From owner-chemistry@ccl.net Mon Feb 20 02:57:00 2006 From: "Eric Scerri scerri_-_chem.ucla.edu" To: CCL Subject: CCL: eugen schwarz on orbitals Message-Id: <-30931-060220025544-6227-DOdPtMNg4UTE9qECz8C22w]|[server.ccl.net> X-Original-From: Eric Scerri Content-Type: multipart/alternative; boundary=Apple-Mail-53-1042516110 Date: Sun, 19 Feb 2006 20:49:49 -0800 Mime-Version: 1.0 (Apple Message framework v746.2) Sent to CCL by: Eric Scerri [scerri|*|chem.ucla.edu] --Apple-Mail-53-1042516110 Content-Transfer-Encoding: 7bit Content-Type: text/plain; charset=US-ASCII; delsp=yes; format=flowed Sorry. I assumed it would be in the latest issue. I was sent a proof copy by a colleague. Maybe the next issue? I will check. regards, eric scerri On Feb 19, 2006, at 7:59 PM, Brian Salter-Duke b_duke/aocta4.net.au wrote: > Sent to CCL by: Brian Salter-Duke [b_duke###octa4.net.au] > Eric, > > Could you give us an actual reference? It is not in the latest issue I > can access on the web. > > Regards, Brian. > > On Sun, Feb 19, 2006 at 08:32:53PM -0500, Eric Scerri scerri * > chem.ucla.edu wrote: >> Sent to CCL by: Eric Scerri [scerri:_:chem.ucla.edu] >> >> >> --Apple-Mail-3-872680420 >> Content-Transfer-Encoding: 7bit >> Content-Type: text/plain; >> charset=US-ASCII; >> delsp=yes; >> format=flowed >> >> >> >> I am wondering what list members think about the article on >> observation of orbitals in the latest issue of Angewandte Chemie (Int >> Ed')? >> >> If indeed orbitals can be observed in the various senses that Schwarz >> indicates, how should textbook accounts on the unobservability of >> orbitals be modified? This is not something that the author >> addresses. >> >> regards, >> >> >> >> Dr. Eric Scerri >> Department of Chemistry & Biochemistry, >> Charles Young Drive, >> Los Angeles, >> CA 90095. >> >> 310 206 7443 >> fax: 310 206 2061 >> >> UCLA faculty web page: http://www.chem.ucla.edu/dept/Faculty/ >> scerri/ >> >> Editor of Foundations of Chemistry, >> http://www.springer.com/sgw/cda/frontpage/ >> 0,11855,4-40399-70-35545882- >> detailsPage%253Djournal%257CmostViewedArticles% >> 257CmostViewedArticles, >> 00.html >> >> International Society for the Philosophy of Chemistry, >> http://ispc.sas.upenn.edu/ >> >> >> >> >> >> --Apple-Mail-3-872680420 >> Content-Transfer-Encoding: quoted-printable >> Content-Type: text/html; >> charset=ISO-8859-1 >> >> > space; = >> -khtml-line-break: after-white-space; ">

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I am wondering what list >> members = >> think about the article on observation of orbitals in the latest >> issue = >> of Angewandte Chemie (Int Ed')?

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If indeed orbitals >> can be = >> observed in the various senses that Schwarz indicates, how should = >> textbook accounts on the unobservability of orbitals be modified? >> =A0 = >> This is not something that the author addresses.=A0=A0> DIV>

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regards,

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> class=3D"Apple-style-span" style=3D"border-collapse: separate; = >> border-spacing: 0px 0px; color: rgb(0, 0, 0); font-family: >> Helvetica; = >> font-size: 16px; font-style: normal; font-variant: normal; font- >> weight: = >> normal; letter-spacing: normal; line-height: normal; text-align: >> auto; = >> -khtml-text-decorations-in-effect: none; text-indent: 0px; = >> -apple-text-size-adjust: auto; text-transform: none; orphans: 2; = >> white-space: normal; widows: 2; word-spacing: 0px; ">> class=3D"Apple-style-span" style=3D"border-collapse: separate; = >> border-spacing: 0px 0px; color: rgb(0, 0, 0); font-family: >> Helvetica; = >> font-size: 16px; font-style: normal; font-variant: normal; font- >> weight: = >> normal; letter-spacing: normal; line-height: normal; text-align: >> auto; = >> -khtml-text-decorations-in-effect: none; text-indent: 0px; = >> -apple-text-size-adjust: auto; text-transform: none; orphans: 2; = >> white-space: normal; widows: 2; word-spacing: 0px; ">> class=3D"Apple-style-span" style=3D"border-collapse: separate; = >> border-spacing: 0px 0px; color: rgb(0, 0, 0); font-family: >> Helvetica; = >> font-size: 16px; font-style: normal; font-variant: normal; font- >> weight: = >> normal; letter-spacing: normal; line-height: normal; text-align: >> auto; = >> -khtml-text-decorations-in-effect: none; text-indent: 0px; = >> -apple-text-size-adjust: auto; text-transform: none; orphans: 2; = >> white-space: normal; widows: 2; word-spacing: 0px; ">> class=3D"Apple-style-span" style=3D"border-collapse: separate; = >> border-spacing: 0px 0px; color: rgb(0, 0, 0); font-family: >> Helvetica; = >> font-size: 16px; font-style: normal; font-variant: normal; font- >> weight: = >> normal; letter-spacing: normal; line-height: normal; text-align: >> auto; = >> -khtml-text-decorations-in-effect: none; text-indent: 0px; = >> -apple-text-size-adjust: auto; text-transform: none; orphans: 2; = >> white-space: normal; widows: 2; word-spacing: 0px; ">> class=3D"Apple-style-span" style=3D"border-collapse: separate; = >> border-spacing: 0px 0px; color: rgb(0, 0, 0); font-family: >> Helvetica; = >> font-size: 16px; font-style: normal; font-variant: normal; font- >> weight: = >> normal; letter-spacing: normal; line-height: normal; text-align: >> auto; = >> -khtml-text-decorations-in-effect: none; text-indent: 0px; = >> -apple-text-size-adjust: auto; text-transform: none; orphans: 2; = >> white-space: normal; widows: 2; word-spacing: 0px; ">> class=3D"Apple-style-span" style=3D"border-collapse: separate; = >> border-spacing: 0px 0px; color: rgb(0, 0, 0); font-family: >> Helvetica; = >> font-size: 16px; font-style: normal; font-variant: normal; font- >> weight: = >> normal; letter-spacing: normal; line-height: normal; text-align: >> auto; = >> -khtml-text-decorations-in-effect: none; text-indent: 0px; = >> -apple-text-size-adjust: auto; text-transform: none; orphans: 2; = >> white-space: normal; widows: 2; word-spacing: 0px; ">
Dr. Eric = >> Scerri
Department of Chemistry & = >> Biochemistry,
Charles Young Drive,
Los = >> Angeles,
CA 90095.

> class=3D"khtml-block-placeholder">
310 206 7443> DIV>
fax: = >> 310 206 2061

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UCLA faculty web >> page:=A0=A0=A0= >> > class=3D"Apple-style-span" color=3D"#0021E7">> class=3D"Apple-style-span" style=3D"color: rgb(0, 33, 231); = >> -khtml-text-decorations-in-effect: underline; ">> class=3D"Apple-style-span" style=3D"color: rgb(0, 33, 231); = >> -khtml-text-decorations-in-effect: underline; = >> ">http://www.chem.ucla.edu/dept/Faculty/scerri/> FONT>> DIV>

Editor of = >> Foundations of Chemistry,

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International Society >> for = >> the Philosophy of Chemistry,

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> class=3D"Apple-interchange-newline">> SPAN>> PAN>

= >> >> --Apple-Mail-3-872680420--> >> >> > > -- > Brian Salter-Duke (Brian Duke) b_duke(-)octa4.net.au > Post: 626 Melbourne Rd, Spotswood, VIC, 3015, Australia > Phone 03-93992847. http://members.iinet.net.au/~linden1/brian/ > Honorary Researcher Fellow, Dept. of Medicinal Chemistry, Monash Univ. > > > > -= This is automatically added to each message by the mailing > script =- > To recover the email address of the author of the message, please > change> Conferences: http://server.ccl.net/chemistry/announcements/ > conferences/ > > Search Messages: http://www.ccl.net/htdig (login: ccl, Password: > search)> > -+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+- > +-+-+ > > Dr. Eric Scerri Department of Chemistry & Biochemistry, Charles Young Drive, Los Angeles, CA 90095. 310 206 7443 fax: 310 206 2061 UCLA faculty web page: http://www.chem.ucla.edu/dept/Faculty/scerri/ Editor of Foundations of Chemistry, http://www.springer.com/sgw/cda/frontpage/0,11855,4-40399-70-35545882- detailsPage%253Djournal%257CmostViewedArticles%257CmostViewedArticles, 00.html International Society for the Philosophy of Chemistry, http://ispc.sas.upenn.edu/ --Apple-Mail-53-1042516110 Content-Transfer-Encoding: quoted-printable Content-Type: text/html; charset=ISO-8859-1


Sorry.=A0 I assumed it would be = in the latest issue.=A0 I was sent a proof copy by a colleague.

Maybe the next issue?=A0 I = will check.



regards,
eric = scerri




On Feb 19, = 2006, at 7:59 PM, Brian Salter-Duke b_duke/aocta4.net.au wrote:

Sent to CCL by: Brian Salter-Duke = [b_duke###octa4.net.au]

Could you give us an actual reference? It is not in = the latest issue I
can access on the = web.

Regards, Brian.

On Sun, Feb 19, 2006 at = 08:32:53PM -0500, Eric Scerri scerri * chem.ucla.edu wrote:
=
Sent to CCL by: Eric Scerri = [scerri:_:chem.ucla.edu]


--Apple-Mail-3-872680420
Content-Transfer-Encoding: 7bit
Content-Type: text/plain;
charset=3DUS-ASCII;
delsp=3Dyes;
format=3Dflowed



I am wondering what list members = think about the article on =A0
=A0
Ed')?

If indeed orbitals can be = observed in the various senses that Schwarz =A0
=A0
orbitals be modified?=A0 This is not something that = the author addresses.
regards,



Dr. Eric Scerri
Department of Chemistry & = Biochemistry,
Charles Young Drive,
Los Angeles,
CA = 90095.

310 206 7443
fax: 310 206 = 2061


Editor of Foundations of = Chemistry,
=A0
00.html

International Society for the = Philosophy of Chemistry,





Content-Type: text/html;
charset=3DISO-8859-1

think about the article on = observation of orbitals in the latest issue =3D
of Angewandte Chemie (Int Ed')?<DIV><BR = =3D
observed in = the various senses that Schwarz indicates, how should =3D
textbook accounts on the unobservability of orbitals = be modified?=3DA0 =3D
This is not something that = the author addresses.=3DA0=3DA0</DIV><DIV><BR =3D
border-spacing: 0px 0px; color: = rgb(0, 0, 0); font-family: Helvetica; =3D
normal; letter-spacing: normal; = line-height: normal; text-align: auto; =3D
-apple-text-size-adjust: auto; text-transform: none; = orphans: 2; =3D
white-space: normal; widows: 2; = word-spacing: 0px; "><SPAN =3D
border-spacing: 0px 0px; color: = rgb(0, 0, 0); font-family: Helvetica; =3D
normal; letter-spacing: normal; = line-height: normal; text-align: auto; =3D
-apple-text-size-adjust: auto; text-transform: none; = orphans: 2; =3D
white-space: normal; widows: 2; = word-spacing: 0px; "><SPAN =3D
border-spacing: 0px 0px; color: = rgb(0, 0, 0); font-family: Helvetica; =3D
normal; letter-spacing: normal; = line-height: normal; text-align: auto; =3D
-apple-text-size-adjust: auto; text-transform: none; = orphans: 2; =3D
white-space: normal; widows: 2; = word-spacing: 0px; "><SPAN =3D
border-spacing: 0px 0px; color: = rgb(0, 0, 0); font-family: Helvetica; =3D
normal; letter-spacing: normal; = line-height: normal; text-align: auto; =3D
-apple-text-size-adjust: auto; text-transform: none; = orphans: 2; =3D
white-space: normal; widows: 2; = word-spacing: 0px; "><SPAN =3D
border-spacing: 0px 0px; color: = rgb(0, 0, 0); font-family: Helvetica; =3D
normal; letter-spacing: normal; = line-height: normal; text-align: auto; =3D
-apple-text-size-adjust: auto; text-transform: none; = orphans: 2; =3D
white-space: normal; widows: 2; = word-spacing: 0px; "><SPAN =3D
border-spacing: 0px 0px; color: = rgb(0, 0, 0); font-family: Helvetica; =3D
normal; letter-spacing: normal; = line-height: normal; text-align: auto; =3D
-apple-text-size-adjust: auto; text-transform: none; = orphans: 2; =3D
white-space: normal; widows: 2; = word-spacing: 0px; "><DIV>Dr. Eric =3D
Scerri</DIV><DIV>Department of Chemistry = &amp; =3D
310 206 = 2061</DIV><DIV><BR =3D
class=3D3D"Apple-style-span" = color=3D3D"#0021E7"><SPAN =3D
class=3D3D"Apple-style-span" = style=3D3D"color: rgb(0, 33, 231); =3D
">http://www.chem.ucl= a.edu/dept/Faculty/scerri/</SPAN></SPAN></FONT></= A></=3D
DIV><DIV><BR = class=3D3D"khtml-block-placeholder"></DIV><DIV>Editor of = =3D
Foundations of = Chemistry,</DIV><DIV style=3D3D"margin-top: 0px; =3D
margin-right: 0px; margin-bottom: 0px; margin-left: = 0px; "><A =3D
00.html"><SPAN = class=3D3D"Apple-style-span" style=3D3D"color: rgb(0, 0, =3D
238); -khtml-text-decorations-in-effect: underline; = "><SPAN =3D
class=3D3D"Apple-style-span" = style=3D3D"color: rgb(0, 0, 238); =3D
class=3D3D"Apple-style-span" = style=3D3D"color: rgb(0, 0, 238); =3D
the Philosophy of = Chemistry,</DIV><DIV><A =3D
http://ispc.sas.upenn.edu">http://ispc.sas.upenn.edu</A>= /</DIV><DI=3D
V><BR = class=3D3D"khtml-block-placeholder"></DIV><DIV><BR = =3D
PAN> = </DIV><BR></DIV></BODY></HTML>=3D

=A0



--=A0
=A0=A0 =A0 =A0 =A0 Brian = Salter-Duke (Brian Duke) b_duke(-)octa4.net.au =A0
=A0=A0 =A0 =A0 Post: 626 = Melbourne Rd, Spotswood, VIC, 3015, Australia
Honorary = Researcher Fellow, Dept. of Medicinal Chemistry, Monash Univ.



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=

Dr. Eric = Scerri
Department of Chemistry & = Biochemistry,
Charles Young Drive,
Los = Angeles,
CA 90095.

310 206 7443
fax: = 310 206 2061

UCLA faculty web page:=A0=A0=A0=




= --Apple-Mail-53-1042516110-- From owner-chemistry@ccl.net Mon Feb 20 04:07:00 2006 From: "Eric Scerri scerri\a/chem.ucla.edu" To: CCL Subject: CCL: eugen schwarz on orbitals Message-Id: <-30933-060220032245-20214-zTV5VF5YMz6Wvdq1m3XSMQ###server.ccl.net> X-Original-From: Eric Scerri Content-Type: multipart/alternative; boundary=Apple-Mail-72-1055284807 Date: Mon, 20 Feb 2006 00:22:38 -0800 Mime-Version: 1.0 (Apple Message framework v746.2) Sent to CCL by: Eric Scerri [scerri[#]chem.ucla.edu] --Apple-Mail-72-1055284807 Content-Transfer-Encoding: 7bit Content-Type: text/plain; charset=US-ASCII; delsp=yes; format=flowed It will appear in the next issue, 10/2006 under the section entitled, Essays. The table of contents for this issue is previewed in the current issue. regards, eric scerri On Feb 19, 2006, at 7:59 PM, Brian Salter-Duke b_duke/aocta4.net.au wrote: > Sent to CCL by: Brian Salter-Duke [b_duke###octa4.net.au] > Eric, > > Could you give us an actual reference? It is not in the latest issue I > can access on the web. > > Regards, Brian. > --Apple-Mail-72-1055284807 Content-Transfer-Encoding: quoted-printable Content-Type: text/html; charset=ISO-8859-1


It will appear in the next = issue,=A0 10/2006=A0 =A0under the section entitled,=A0 =A0

Essays.
The table of contents for = this issue is previewed in the current issue.




regards,
eric = scerri




On Feb 19, 2006, at 7:59 = PM, Brian Salter-Duke b_duke/aocta4.net.au wrote:

Sent to CCL by: Brian Salter-Duke = [b_duke###octa4.net.au]

Could you give us an actual reference? It is not in = the latest issue I
can access on the = web.

Regards, Brian.

= --Apple-Mail-72-1055284807-- From owner-chemistry@ccl.net Mon Feb 20 03:31:23 2006 From: "Mikael Johansson mikael.johansson^helsinki.fi" To: CCL Subject: CCL: eugen schwarz on orbitals Message-Id: <-30932-060220025739-6862-7ybO2v8PY+5DtRaY50pQDQ[]server.ccl.net> X-Original-From: Mikael Johansson Content-Type: TEXT/PLAIN; charset=US-ASCII; format=flowed Date: Mon, 20 Feb 2006 09:21:29 +0200 (EET) MIME-Version: 1.0 Sent to CCL by: Mikael Johansson [mikael.johansson~~helsinki.fi] Hello Brian and All! On Sun, 19 Feb 2006, Brian Salter-Duke b_duke/aocta4.net.au wrote: > Could you give us an actual reference? It is not in the latest issue I > can access on the web. It's in the early view section. The following link works for me right now at least: http://www3.interscience.wiley.com/cgi-bin/abstract/112404061/ABSTRACT The title is "Measuring Orbitals: Provocation or Reality?". Looks line an interesting read. Have a nice day, Mikael J. http://www.helsinki.fi/~mpjohans/ From owner-chemistry@ccl.net Mon Feb 20 04:53:02 2006 From: "Pablo Echenique pnique..unizar.es" To: CCL Subject: CCL: Methods and basis sets comparison Message-Id: <-30934-060220045124-4553-Dz/DSR6zbs1p1wuH+j+Abw(-)server.ccl.net> X-Original-From: "Pablo Echenique" Date: Mon, 20 Feb 2006 04:51:22 -0500 Sent to CCL by: "Pablo Echenique" [pnique(a)unizar.es] Hello all, I am planning to carry out an extensive computational study of the accuracy of different methods (HF, MP2 and B3LYP) and different basis sets in the description of the conformational properties of small flexible peptides. I would thank very much any one that could suggest me references in which methods and basis sets are extensively compared (even if it is done on different molecules, i.e., which are not peptides). Thank you very much in advance, Pablo Echenique ------------------------------------ Pablo Echenique Robba Departamento de Fisica Teorica & Instituto de Biocomputacion y Fisica de los Sistemas Complejos BIFI Universidad de Zaragoza 50009 Zaragoza Spain Tel.: +34 976761260 E-mail: pnique*o*unizar.es ------------------------------------ From owner-chemistry@ccl.net Mon Feb 20 05:48:36 2006 From: "Tanja van Mourik t.vanmourik-#-ucl.ac.uk" To: CCL Subject: CCL: Methods and basis sets comparison Message-Id: <-30935-060220054539-5094-ZWRW2t5blh62dMU1PTqiKw..server.ccl.net> X-Original-From: Tanja van Mourik Content-Transfer-Encoding: 7bit Content-Type: text/plain; charset=us-ascii Date: Mon, 20 Feb 2006 10:44:18 +0000 (GMT) MIME-Version: 1.0 Sent to CCL by: Tanja van Mourik [t.vanmourik.(a).ucl.ac.uk] Dear Pablo, > I am planning to carry out an extensive computational study of the accuracy of different methods (HF, MP2 and B3LYP) and different basis sets in the description of the conformational properties of small flexible peptides. I would thank very much any one that could suggest me references in which methods and basis sets are extensively compared (even if it is done on different molecules, i.e., which are not peptides). > We have recently studied the conformation of a dipeptide, Tyr-Gly, and found that for some conformers MP2 and B3LYP give strikingly different structures, see: "The structure of the gas-phase tyrosine-glycine dipeptide" D. Toroz and T. van Mourik, Mol. Phys. 104, 559-570 (2006). "Molecular conformations and relative stabilities can be as demanding of electronic structure method as intermolecular calculations" T. van Mourik, P. Panagiotis and S.L. Price, J. Phys. Chem. A 110, 8-12 (2006). The following papers on flexible neurotransmitters may also be of interest: T. van Mourik and L.E.V. Emson, Phys. Chem. Chem. Phys. 4, 5863-5871 (2002) (contains some HF/B3LYP comparison of different serotonin conformers) T. van Mourik, Chem. Phys. Lett. 414, 365-368 (2005) (relative stability of the two most stable noradrenaline conformers differs for MP2 anfd B3LYP). Hope this helps, Tanja -- ================================================================= Tanja van Mourik Royal Society University Research Fellow Chemistry Department University College London phone: +44 (0)20-7679-4663 20 Gordon Street e-mail: work: T.vanMourik(a)ucl.ac.uk London WC1H 0AJ, UK home: tanja(a)van-mourik.me.uk http://www.chem.ucl.ac.uk/people/vanmourik/index.html !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! ! Please note new address from 1 April 2006 ! ! email: tanja.vanmourik(a)st-andrews.ac.uk ! ================================================================= From owner-chemistry@ccl.net Mon Feb 20 08:09:00 2006 From: "Arvydas Tamulis tamulis^^mserv.itpa.lt" To: CCL Subject: CCL: References on electronic structure of [Ru(bipyridine)3]+2 Message-Id: <-30936-060219143926-21419-tj+775NnS7/RvPy7U9iqNg::server.ccl.net> X-Original-From: Arvydas Tamulis Content-Type: TEXT/PLAIN; charset=US-ASCII; format=flowed Date: Sun, 19 Feb 2006 21:39:03 +0200 (EET) MIME-Version: 1.0 Sent to CCL by: Arvydas Tamulis [tamulis^^mserv.itpa.lt] Dear Colleagues, Would you please to send me references on electronic structure investigations of [Ru(bipyridine)3)]+2 molecule using quantum mechanical electron correlations methods (including DFT). I am using DFT B3LYP/LanL2DZ model and can share with my preliminary results. With best regards, Arvydas Tamulis From owner-chemistry@ccl.net Mon Feb 20 08:43:00 2006 From: "Roger Kevin Robinson r.robinson .. imperial.ac.uk" To: CCL Subject: CCL: G3B3 Atomization Energy Methane Message-Id: <-30937-060220082108-16549-Sw5dK4FzV/WR+ShAlIIT1A[a]server.ccl.net> X-Original-From: Roger Kevin Robinson Content-Transfer-Encoding: 7bit Content-Type: text/plain; charset=ISO-8859-1; format=flowed Date: Mon, 20 Feb 2006 13:24:10 +0000 MIME-Version: 1.0 Sent to CCL by: Roger Kevin Robinson [r.robinson,,imperial.ac.uk] Hi, I've asked about this before but i still seem to be having some trouble. Im just using Methane as an example. Using G3B3 methods. At 298K I get Name G3-Energy(G3B3) ZPE C -37.778738 H -0.499671 CH4 -40.455401 0.043410 Using this values to calculate Atomization Energy = (-37.778738 + 4* -0.499671) - -40.455401 - 0.043410= 0.634569 = 1666.06091 kJ/mol this fits in well with an experimental value of 1663.3 to calculate Enthalpy of formation you need the atomization Energy at 0K as far as im aware. Right at 0K Name G3(0K) - (G3B3) ZPE C -37.780154 H -0.501087 CH4 -40.458277 0.043410 = ( -37.780154 +4 * -0.499671) - -40.455401 - 0.043410 = 0.630365 = 1655.02331. But the experimental value is 1642.27 Does any one know where im making the mistake ? Thanks Roger From owner-chemistry@ccl.net Mon Feb 20 09:40:00 2006 From: "Tony Yuan TYuan~~cambridgesoft.com" To: CCL Subject: CCL:G: NMR database Message-Id: <-30938-060220093736-27278-aMkNXv3htusr6T1unkjBag---server.ccl.net> X-Original-From: "Tony Yuan" Content-class: urn:content-classes:message Content-Transfer-Encoding: 8bit Content-Type: text/plain; charset="us-ascii" Date: Mon, 20 Feb 2006 08:37:13 -0500 MIME-Version: 1.0 Sent to CCL by: "Tony Yuan" [TYuan()cambridgesoft.com] FYI: http://forum.chemih.com/forum/view.asp?aid=607 -----Original Message----- > From: owner-chemistry a ccl.net [mailto:owner-chemistry a ccl.net] Sent: Wednesday, February 15, 2006 12:47 PM To: Tony Yuan Subject: CCL:G: NMR database Sent to CCL by: "Wayne Steinmetz" [WES04747-*-pomona.edu] SDBS (http://www.aist.go.jp/RIODB/SDBS/cgi-bin/cre_index.cgi) maintains an excellent database of spectra. For calculations, the gold standard is Gaussian. However, I have found that the current version of Spartan does an excellent job of calculating carbon-13 and proton chemical shifts for medium-sized organic molecules. Wayne E. Steinmetz Carnegie Professor of Chemistry Woodbadge Course Director Chemistry Department Pomona College 645 North College Avenue Claremont, California 91711-6338 USA phone: 1-909-621-8447 FAX: 1-909-707-7726 Email: wsteinmetz|pomona.edu WWW: pages.pomona.edu/~wsteinmetz -----Original Message----- > From: owner-chemistry|ccl.net [mailto:owner-chemistry|ccl.net] Sent: Tuesday, February 14, 2006 10:29 PM To: Wayne Steinmetz Subject: CCL: NMR database Sent to CCL by: "Fuji yama" [yamafuji6-x-yahoo.com] Hello All, I wanted to compare the NMR of some of the ligands. Can any one tell me where can I find the NMR database (Both Theoretical and Experimental). Is there any user friendly software on windows platform to calculate the Proton, 13C and 2D NMR? Thank you very much. Sincerely, Fuji.http://www.ccl.net/cgi-bin/ccl/send_ccl_messagehttp://www.ccl.net/c hemistry/sub_unsub.shtmlhttp://www.ccl.net/spammers.txt----------------- -------------------------------------------- This message has been scanned by Postini anti-virus software.http://www.ccl.net/cgi-bin/ccl/send_ccl_messagehttp://www.ccl.net/chemistry/sub_unsub.shtmlhttp://www.ccl.net/spammers.txt From owner-chemistry@ccl.net Mon Feb 20 12:02:01 2006 From: "Miklos Kertesz kertesz**georgetown.edu" To: CCL Subject: CCL: Methods and basis sets comparison Message-Id: <-30939-060220105832-20014-skPRL3w4qbbqkNcaM5MC5g[A]server.ccl.net> X-Original-From: Miklos Kertesz Content-Language: en Content-Type: multipart/mixed; boundary="--5ce1f9243fb6336" Date: Mon, 20 Feb 2006 08:38:52 -0500 MIME-Version: 1.0 Sent to CCL by: Miklos Kertesz [kertesz#,#georgetown.edu] This is a multi-part message in MIME format. ----5ce1f9243fb6336 Content-Type: text/plain; charset=us-ascii Content-Disposition: inline Content-Transfer-Encoding: 7bit Check papers by Alfred Karpfen with various co-authors. The Web of Science is a good starting point. -- Miklos Kertesz Professor of Chemistry Georgetown University 606 Reiss Washington DC 20057-1227 Office: 202-687-5761 Fax: 202-687-6209 Email: kertesz,georgetown.edu http://www.georgetown.edu/departments/chemistry/faculty/kertesz.htm Pablo Echenique pnique..unizar.es wrote: > Sent to CCL by: "Pablo Echenique" [pnique(a)unizar.es] > Hello all, > > I am planning to carry out an extensive computational study of the accuracy of different methods (HF, MP2 and B3LYP) and different basis sets in the description of the conformational properties of small flexible peptides. I would thank very much any one that could suggest me references in which methods and basis sets are extensively compared (even if it is done on different molecules, i.e., which are not peptides). > > Thank you very much in advance, > > Pablo Echenique > > ------------------------------------ > Pablo Echenique Robba > > Departamento de Fisica Teorica > & > Instituto de Biocomputacion y > Fisica de los Sistemas Complejos > BIFI > > Universidad de Zaragoza > 50009 Zaragoza > Spain > > Tel.: +34 976761260 > E-mail: pnique[#]unizar.es > ------------------------------------> > > ----5ce1f9243fb6336 Content-Type: text/x-vcard; name="kertesz.vcf"; charset="windows-1252" Content-Disposition: attachment; filename="kertesz.vcf" Content-Description: Card for Miklos Kertesz Content-Transfer-Encoding: quoted-printable begin=3Avcard n=3AKertesz=3BMiklos fn=3AMiklos Kertesz tel=3Bfax=3A202-687-6209 tel=3Bwork=3A202-687-5761 url=3Ahttp=3A//www=2Egeorgetown=2Eedu/departments/chemistry/faculty/kerte= sz=2Ehtm org=3AGeorgetown University=3BChemistry version=3A2=2E1 email=3Binternet=3Akertesz=40georgetown=2Eedu title=3AProfessor = end=3Avcard ----5ce1f9243fb6336-- From owner-chemistry@ccl.net Mon Feb 20 13:18:00 2006 From: "Goedele Roos groos|a|vub.ac.be" To: CCL Subject: CCL: 6-31G basis set Message-Id: <-30940-060220131645-24695-/o8P1ibP953CLaG6M4rXRw a server.ccl.net> X-Original-From: Goedele Roos Date: Mon, 20 Feb 2006 19:16:38 +0100 (CET) Sent to CCL by: Goedele Roos [groos]^[vub.ac.be] Dear all, I've read somewhere that the 6-31G basis set in combination with HF is a bit tricky and that one can better use a 6-31G** basis set. Is thit correct? And what is the reason therefore? Thanks in advance for considering my question, Best regards, goedele Drs. Goedele Roos Dienst Algemene Chemie (ALGC) Vrije Universiteit Brussel (VUB) Pleinlaan 2 B-1050 Brussels Tel: 0032-2-629 35 16 Fax: 0032-2-629 33 17 From owner-chemistry@ccl.net Mon Feb 20 14:01:01 2006 From: "Mikael Johansson mikael.johansson::helsinki.fi" To: CCL Subject: CCL: 6-31G basis set Message-Id: <-30941-060220135618-15158-9NwgrM30ql1TaCwCoLOVlQ()server.ccl.net> X-Original-From: Mikael Johansson Content-Type: TEXT/PLAIN; charset=US-ASCII; format=flowed Date: Mon, 20 Feb 2006 20:56:07 +0200 (EET) MIME-Version: 1.0 Sent to CCL by: Mikael Johansson [mikael.johansson[-]helsinki.fi] Hello! On Mon, 20 Feb 2006, Goedele Roos groos|a|vub.ac.be wrote: > I've read somewhere that the 6-31G basis set in combination with HF is > a bit tricky and that one can better use a 6-31G** basis set. Is thit > correct? And what is the reason therefore? In short, 6-31G** is larger and thus stands a better chance of describing the Hartree-Fock wave function correctly. I recommend Frank Jensen's book "Introduction to Computational Chemistry", it's quite good: http://bogense.chem.sdu.dk/~icc/ Have a nice day, Mikael J. http://www.helsinki.fi/~mpjohans/ From owner-chemistry@ccl.net Mon Feb 20 14:39:00 2006 From: "Close, David M. CLOSED(!)mail.etsu.edu" To: CCL Subject: CCL: 6-31G basis set Message-Id: <-30942-060220143626-5272-I+IpyBfPZJZgo7cmBTvyQA(_)server.ccl.net> X-Original-From: "Close, David M." Content-class: urn:content-classes:message Content-Transfer-Encoding: 8bit Content-Type: text/plain; charset="us-ascii" Date: Mon, 20 Feb 2006 13:34:17 -0500 MIME-Version: 1.0 Sent to CCL by: "Close, David M." [CLOSED|mail.etsu.edu] Goedele: A lot depends on what you are working on. There have been discussions in this group just the past week on examples of where adding the diffuse functions can cause troubles. There is enough expertise in the CCL to answer just about any question on appropriate basis sets. However you must first specify what you are trying to accomplish. Regards, Dave Close. -----Original Message----- > From: owner-chemistry{}ccl.net [mailto:owner-chemistry{}ccl.net] Sent: Monday, February 20, 2006 1:18 PM To: Close, David M. Subject: CCL: 6-31G basis set Sent to CCL by: Goedele Roos [groos]^[vub.ac.be] Dear all, I've read somewhere that the 6-31G basis set in combination with HF is a bit tricky and that one can better use a 6-31G** basis set. Is thit correct? And what is the reason therefore? Thanks in advance for considering my question, Best regards, goedele Drs. Goedele Roos Dienst Algemene Chemie (ALGC) Vrije Universiteit Brussel (VUB) Pleinlaan 2 B-1050 Brussels Tel: 0032-2-629 35 16 Fax: 0032-2-629 33 17http://www.ccl.net/cgi-bin/ccl/send_ccl_messagehttp://www.ccl.net/chemistry/sub_unsub.shtmlhttp://www.ccl.net/spammers.txt From owner-chemistry@ccl.net Mon Feb 20 15:41:01 2006 From: "Stefan Grimme grimmes:_:uni-muenster.de" To: CCL Subject: CCL:G: Methods and basis sets comparison Message-Id: <-30943-060220111301-21286-z5416we8AKZrGd2PVZhJXA=server.ccl.net> X-Original-From: Stefan Grimme Content-Transfer-Encoding: 8bit Content-Type: text/plain; charset=iso-8859-1 Date: Mon, 20 Feb 2006 16:07:57 +0100 (MEZ) MIME-Version: 1.0 Sent to CCL by: Stefan Grimme [grimmes*|*uni-muenster.de] > I am planning to carry out an extensive computational study of the > accuracy of different methods (HF, MP2 and B3LYP) and different basis > sets in the description of the conformational properties of small > flexible peptides. I would thank very much any one that could suggest > me references in which methods and basis sets are extensively > compared (even if it is done on different molecules, i.e., which are > not peptides). Dear Pablo, in addition to MP2 you should try also SCS-MP2 with improves in almost all respects on MP2, see "Improved second-order Møller-Plesset pertubation theory by seperate scaling of parallel- and antiparallel-spin pair correlation energies", J. Chem. Phys., 118, (2003), 9095-9102. In particular the systematic overestimation of van der Waals interactions in larger (unsaturated) systems by MP2 is corrected for. These interactions are also important in intramolecular situations, see e.g. "The importance of inter- and intramolecular van der Waals interactions in organic reactions: the dimerization of anthracene revisited", Angew. Chem. Int. Ed. 45, (2006), 625-629. SCS-MP2 energies can be calculated directly from a standard Gaussian output. Best wishes Stefan _________________________________________________________ Prof. Dr. Stefan Grimme Organisch-Chemisches Institut (Abt. Theoretische Chemie) Westfaelische Wilhelms-Universitaet, Corrensstrasse 40 D-48149 Muenster, Tel (+49)-251-83 36512/33241/36515(Fax) Email:grimmes-*-uni-muenster.de http://www.uni-muenster.de/Chemie/OC/research/grimme/ _________________________________________________________ From owner-chemistry@ccl.net Mon Feb 20 17:02:00 2006 From: "HAO JIANG jianghao-.-pitt.edu" To: CCL Subject: CCL: Help on Molecular Dynamics software Message-Id: <-30944-060220170039-25719-vv5UfkjHHTB0ToC2o2Ctrw[a]server.ccl.net> X-Original-From: "HAO JIANG" Date: Mon, 20 Feb 2006 17:00:33 -0500 Sent to CCL by: "HAO JIANG" [jianghao%%pitt.edu] Hi, all, Thanks a lot for all replies to my questions. Here please allow me to make a summary of the information that I got: 1. We can make movies for TINKER trajectory (.arc) files using the VMD software (version 1.8.3 or later). The web page of VMD is http://www.ks.uiuc.edu/Research/vmd/. 2. Parallel computing using the AMOEBA polarizable force field will be supported in AMBER v9 (http://amber.scripps.edu), which is scheduled for release at the end of March. Thanks again for all the help! Regards, Hao Jiang Department of Chemistry University of Pittsburgh From owner-chemistry@ccl.net Mon Feb 20 19:32:01 2006 From: "John Bushnell bushnell,+,chem.ucsb.edu" To: CCL Subject: CCL: G3B3 Atomization Energy Methane Message-Id: <-30945-060220192833-21829-2KJSg84hV53WOP19UJg3cw]|[server.ccl.net> X-Original-From: John Bushnell Content-Type: TEXT/PLAIN; charset=US-ASCII; format=flowed Date: Mon, 20 Feb 2006 15:19:16 -0800 (PST) MIME-Version: 1.0 Sent to CCL by: John Bushnell [bushnell**chem.ucsb.edu] I'm not at all familiar with the "G3B3" method, but right off hand I would think that this is very good agreement with experiment. You show an error of 13 kJ/mol at zero K. But the calculation involves the difference of some very large numbers. The difference of only 3 kJ/mol at 298 K seems fortuitously small in fact. If enthalpies of formation could be routinely calculated to this accuracy, we wouldn't have to do so many experiments. :-) Just my offhand impression... - John On Mon, 20 Feb 2006, Roger Kevin Robinson r.robinson .. imperial.ac.uk wrote: > Sent to CCL by: Roger Kevin Robinson [r.robinson,,imperial.ac.uk] > Hi, > > I've asked about this before but i still seem to be having some > trouble. Im just using Methane as an example. > > Using G3B3 methods. > > At 298K I get > > Name G3-Energy(G3B3) ZPE > > C -37.778738 > > H -0.499671 > > CH4 -40.455401 0.043410 > > Using this values to calculate Atomization Energy > > = (-37.778738 + 4* -0.499671) - -40.455401 - 0.043410= 0.634569 = > 1666.06091 kJ/mol > > this fits in well with an experimental value of 1663.3 > > to calculate Enthalpy of formation you need the atomization Energy at 0K > as far as im aware. > > Right at 0K > > > Name G3(0K) - (G3B3) ZPE > > C -37.780154 > > H -0.501087 > > CH4 -40.458277 0.043410 > > = ( -37.780154 +4 * -0.499671) - -40.455401 - 0.043410 = 0.630365 = > 1655.02331. > > But the experimental value is 1642.27 > > Does any one know where im making the mistake ? > > Thanks Roger > From owner-chemistry@ccl.net Mon Feb 20 23:03:00 2006 From: "Xiaodong Zhang xdzhang(_)chem.ucsb.edu" To: CCL Subject: CCL: parameters of mTHF Message-Id: <-30946-060220210154-15094-SDvZVsytDiydtjwew10+SA|server.ccl.net> X-Original-From: Xiaodong Zhang Content-Transfer-Encoding: 7bit Content-Type: text/plain; charset=US-ASCII; format=flowed Date: Mon, 20 Feb 2006 17:11:30 -0800 Mime-Version: 1.0 (Apple Message framework v623) Sent to CCL by: Xiaodong Zhang [xdzhang:_:chem.ucsb.edu] Hi, Do you have the parameters of mTHF (N5,N10-methylenetetrahydrofolate) for MD simualtions? or tell me how to obtain these parameter with very simple method? Thanks, Xiaodong