barrier for successful interaction between theory and experiment, quantum chemists do not investigate and develop new methdods just because they do not know what else to do with their time. I would rather say that this discussion highlights a lack of communication between method developers and the users of QM methods and as always the fault for that lies probably on both sides; one consequence of that is that B3LYP/6-31G* is still so popular in the year 2015. Giving a general answer to your question is difficult, as it is not quite sure what property you want to calculate, which is exactly why the various answers to your question differ so much. However, there are numerous benchmark studies out there that provide some guidance on which methods to use and which to avoid; I have given some hints on reliable methods above. Of course, there is never 100% certainty that your predictions are right because in the end you try to describe a highly complex system with a theoretical model, which by definition is only a simplification of the real world. That complexity also means that there is not one sole, easy solution to your question. Therefore, it is probably wise to run calculations at two different levels of theory to distinguish between general trends and methodological artifacts. By carefully choosing a statistically reliable level of theory, you can at least minimise the possibilibity of making wrong predictions, and that is something that also industry people will accept if properly explained. I hope some of these hints were helpful. Finally, I hope you forgive me for saying that having efficient and ever improving QM methods is something that would not be possible without all those dedicated level nerds out there, which is why we should regard that term as a compliment. Cheers, Lars --- Dr. Lars Goerigk ARC DECRA Fellow School of Chemistry The University of Melbourne VIC 3010 Australia Research profile: http://www.chemistry.unimelb.edu.au/dr-lars-goerigk List of my publications: http://www.researcherid.com/rid/D-3717-2009 Follow me on Twitter: https://twitter.com/lgoer_compchem From owner-chemistry@ccl.net Wed Sep 9 12:04:00 2015 From: "Susi Lehtola susi.lehtola_-_alumni.helsinki.fi" To: CCL Subject: CCL: Case Studies of QM Computational Chemistry in Reactivity Message-Id: <-51680-150909103219-8074-D4wf5evuzSHrKN9jYUzeHQ_-_server.ccl.net> X-Original-From: Susi Lehtola Content-Transfer-Encoding: 7bit Content-Type: text/plain; charset=utf-8; format=flowed Date: Wed, 9 Sep 2015 07:31:20 -0700 MIME-Version: 1.0 Sent to CCL by: Susi Lehtola [susi.lehtola:+:alumni.helsinki.fi] On 09/08/2015 11:19 PM, Peter Jarowski peterjarowski###gmail.com wrote: > Hello Susi, > > Thanks for the snarky comment it highlights an important point. I am really > not interested in methodology for this present work and neither is > industry. They care about prediction and having it fast. I see level nerds > as being a barrier to a better interaction between theory and experiment. > So, people, if you have HF/sto-3g calcs that do the job, I want to know. My pleasure ;) However, 6-31G*/B3LYP is seen much too often in experimental papers, even for systems where a much higher quality calculation could be done routinely without problems. Way too many people still see 6-31G*/B3LYP as current state-of-the-art, although this has not been the case for at least a decade. Especially appalling is the case where a discrepancies are seen between experiment and 6-31G*/B3LYP theory, but no effort is put into seeing how wrong the latter result is. After all, 6-31G* is a minimalistic basis set, far from the basis set limit. It has S=P exponents that were useful in the 1980s because integral evaluation was in its infancy and couldn't handle polarization functions all that well. B3LYP is a functional from the mid-90s. Much more accurate functionals have been developed in the past 20 years, with a comparable or slightly larger cost. For instance, Jensen's pc-2 basis set is roughly two times larger than 6-31G*, but already gives highly accurate results with respect to the basis set limit. A modern range-separated hybrid functional costs roughly twice as much as B3LYP, but with significantly less self-interaction error. You can also do van der Waals type interactions in ab initio style today, using e.g. functionals that build on the VV10 model [Vydrov and van Voorhis, JCP 133, 244103 (2010)]. The evaluation of VV10 may add a noticeable increase in the compute time for small systems, but for larger ones VV10 is basically free compared to the evaluation of exact exchange. One of the most accurate functionals today is wB97X-V [Mardirossian and Head-Gordon, PCCP 16, 9904 (2014)], which is a range separated hybrid including VV10 non-local correlation, and performs extremely well in a wide variety of systems. The only two things that are still a problem for modern functionals like wB97X-V are 1) systems with large sensitivity to self-interaction error 2) systems that exhibit strong correlation and out of these no 2) is outside the scope of Kohn-Sham DFT [Kurzweil et al, Mol Phys 107, 2103 (2009)]. -- ----------------------------------------------------------------------- Mr. Susi Lehtola, PhD Chemist Postdoctoral Fellow susi.lehtola]![alumni.helsinki.fi Lawrence Berkeley National Laboratory http://www.helsinki.fi/~jzlehtol USA ----------------------------------------------------------------------- From owner-chemistry@ccl.net Wed Sep 9 12:52:01 2015 From: "Dr. Robert Molt Jr. r.molt.chemical.physics{=}gmail.com" To: CCL Subject: CCL: Case Studies of QM Computational Chemistry in Reactivity Message-Id: <-51681-150909105242-10993-TrpbKdocZqd4gHZhuiHQkQ-.-server.ccl.net> X-Original-From: "Dr. Robert Molt Jr." Content-Type: multipart/alternative; boundary="------------070107070801010000000207" Date: Wed, 09 Sep 2015 10:51:49 -0400 MIME-Version: 1.0 Sent to CCL by: "Dr. Robert Molt Jr." [r.molt.chemical.physics%%gmail.com] This is a multi-part message in MIME format. --------------070107070801010000000207 Content-Type: text/plain; charset=utf-8; format=flowed Content-Transfer-Encoding: 7bit What Dr. Jarowski clearly does not understand is that "level nerds" (since this is clearly a forum for pejorative comments, very professional indeed) are the ones who CAN tell you whether or not "HF/STO-3G calcs that do the job." Insulting people who understand the reliability of calculation methods is a great way to find the best calculation methods for your purposes. Moreover, you are coming onto this forum asking other people to do a literature review for you because you do not feel like it. Dr. Robert Molt Jr. r.molt.chemical.physics-x-gmail.com On 09/09/2015 02:19 AM, Peter Jarowski peterjarowski###gmail.com wrote: > Hello Susi, > > Thanks for the snarky comment it highlights an important point. I am > really not interested in methodology for this present work and neither > is industry. They care about prediction and having it fast. I see > level nerds as being a barrier to a better interaction between theory > and experiment. So, people, if you have HF/sto-3g calcsthat do the > job, I want to know. > > Best, > > Peter > > On Tuesday, September 8, 2015, Susi Lehtola susi.lehtola a > alumni.helsinki.fi > > wrote: > > > Sent to CCL by: Susi Lehtola [susi.lehtola.^.alumni.helsinki.fi > ] > On 09/07/2015 12:39 AM, Peter Damian Jarowski > peterjarowski[-]gmail.com wrote: > > I am looking to collect case studies of how computational > chemistry (specifically QM) has been able to predict or > refine/optimize chemical reactions, especially cases where > experimental work has followed this theoretical work up to > achieve higher yields or selectivity. Any references or > descriptions would be much appreciated and I would use them to > build an argument for QM. I would of course give references > and credit and then I will share a report here. > > A good example would be my own work where we were able to > predict the existence of an isolable intermediate and then > prove this with experiment and XRD: > > Wu, Y.-L.; Jarowski, P. D.; Schweizer, W. B.; Diederich, F. > "Mechanistic Investigation of the Formal [2+2] > Cycloaddition-Cycloreversion Reaction between > 4-(N,N-Dimethylamino)phenylacetylene and Arylated > 1,1-Dicyanovinyl Derivatives to Form Intramolecular > Charge-Transfer Chromophores." Chem. Eur. J. 2009, 16, 202-211. > > However, I am looking for industry relevant examples. I would > love to hear > from the community about this and I think it > would benefit everyone to have at hand such examples. > > > > from the abstract: > > "have been studied experimentally by the method of initial rates > and computationally at the unrestricted B3LYP/6-31G(d) level." > > What is this, the 1990s? :P > -- > ----------------------------------------------------------------------- > Mr. Susi Lehtola, PhD Chemist Postdoctoral Fellow > susi.lehtola : alumni.helsinki.fi > Lawrence Berkeley National Laboratory > http://www.helsinki.fi/~jzlehtol > USA > ----------------------------------------------------------------------- > > > > -= This is automatically added to each message by the mailing > script =- > E-mail to subscribers: CHEMISTRY^ccl.net or use:> > E-mail to administrators: CHEMISTRY-REQUEST^ccl.net or usehttp://www.ccl.net/chemistry/sub_unsub.shtmlConferences: > http://server.ccl.net/chemistry/announcements/conferences/> > --------------070107070801010000000207 Content-Type: text/html; charset=utf-8 Content-Transfer-Encoding: 8bit What Dr. Jarowski clearly does not understand is that "level nerds" (since this is clearly a forum for pejorative comments, very professional indeed) are the ones who CAN tell you whether or not "HF/STO-3G calcs that do the job." Insulting people who understand the reliability of calculation methods is a great way to find the best calculation methods for your purposes.

Moreover, you are coming onto this forum asking other people to do a literature review for you because you do not feel like it.

Dr. Robert Molt Jr.
r.molt.chemical.physics-x-gmail.com

On 09/09/2015 02:19 AM, Peter Jarowski peterjarowski###gmail.com wrote:

Hello Susi,

Thanks for the snarky comment it highlights an important point. I am really not interested in methodology for this present workÂ and neither is industry. They care about prediction and having it fast. I see level nerds as being a barrier to aÂ better interaction between theory and experiment. So, people, if you have HF/sto-3g calcs that do the job, I want to know.

Best,

Peter

On Tuesday, September 8, 2015, Susi Lehtola susi.lehtola a alumni.helsinki.fi <owner-chemistry^ccl.net> wrote:

Sent to CCL by: Susi Lehtola [susi.lehtola.^.alumni.helsinki.fi]
On 09/07/2015 12:39 AM, Peter Damian Jarowski peterjarowski[-]gmail.com wrote:

I am looking to collect case studies of how computational chemistry (specifically QM) has been able to predict or refine/optimize chemical reactions, especially cases where experimental work has followed this theoretical work up to achieve higher yields or selectivity. Any references or descriptions would be much appreciated and I would use them to build an argument for QM. I would of course give references and credit and then I will share a report here.

A good example would be my own work where we were able to predict the existence of an isolable intermediate and then prove this with experiment and XRD:

Wu, Y.-L.; Jarowski, P. D.; Schweizer, W. B.; Diederich, F. "Mechanistic Investigation of the Formal [2+2] Cycloaddition-Cycloreversion Reaction between 4-(N,N-Dimethylamino)phenylacetylene and Arylated 1,1-Dicyanovinyl Derivatives to Form Intramolecular Charge-Transfer Chromophores." Chem. Eur. J. 2009, 16, 202-211.

However, I am looking for industry relevant examples. I would love to hear > from the community about this and I think it would benefit everyone to have at hand such examples.

> from the abstract:

"have been studied experimentally by the method of initial rates and computationally at the unrestricted B3LYP/6-31G(d) level."

What is this, the 1990s? :P
--
-----------------------------------------------------------------------
Mr. Susi Lehtola, PhDÂ Â Â Â Â Â Â Chemist Postdoctoral Fellow
susi.lehtola : alumni.helsinki.fiÂ Â Lawrence Berkeley National Laboratory
http://www.helsinki.fi/~jzlehtolÂ USA
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--------------070107070801010000000207-- From owner-chemistry@ccl.net Wed Sep 9 16:22:00 2015 From: "Tom Albright talbright1234]=[gmail.com" To: CCL Subject: CCL: Case Studies of QM Computational Chemistry in Reactivity Message-Id: <-51682-150909132911-31588-i3YS0I4O7yaRYkFHVQn6Gg() server.ccl.net> X-Original-From: Tom Albright Content-Type: multipart/alternative; boundary=Apple-Mail-9--343953773 Date: Wed, 9 Sep 2015 12:28:33 -0500 Mime-Version: 1.0 (Apple Message framework v1085) Sent to CCL by: Tom Albright [talbright1234]^[gmail.com] --Apple-Mail-9--343953773 Content-Transfer-Encoding: quoted-printable Content-Type: text/plain; charset=iso-8859-1 I wholeheartedly agree with you Victor. Too often I see "how high can I = go" rather than a coherent explanation of why I got the results that I = did and can I extrapolate this "understanding" to other examples. And no = this is not the '90s. On Sep 9, 2015, at 8:28 AM, V=EDctor Lua=F1a Cabal = victora/fluor.quimica.uniovi.es wrote: >=20 > Sent to CCL by: =3D?iso-8859-1?Q?V=3DEDctor_Lua=3DF1a?=3D Cabal = [victor:+:fluor.quimica.uniovi.es] > On Wed, Sep 09, 2015 at 07:19:58AM +0100, Peter Jarowski = peterjarowski###gmail.com wrote: >> Thanks for the snarky comment it highlights an important point. I am = really >> not interested in methodology for this present work and neither is >> industry. They care about prediction and having it fast. I see level = nerds >> as being a barrier to a better interaction between theory and = experiment. >> So, people, if you have HF/sto-3g calcs that do the job, I want to = know. >=20 > Peter, >=20 > Your remark points to a important quastion about the role of theory > in science, and particularly in scientific simulation. >=20 > This is a debatable subject, certainly, but my opinion is that the > objective of theory is not reproducing experiments. Nothing surpasses > experimental measurement on that. The role of theory is insight on > understanding what experiments produce and what influences the > experimental properties. >=20 > You point to HF/sto-3g calcs as a good example of demod=E9 techniques = that > can be useful for a purpose. I point to the H=FCckel and = extended-H=FCckel > techniques that were used by a Nobel prize school: Roald Hoffmann. >=20 > Good luck in your chase for heroic examples of theoretical chemistry > examples, > V=EDctor > -- > . . "In science a person can be convinced by a good argument. > / `' \ That is almost impossible in politics or religion" > /(o)(o)\ (Adapted from Carl Sagan) > /`. \/ .'\ "Lo mediocre es peor que lo bueno, pero tambi=E9n es peor > / '`'` \ que lo malo, porque la mediocridad no es un grado, es una > | \'`'`/ | actitud" -- Jorge Wasenberg, 2015 > | |'`'`| | (Mediocre is worse than good, but it is also worse than > \/`'`'`'\/ bad, because mediocrity is not a grade, it is an = attitude) > = =3D=3D=3D(((=3D=3D)))=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D= =3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D+=3D=3D=3D=3D=3D=3D=3D=3D=3D= =3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D > ! Dr.V=EDctor Lua=F1a, in silico chemist & prof. !"I have two kinds of = problems, > ! Departamento de Qu=EDmica F=EDsica y Anal=EDtica ! the urgent and = the important. > ! Universidad de Oviedo, 33006-Oviedo, Spain ! The urgent are not = important, > ! e-mail: victor###fluor.quimica.uniovi.es ! and the important are = never > ! phone: +34-985-103491 fax: +34-985-103125 ! urgent. > +--------------------------------------------+ (Dwight D. = Eisenhower) > GroupPage : http://azufre.quimica.uniovi.es/ >=20 >=20 >=20 > -=3D This is automatically added to each message by the mailing script = =3D- > To recover the email address of the author of the message, please = change>=20>=20>=20 > Subscribe/Unsubscribe:=20>=20>=20 > Job: http://www.ccl.net/jobs=20 > Conferences: = http://server.ccl.net/chemistry/announcements/conferences/ >=20>=20>=20>=20 >=20 With Best Regards Tom Albright --Apple-Mail-9--343953773 Content-Transfer-Encoding: quoted-printable Content-Type: text/html; charset=iso-8859-1 I = wholeheartedly agree with you Victor. Too often I see "how high can I = go" rather than a coherent explanation of why I got the results that I = did and can I extrapolate this "understanding" to other examples. And no = this is not the '90s.

On Sep 9, 2015, at 8:28 AM, V=EDctor = Lua=F1a Cabal victora/fluor.quimica.uniovi.es wrote:

Sent to CCL by: =3D?iso-8859-1?Q?V=3DEDctor_Lua=3DF= 1a?=3D Cabal [victor:+:fluor.quimica.uniovi.es]
On Wed, Sep 09, 2015 = at 07:19:58AM +0100, Peter Jarowski peterjarowski###gmail.com = wrote:
Thanks for the snarky comment it = highlights an important point. I am really
not interested in methodology for this present work and = neither is
industry. They care = about prediction and having it fast. I see level = nerds
as being a barrier to a = better interaction between theory and = experiment.
So, people, if you = have HF/sto-3g calcs that do the job, I want to = know.

Peter,

Your remark points to a = important quastion about the role of theory
in science, and = particularly in scientific simulation.

This is a debatable = subject, certainly, but my opinion is that the
objective of theory is = not reproducing experiments. Nothing surpasses
experimental = measurement on that. The role of theory is insight on
understanding = what experiments produce and what influences the
experimental = properties.

You point to HF/sto-3g calcs as a good example of = demod=E9 techniques that
can be useful for a purpose. I point to the = H=FCckel and extended-H=FCckel
techniques that were used by a Nobel = prize school: Roald Hoffmann.

Good luck in your chase for heroic = examples of theoretical chemistry
examples,
=           V=EDctor
--=
    . .    "In science a = person can be convinced by a good argument.
   / `' \ =   That is almost impossible in politics or religion"
=   /(o)(o)\ (Adapted from Carl Sagan)
/`. \/ = .'\ "Lo mediocre es peor que lo bueno, pero tambi=E9n es peor
= /   '`'`   \ que lo malo, porque la mediocridad no = es un grado, es una
| \'`'`/ | actitud" -- Jorge = Wasenberg, 2015
| |'`'`| | (Mediocre is worse than good, = but it is also worse than
\/`'`'`'\/ bad, because = mediocrity is not a grade, it is an = attitude)
=3D=3D=3D(((=3D=3D)))=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D= =3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D+=3D=3D=3D=3D=3D= =3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D
! = Dr.V=EDctor Lua=F1a, in silico chemist & prof. !"I have two kinds of = problems,
! Departamento de Qu=EDmica F=EDsica y Anal=EDtica ! the = urgent and the important.
! Universidad de Oviedo, 33006-Oviedo, = Spain ! The urgent are not important,
! e-mail: =   victor###fluor.quimica.uniovi.es   ! and the = important are never
! phone: +34-985-103491 fax: +34-985-103125 = ! urgent.
+--------------------------------------------+ =        (Dwight D. Eisenhower)
= GroupPage : http://azufre.quimica.uniovi.es/=

-=3D This is automatically added to each message by = the mailing script =3D-
To recover the email address of the author of = the message, please change
the strange characters on the top line to = the : sign. You can also
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With = Best Regards

Tom Albright

= --Apple-Mail-9--343953773-- From owner-chemistry@ccl.net Wed Sep 9 16:57:00 2015 From: "Peeter Burk peeter.burk|a|ut.ee" To: CCL Subject: CCL: Case Studies of QM Computational Chemistry in Reactivity Message-Id: <-51683-150909134940-9301-A8EkbBD9/gMINN3xCPEd1g[a]server.ccl.net> X-Original-From: Peeter Burk Content-Transfer-Encoding: 8bit Content-Type: text/plain; charset=windows-1252; format=flowed Date: Wed, 9 Sep 2015 20:48:53 +0300 MIME-Version: 1.0 Sent to CCL by: Peeter Burk [peeter.burk-$-ut.ee] Sorry, could not hold me back! Any theory that explains or gives "insight on understanding what experiments produce and what influences the experimental properties" is theoretically useless. The only useful theory PREDICTS something that has not yet been measured and can thus been verified or falsified. If the HF/STO-3G can predict, let's say dipole moments (or HF/6-31G* the harmonic frequencies) with given/known accuracy, then it is a valid and useful theory. Chasing for newest (and thus usually more expensive) and often uncalibrated (unverified against experiment) theories seems to be a common mistake... In that sense also the earlier discussion on which atomic charges are better was a bit nonsense to me as the atomis charges can not be physically measurable. And if I recall right Eugen Schwarz has allready in 1994 shown that "Only a single principal component of ionicity has been found, which is common to all the various operational charge definitions. " J. Phys.Chem. 98, 1994, p. 8245. Best regards to everybody Peeter Burk University of Tartu, Estonia On 09/09/2015 04:28 PM, Víctor Luaña Cabal victora/fluor.quimica.uniovi.es wrote: > > Sent to CCL by: =?iso-8859-1?Q?V=EDctor_Lua=F1a?= Cabal [victor:+:fluor.quimica.uniovi.es] > On Wed, Sep 09, 2015 at 07:19:58AM +0100, Peter Jarowski peterjarowski###gmail.com wrote: >> Thanks for the snarky comment it highlights an important point. I am really >> not interested in methodology for this present work and neither is >> industry. They care about prediction and having it fast. I see level nerds >> as being a barrier to a better interaction between theory and experiment. >> So, people, if you have HF/sto-3g calcs that do the job, I want to know. > > Peter, > > Your remark points to a important quastion about the role of theory > in science, and particularly in scientific simulation. > > This is a debatable subject, certainly, but my opinion is that the > objective of theory is not reproducing experiments. Nothing surpasses > experimental measurement on that. The role of theory is insight on > understanding what experiments produce and what influences the > experimental properties. > > You point to HF/sto-3g calcs as a good example of demodé techniques that > can be useful for a purpose. I point to the Hückel and extended-Hückel > techniques that were used by a Nobel prize school: Roald Hoffmann. > > Good luck in your chase for heroic examples of theoretical chemistry > examples, > Víctor > -- > . . "In science a person can be convinced by a good argument. > / `' \ That is almost impossible in politics or religion" > /(o)(o)\ (Adapted from Carl Sagan) > /`. \/ .'\ "Lo mediocre es peor que lo bueno, pero también es peor > / '`'` \ que lo malo, porque la mediocridad no es un grado, es una > | \'`'`/ | actitud" -- Jorge Wasenberg, 2015 > | |'`'`| | (Mediocre is worse than good, but it is also worse than > \/`'`'`'\/ bad, because mediocrity is not a grade, it is an attitude) > ===(((==)))==================================+========================= > ! Dr.Víctor Luaña, in silico chemist & prof. !"I have two kinds of problems, > ! Departamento de Química Física y Analítica ! the urgent and the important. > ! Universidad de Oviedo, 33006-Oviedo, Spain ! The urgent are not important, > ! e-mail: victor###fluor.quimica.uniovi.es ! and the important are never > ! phone: +34-985-103491 fax: +34-985-103125 ! urgent. > +--------------------------------------------+ (Dwight D. Eisenhower) > GroupPage : http://azufre.quimica.uniovi.es/> From owner-chemistry@ccl.net Wed Sep 9 17:32:01 2015 From: "Peter Jarowski peterjarowski%gmail.com" To: CCL Subject: CCL: Case Studies of QM Computational Chemistry in Reactivity Message-Id: <-51684-150909143001-21458-LHMEcshjAE91Fd4PhkU8DA~!~server.ccl.net> X-Original-From: Peter Jarowski Content-Type: multipart/alternative; boundary=001a11c3b9087406e8051f54a93b Date: Wed, 9 Sep 2015 20:29:24 +0200 MIME-Version: 1.0 Sent to CCL by: Peter Jarowski [peterjarowski a gmail.com] --001a11c3b9087406e8051f54a93b Content-Type: text/plain; charset=UTF-8 Content-Transfer-Encoding: quoted-printable Hi Victor: Very much agreed. I remind readers that I was looking for cases where theory predicted something that had not been experimentally performed and then was later verified by experiment. Reproducing experiment with theory is useful for verification, but doesn't go much beyond that. I would argue though that theory can do something experiment can not: it can provide "error-less" results. More specifically, experiments present so many confounds, known and unknown, whereas theory can model the heart of the matter. Heats of formation, for example, may be more accurate and more readily comparable by very robust theory versus trolling the literature for these data derived under varied conditions, at various times, and using different approaches. So lets keep them coming and later on I will summarize what was sent to me here and on linkedin/researchgate and see what we all think. Best Regards, Peter On Wed, Sep 9, 2015 at 3:28 PM, V=C3=ADctor Lua=C3=B1a Cabal victora/ fluor.quimica.uniovi.es wrote: > > Sent to CCL by: =3D?iso-8859-1?Q?V=3DEDctor_Lua=3DF1a?=3D Cabal [victor:+= : > fluor.quimica.uniovi.es] > On Wed, Sep 09, 2015 at 07:19:58AM +0100, Peter Jarowski peterjarowski### > gmail.com wrote: > > Thanks for the snarky comment it highlights an important point. I am > really > > not interested in methodology for this present work and neither is > > industry. They care about prediction and having it fast. I see level > nerds > > as being a barrier to a better interaction between theory and experimen= t. > > So, people, if you have HF/sto-3g calcs that do the job, I want to know= . > > Peter, > > Your remark points to a important quastion about the role of theory > in science, and particularly in scientific simulation. > > This is a debatable subject, certainly, but my opinion is that the > objective of theory is not reproducing experiments. Nothing surpasses > experimental measurement on that. The role of theory is insight on > understanding what experiments produce and what influences the > experimental properties. > > You point to HF/sto-3g calcs as a good example of demod=C3=A9 techniques = that > can be useful for a purpose. I point to the H=C3=BCckel and extended-H=C3= =BCckel > techniques that were used by a Nobel prize school: Roald Hoffmann. > > Good luck in your chase for heroic examples of theoretical chemistry > examples, > V=C3=ADctor > -- > . . "In science a person can be convinced by a good argument. > / `' \ That is almost impossible in politics or religion" > /(o)(o)\ (Adapted from Carl Sagan) > /`. \/ .'\ "Lo mediocre es peor que lo bueno, pero tambi=C3=A9n es peo= r > / '`'` \ que lo malo, porque la mediocridad no es un grado, es una > | \'`'`/ | actitud" -- Jorge Wasenberg, 2015 > | |'`'`| | (Mediocre is worse than good, but it is also worse than > \/`'`'`'\/ bad, because mediocrity is not a grade, it is an attitude) > =3D=3D=3D(((=3D=3D)))=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D= =3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D+=3D=3D=3D=3D=3D=3D=3D= =3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D > ! Dr.V=C3=ADctor Lua=C3=B1a, in silico chemist & prof. !"I have two kinds= of > problems, > ! Departamento de Qu=C3=ADmica F=C3=ADsica y Anal=C3=ADtica ! the urgent = and the > important. > ! Universidad de Oviedo, 33006-Oviedo, Spain ! The urgent are not > important, > ! e-mail: victor###fluor.quimica.uniovi.es ! and the important are > never > ! phone: +34-985-103491 fax: +34-985-103125 ! urgent. > +--------------------------------------------+ (Dwight D. > Eisenhower) > GroupPage : http://azufre.quimica.uniovi.es/ > > > > -=3D This is automatically added to each message by the mailing script = =3D-> > > --001a11c3b9087406e8051f54a93b Content-Type: text/html; charset=UTF-8 Content-Transfer-Encoding: quoted-printable

Hi Victor:

Very much= agreed. I remind readers that I was looking for cases where theory predict= ed something that had not been experimentally performed and then was later = verified by experiment. Reproducing experiment with theory is useful for ve= rification, but doesn't go much beyond that.

I would argu= e though that theory can do something experiment can not: it can provide &q= uot;error-less" results. More specifically, experiments present so man= y confounds, known and unknown, whereas theory can model the heart of the m= atter. Heats of formation, for example, may be more accurate and more readi= ly comparable by very robust theory versus trolling the literature for thes= e data derived under varied conditions, at various times, and using differe= nt approaches.

So lets keep them coming and later on I will su= mmarize what was sent to me here and on linkedin/researchgate and see what = we all think.

Best Regards,

Peter

On Wed, Sep 9, 2015 at = 3:28 PM, V=C3=ADctor Lua=C3=B1a Cabal victora/fluor.quimica.uniovi.es <owner-chemistry[-]ccl.net> wrote:

Sent to CCL by: =3D?iso-8859-1?Q?V=3DEDctor_Lua=3DF1a?=3D Cabal [victor:+:<= a href=3D"http://fluor.quimica.uniovi.es" rel=3D"noreferrer" target=3D"_bla= nk">fluor.quimica.uniovi.es]
On Wed, Sep 09, 2015 at 07:19:58AM +0100, Peter Jarowski peterjarowski###gmail.com wrote:
> Thanks for the snarky comment it highlights an important point. I am r= eally
> not interested in methodology for this present work and neither is
> industry. They care about prediction and having it fast. I see level n= erds
> as being a barrier to a better interaction between theory and experime= nt.
> So, people, if you have HF/sto-3g calcs that do the job, I want to kno= w.

Peter,

Your remark points to a important quastion about the role of theory
in science, and particularly in scientific simulation.

This is a debatable subject, certainly, but my opinion is that the
objective of theory is not reproducing experiments. Nothing surpasses
experimental measurement on that. The role of theory is insight on
understanding what experiments produce and what influences the
experimental properties.

You point to HF/sto-3g calcs as a good example of demod=C3=A9 techniques th= at
can be useful for a purpose. I point to the H=C3=BCckel and extended-H=C3= =BCckel
techniques that were used by a Nobel prize school: Roald Hoffmann.

Good luck in your chase for heroic examples of theoretical chemistry
examples,
=C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0V=C3=ADctor
--
=C2=A0 =C2=A0 =C2=A0.=C2=A0 .=C2=A0 =C2=A0 "In science a person can be= convinced by a good argument.
=C2=A0 =C2=A0 / `' \=C2=A0 =C2=A0That is almost impossible in politics = or religion"
=C2=A0 =C2=A0/(o)(o)\=C2=A0 (Adapted from Carl Sagan)
=C2=A0 /`. \/ .'\=C2=A0 "Lo mediocre es peor que lo bueno, pero ta= mbi=C3=A9n es peor
=C2=A0/=C2=A0 =C2=A0'`'`=C2=A0 =C2=A0\ que lo malo, porque la medio= cridad no es un grado, es una
=C2=A0|=C2=A0 \'`'`/=C2=A0 | actitud" -- Jorge Wasenberg, 2015=
=C2=A0|=C2=A0 |'`'`|=C2=A0 | (Mediocre is worse than good, but it i= s also worse than
=C2=A0 \/`'`'`'\/=C2=A0 bad, because mediocrity is not a grade,= it is an attitude)
=3D=3D=3D(((=3D=3D)))=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D= =3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D+=3D=3D=3D=3D=3D=3D=3D=3D= =3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D
! Dr.V=C3=ADctor Lua=C3=B1a, in silico chemist & prof. !"I have tw= o kinds of problems,
! Departamento de Qu=C3=ADmica F=C3=ADsica y Anal=C3=ADtica ! the urgent an= d the important.
! Universidad de Oviedo, 33006-Oviedo, Spain ! The urgent are not important= ,
! e-mail:=C2=A0 =C2=A0victor###fluor.quimica.uniovi.es=C2=A0 =C2= =A0! and the important are never
! phone: +34-985-10= 3491=C2=A0 fax: +34-985-103125 ! urgent.
+--------------------------------------------+=C2=A0 =C2=A0 =C2=A0 =C2=A0 (= Dwight D. Eisenhower)
=C2=A0GroupPage : http://azufre.quimica.uniovi.es/

-=3D This is automatically added to each message by the mailing script =3D-=
E-mail to subscribers: CHEMISTRY[-]ccl.n= et or use:
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--001a11c3b9087406e8051f54a93b-- From owner-chemistry@ccl.net Wed Sep 9 18:08:00 2015 From: "darren.rhodes darren.rhodes^gmail.com" To: CCL Subject: CCL: Case Studies of QM Computational Chemistry in Reactivity Message-Id: <-51685-150909160128-9842-bAryKcaXWvkPKcgDcn2Q5w[A]server.ccl.net> X-Original-From: "darren.rhodes" Content-Type: text/plain; charset=UTF-8 Date: Wed, 9 Sep 2015 21:00:52 +0100 MIME-Version: 1.0 Sent to CCL by: "darren.rhodes" [darren.rhodes*|*gmail.com] Hi Peter If you broaden your criteria to include NMR prediction (I'm thinking of Goodman's work - http://www-jmg.ch.cam.ac.uk/tools/nmr/DP4/ ) you may get some more responses. Very interesting thread you've started ... a bit disappointing there aren't more examples coming to light but commercial confidentiality obviously causes difficulties. All the best Darren. On 9 September 2015 at 15:31, Susi Lehtola susi.lehtola_-_alumni.helsinki.fi wrote: > > Sent to CCL by: Susi Lehtola [susi.lehtola:+:alumni.helsinki.fi] > On 09/08/2015 11:19 PM, Peter Jarowski peterjarowski###gmail.com wrote: >> >> Hello Susi, >> >> Thanks for the snarky comment it highlights an important point. I am >> really >> not interested in methodology for this present work and neither is >> industry. They care about prediction and having it fast. I see level nerds >> as being a barrier to a better interaction between theory and experiment. >> So, people, if you have HF/sto-3g calcs that do the job, I want to know. > > > My pleasure ;) > > However, 6-31G*/B3LYP is seen much too often in experimental papers, even > for systems where a much higher quality calculation could be done routinely > without problems. > > Way too many people still see 6-31G*/B3LYP as current state-of-the-art, > although this has not been the case for at least a decade. Especially > appalling is the case where a discrepancies are seen between experiment and > 6-31G*/B3LYP theory, but no effort is put into seeing how wrong the latter > result is. > > After all, 6-31G* is a minimalistic basis set, far from the basis set limit. > It has S=P exponents that were useful in the 1980s because integral > evaluation was in its infancy and couldn't handle polarization functions all > that well. > > B3LYP is a functional from the mid-90s. Much more accurate functionals have > been developed in the past 20 years, with a comparable or slightly larger > cost. > > For instance, Jensen's pc-2 basis set is roughly two times larger than > 6-31G*, but already gives highly accurate results with respect to the basis > set limit. > > A modern range-separated hybrid functional costs roughly twice as much as > B3LYP, but with significantly less self-interaction error. You can also do > van der Waals type interactions in ab initio style today, using e.g. > functionals that build on the VV10 model [Vydrov and van Voorhis, JCP 133, > 244103 (2010)]. The evaluation of VV10 may add a noticeable increase in the > compute time for small systems, but for larger ones VV10 is basically free > compared to the evaluation of exact exchange. > > One of the most accurate functionals today is wB97X-V [Mardirossian and > Head-Gordon, PCCP 16, 9904 (2014)], which is a range separated hybrid > including VV10 non-local correlation, and performs extremely well in a wide > variety of systems. The only two things that are still a problem for modern > functionals like wB97X-V are > 1) systems with large sensitivity to self-interaction error > 2) systems that exhibit strong correlation > and out of these no 2) is outside the scope of Kohn-Sham DFT [Kurzweil et > al, Mol Phys 107, 2103 (2009)]. > -- > ----------------------------------------------------------------------- > Mr. Susi Lehtola, PhD Chemist Postdoctoral Fellow > susi.lehtola .. alumni.helsinki.fi Lawrence Berkeley National Laboratory > http://www.helsinki.fi/~jzlehtol USA > -----------------------------------------------------------------------http://www.ccl.net/chemistry/sub_unsub.shtmlConferences: > http://server.ccl.net/chemistry/announcements/conferences/> > -- "I have no doubt that if a party creates and sends an electronically created document then he will be treated as having signed it to the same extent that he would in law be treated as having signed a hard copy of the same document. The fact that the document is created electronically as opposed to as a hard copy can make no difference." Pelling J in Mehta v J Pereira Fernandes SA [2006] EWHC 813 (Ch) Key ID:- 0xB76FE0B9 http://pgpkeys.mit.edu:11371/ From owner-chemistry@ccl.net Wed Sep 9 21:33:00 2015 From: "Tobias Schwabe schwabe__zbh.uni-hamburg.de" To: CCL Subject: CCL: Case Studies of QM Computational Chemistry in Reactivity Message-Id: <-51686-150909212516-9273-LhHtfAj2o+ys7OPcWSvjKQ!^!server.ccl.net> X-Original-From: Tobias Schwabe Content-Transfer-Encoding: 8bit Content-Type: text/plain; charset=utf-8; format=flowed Date: Thu, 10 Sep 2015 11:24:27 +1000 MIME-Version: 1.0 Sent to CCL by: Tobias Schwabe [schwabe++zbh.uni-hamburg.de] Okay, maybe it'd be best to get back to topic. Luckily, some people already did the work for us and reviewed quantum chemistry applications with industrial relevance. For who are interested, you might find this article helpful: Peter Deglmann, Ansgar SchÃ¤fer, and Christian Lennartz, "Application of Quantum Calculations in the Chemical Industryâ€”An Overview", International Journal of Quantum Chemistry 2015, 115, 107â€“136 http://dx.doi.org/10.1002/qua.24811 They are experts in the field working for BASF. Enjoy reading. Regards, Tobias From owner-chemistry@ccl.net Wed Sep 9 22:07:01 2015 From: "Susi Lehtola susi.lehtola ~~ alumni.helsinki.fi" To: CCL Subject: CCL: Case Studies of QM Computational Chemistry in Reactivity Message-Id: <-51687-150909213155-10694-ZEtApOORuJwEnBkHTw+nog+*+server.ccl.net> X-Original-From: Susi Lehtola Content-Transfer-Encoding: 7bit Content-Type: text/plain; charset=windows-1252; format=flowed Date: Wed, 9 Sep 2015 18:31:00 -0700 MIME-Version: 1.0 Sent to CCL by: Susi Lehtola [susi.lehtola%a%alumni.helsinki.fi] On 09/09/2015 10:28 AM, Tom Albright talbright1234]=[gmail.com wrote: > I wholeheartedly agree with you Victor. Too often I see "how high can I go" rather than a coherent explanation of why I got the results that I did and can I extrapolate this "understanding" to other examples. And no this is not the '90s. That's simply not true. If you use a crappy method (like 6-31G*/B3LYP really is), then you are in no position to make any claims on why you get the results you get, because you're relying on fortuitous error cancellation between the method and the basis set. You're so far from the basis set limit that you can't make real quantitative judgements whatever the method is you're using. Yes, it's not the 90s, but too many people act like if it were. Computational methods have progressed a whole lot since those days, but still way too many people stick to old habits without so much as an afterthought. -- ----------------------------------------------------------------------- Mr. Susi Lehtola, PhD Chemist Postdoctoral Fellow susi.lehtola%x%alumni.helsinki.fi Lawrence Berkeley National Laboratory http://www.helsinki.fi/~jzlehtol USA -----------------------------------------------------------------------