From owner-chemistry@ccl.net Tue Jun 26 00:49:00 2012 From: "Salomon Turgman Cohen sturgman|gmail.com" To: CCL Subject: CCL:G: Methyl Carbamic Acid, collinearity and relaxed PES Message-Id: <-47131-120625214747-22389-jPuzSoD7aJg1RZFjCuSU3Q(~)server.ccl.net> X-Original-From: Salomon Turgman Cohen Content-Type: multipart/alternative; boundary=047d7b15fcffad7fa704c356482c Date: Mon, 25 Jun 2012 21:47:40 -0400 MIME-Version: 1.0 Sent to CCL by: Salomon Turgman Cohen [sturgman**gmail.com] --047d7b15fcffad7fa704c356482c Content-Type: text/plain; charset=ISO-8859-1 Hello, I just started using QM software in my work and I am running into a problem when attempting optimization of molecules with carbon oxygen double bonds. I am using Gaussian 09 software and I am attempting to obtain a relaxed PES by scanning through a dihedral angle. My input file looks like this: ======================= %chk=checkpoint.out # opt=modredundant # MP2/3-21G Methyl Carbamic Acid -1 1 C -1.138918 0.893653 -0.049356 H -2.079107 0.544512 -0.478804 H -1.021588 1.947417 -0.306449 H -1.280611 0.865522 1.032038 N -0.023046 0.089597 -0.511660 H 0.244819 -0.107547 -1.462151 C 0.759629 -0.614681 0.333273 O 1.812834 0.147724 0.752146 O 0.484148 -1.759325 0.621099 D * 5 7 * R D 1 5 7 8 S 18 10.0 ========================= If I remove the "D * 5 7 * R" line the program runs properly, but with the line I get the error relating to internal coordinates: NTrRot= -1 NTRed= 27 NAtoms= 9 NSkip= 6 IsLin=F Error in internal coordinate system. Error termination via Lnk1e in /usr/local/g09/g09/l103.exe at Mon Jun 25 21:24:51 2012. The reason I try to remove the coordinates related to that bond is that Gaussian manual suggests this is necessary to obtain relaxed PES (although I do not understand exactly why and could not find the answer in Jensen's Intro. or Lewars' book) Searching through your website (what seemed like the archives) I found this paragraph that may be related: "It is important to realize that the torsional angle is undefined if either atoms *i*, *j* and *k*, or *j*, *k* and *l* are collinear (i.e., a straight line is passing through three consecutive atoms) because an infinite number of planes can pass through three collinear points. For this reason, it does not make sense to talk about a torsional angle in acetylene. " Is this related to the problem I am having. While visualizing the molecule it is not clear to me how it is becoming collinear during the optimization and scanning. Can anyone provide a hint on what concept I am missing here? -- Salomon Turgman Cohen Postdoctoral Associate Cornell University (919) 341-9650 --047d7b15fcffad7fa704c356482c Content-Type: text/html; charset=ISO-8859-1 Content-Transfer-Encoding: quoted-printable Hello,
=A0=A0 I just started using QM software in my work and I am runni= ng into a problem when attempting optimization of molecules with carbon oxy= gen double bonds. I am using Gaussian 09 software and I am attempting to ob= tain a relaxed PES by scanning through a dihedral angle. My input file look= s like this:

=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D
%chk=3Dcheckpoint.out

# opt=3Dmodredundant
# MP2/3-21G
<= br>Methyl Carbamic Acid

-1 1
C=A0=A0=A0=A0=A0=A0=A0=A0 -1.138918= =A0=A0=A0=A0 0.893653=A0=A0=A0 -0.049356
H=A0=A0=A0=A0=A0=A0=A0=A0 -2.07= 9107=A0=A0=A0=A0 0.544512=A0=A0=A0 -0.478804
H=A0=A0=A0=A0=A0=A0=A0=A0 -1.021588=A0=A0=A0=A0 1.947417=A0=A0=A0 -0.306449=
H=A0=A0=A0=A0=A0=A0=A0=A0 -1.280611=A0=A0=A0=A0 0.865522=A0=A0=A0=A0 1.= 032038
N=A0=A0=A0=A0=A0=A0=A0=A0 -0.023046=A0=A0=A0=A0 0.089597=A0=A0=A0= -0.511660
H=A0=A0=A0=A0=A0=A0=A0=A0=A0 0.244819=A0=A0=A0 -0.107547=A0= =A0=A0 -1.462151
C=A0=A0=A0=A0=A0=A0=A0=A0=A0 0.759629=A0=A0=A0 -0.61468= 1=A0=A0=A0=A0 0.333273
O=A0=A0=A0=A0=A0=A0=A0=A0=A0 1.812834=A0=A0=A0=A0 0.147724=A0=A0=A0=A0 0.75= 2146
O=A0=A0=A0=A0=A0=A0=A0=A0=A0 0.484148=A0=A0=A0 -1.759325=A0=A0=A0= =A0 0.621099

D * 5 7 * R
D 1 5 7 8 S 18 10.0

=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

If I remove the "D *=A0 5 7 * R" line the program runs= properly, but with the line I get the error relating to internal coordinat= es:

=A0NTrRot=3D=A0=A0=A0 -1 NTRed=3D=A0=A0=A0 27 NAtoms=3D=A0=A0=A0=A0 9 N= Skip=3D=A0=A0=A0=A0 6 IsLin=3DF
=A0Error in internal coordinate system.<= br>=A0Error termination via Lnk1e in /usr/local/g09/g09/l103.exe at Mon Jun= 25 21:24:51 2012.

The reason I try to remove the coordinates relate= d to that bond is that Gaussian manual suggests this is necessary to obtain= relaxed PES (although I do not understand exactly why and could not find t= he answer in Jensen's Intro. or Lewars' book)

Searching through your website (what seemed like the archives) I found = this paragraph that may be related:
"It is important to realize tha= t the torsional angle is undefined if either atoms i, j and k, or j, k and l a= re collinear (i.e., a straight line is passing through three consecutive atoms) because an infinite number of planes can pass through three collinear points. For this reason, it does not make sense to talk about a torsional angle in acetylene. "

Is this related to the problem I am having. While visualizing= the molecule it is not clear to me how it is becoming collinear during the= optimization and scanning. Can anyone provide a hint on what concept I am = missing here?


--
Salomon Turgman Cohen
Postdoctoral Associate
Cornell U= niversity
(919) 341-9650
--047d7b15fcffad7fa704c356482c-- From owner-chemistry@ccl.net Tue Jun 26 06:06:00 2012 From: "Kim Hyungjun hyungjun96##kaist.ac.kr" To: CCL Subject: CCL: G09 ESP method dependency Message-Id: <-47132-120626041026-7073-IyYvZceRebjWImuKK6BqgQ- -server.ccl.net> X-Original-From: "Kim Hyungjun" Date: Tue, 26 Jun 2012 04:10:17 -0400 Sent to CCL by: "Kim Hyungjun" [hyungjun96[]kaist.ac.kr] Dear CCL users, This is Hyungjun Kim. I tried ESP charge calculation using G09 at HF and MP2 level. At some papers, the results of HF and MP2 level are different, but my result is same for both calculations. It might be from the fact that both calculations use "Electrostatic properties using SCF density" to obtain ESP charge. How can I get ESP charge of MP2 level? Any comments will be helpful. Thank you in advance. From owner-chemistry@ccl.net Tue Jun 26 07:43:01 2012 From: "berger_-_chem.helsinki.fi" To: CCL Subject: CCL: The aufbau principle in teaching chemistry Message-Id: <-47133-120626012304-20581-BpwcQ6LlZyfDMdTYWPo57g * server.ccl.net> X-Original-From: berger-,-chem.helsinki.fi Content-Transfer-Encoding: 8bit Content-Type: text/plain;charset=iso-8859-1 Date: Tue, 26 Jun 2012 08:22:51 +0300 MIME-Version: 1.0 Sent to CCL by: berger.:.chem.helsinki.fi Dear Prof. Scerri, when I talk aubout the "Aufbau-Prinzip" I say that inspite it is called a "Prinzip" it is fact a "Regel" (rule). And here the german saying "Die Ausnahme bestätigt die Regel." (roughly translated as: if there are exceptions then it is confirmed that we are dealing with a rule [rather than with a law]) applies quite well. Then I discuss the exceptions and the reasons for the exceptions. Rules are in my point of view, one of the possibilities to reduce the complexity of chemistry and to make it easier to memorize a hughe number of facts, which unfortuntaly cannot be avoided when one wants to become a chemist. My teacher called the "Aufbau-Prinzip" not "Regel" but "Mnemotechnische Hilfe", which is also quite helpful. One also should not forget, that the states get closer and closer with increasing Z, that relativity gets more and more important, and also that "one-electron-wavefunction model" is also only an approximation. > From a certain point of view such rules and exception generating effects, can be viewed like a perturbation series, in case the higher order effects are understood. Best regards RB > >> Dear Colleagues, >> >> I have a blog on the question of using the aufbau to 'predict' and teach >> electronic configurations of atoms at, >> >> http://ericscerri.blogspot.com/ >> >> and would be interested in hearing comments on it. >> >> all the best >> eric scerri >> UCLA >> >> ______________________________________________________ > > > > > > ericscerri.com > > On Twitter: > https://twitter.com/#!/ericscerri > > > > > > > > > > > From owner-chemistry@ccl.net Tue Jun 26 08:18:00 2012 From: "psavita savita.pundlik:+:crl-global.com" To: CCL Subject: CCL:G: The aufbau principle in teaching chemistry Message-Id: <-47134-120626015016-13813-PsmWsDb8/FQBJ7qx4xubmw^server.ccl.net> X-Original-From: psavita Content-Type: multipart/related; boundary="=_related 00200D0E65257A29_=" Date: Tue, 26 Jun 2012 11:20:04 +0530 MIME-Version: 1.0 Sent to CCL by: psavita [savita.pundlik * crl-global.com] --=_related 00200D0E65257A29_= Content-Transfer-Encoding: quoted-printable Content-Type: text/html; charset=ISO-8859-1 Hello,

I thoroughly enjoyed reading this blog= .
I remember to have learned this Aufbau technique in high school
bu= t always found it complicated to remember, given the fact that there
ar= e quite a few exceptions. I wouldn't have understood the reason for
eith= er the rule or its exceptions till I learned quantum mechanics
and then = computation of orbitals.
I feel during education, especially in Science= , it is better to highlight
known limitations of rules and/or laws altho= ugh the complete explanation
may be beyond the scope at that level.
<= /span>

Thanks and best wishes,

Savita Pundlik
Computational Materials Re= search & Innovation Group
Computational Research Lab= oratories Ltd.,
Taco House, Damle Path, O= ff Law College Road
P= une - 411004, India.



-----owner-chemistry+savita.pundlik=3D=3Dcrl-= global.com*ccl.net wrote: -----
To: "Pundlik, Savita Sunil " <savita.pundlik*crl-glo= bal.com>
From: "Eric Scerri scerri=5F-=5Fchem.ucla.edu"
Sent by: owner-ch= emistry+savita.pundlik=3D=3Dcrl-global.com*ccl.net
Date: 06/26/2012 = 04:23AM
Subject: CCL:G: The aufbau principle in teaching chemistry

=0D<= span class=3D"Apple-style-span">
Dear Colleagues,

I have a blog on the question of using the aufba= u to 'predict' and teach electronic configurations of atoms at,


and would be interested in hearing comments on it= .

all the best
eric scerri
UCLA

<= /span>=5F=5F=5F=5F=5F=5F=5F=5F=5F=5F=5F=5F=5F=5F=5F=5F= =5F=5F=5F=5F=5F=5F=5F=5F=5F=5F=5F=5F=5F=5F=5F=5F=5F=5F=5F=5F=5F=5F=5F=5F=5F= =5F=5F=5F=5F=5F=5F=5F=5F=5F=5F=5F=5F=5F
=

=

       <= span style=3D"border-collapse: separate; font-family: Helvetica; font-style= : normal; font-variant: normal; font-weight: normal; letter-spacing: normal= ; line-height: normal; text-indent: 0px; text-transform: none; white-space:= normal; word-spacing: 0px; font-size: medium;">ericscerri.com=

On Twitter:  

=

<= div>
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=



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CCL by: "Kim Hyungjun" [hyungjun96+/-gmail.com] Dear CCL users, This is Hyungjun Kim. I tried ESP charge calculation using G09 at HF and MP2 level. At some papers, the results of HF and MP2 level are different, but my result is same for both calculations. It might be from the fact that both calculations use "Electrostatic properties using SCF density" to obtain ESP charge. How can I get ESP charge of MP2 level? Any comments will be helpful. Thank you in advance. From owner-chemistry@ccl.net Tue Jun 26 09:28:00 2012 From: "willsd{}appstate.edu" To: CCL Subject: CCL: G09 ESP method dependency Message-Id: <-47136-120626071438-31100-eXnJ+GzxF0iBnMWOxqhyQg:_:server.ccl.net> X-Original-From: Content-Disposition: inline Content-Language: en Content-Transfer-Encoding: 7bit Content-Type: text/plain; charset=us-ascii Date: Tue, 26 Jun 2012 11:02:30 GMT MIME-Version: 1.0 Sent to CCL by: [willsd^^appstate.edu] try density=current Steve Williams ----- Original Message ----- > From: "Kim Hyungjun hyungjun96##kaist.ac.kr" Date: Tuesday, June 26, 2012 6:45 am Subject: CCL: G09 ESP method dependency To: "Williams, Steve " > > Sent to CCL by: "Kim Hyungjun" [hyungjun96[]kaist.ac.kr] > Dear CCL users, > > This is Hyungjun Kim. > > I tried ESP charge calculation using G09 at HF and MP2 level. > > At some papers, the results of HF and MP2 level are different, but > my result is > same for both calculations. > > It might be from the fact that both calculations use "Electrostatic > properties > using SCF density" to obtain ESP charge. > > How can I get ESP charge of MP2 level? > > Any comments will be helpful. > > Thank you in advance. > > > > -= This is automatically added to each message by the mailing > script =- > To recover the email address of the author of the message, please > changethe strange characters on the top line to the ]-[ sign. You can > also> Conferences: > http://server.ccl.net/chemistry/announcements/conferences/> > > From owner-chemistry@ccl.net Tue Jun 26 10:02:01 2012 From: "willsd+*+appstate.edu" To: CCL Subject: CCL: The aufbau principle in teaching chemistry Message-Id: <-47137-120626071448-31292-IugUI3rUP5BMFx/ti+kD9A^^^server.ccl.net> X-Original-From: Content-Disposition: inline Content-Language: en Content-Transfer-Encoding: 7bit Content-Type: text/plain; charset=us-ascii Date: Tue, 26 Jun 2012 10:59:45 GMT MIME-Version: 1.0 Sent to CCL by: [willsd],[appstate.edu] Thanks for posting this blog, Eric. I've been teaching a general chemistry course about twice a year since the fall of 1983. The "sloppy" aufbau picture you include (diagonal arrows, long jumps, abrupt curves, etc) has appeared in almost every university level text I've used but I do not teach it. Instead, my approach is to use the periodic table, the simple statement of the Pauli principle, and the Schroedinger H atom solutions to rationalize electron configurations. We get quantum numbers (n, l, ml, and ms, neglecting the fact ms is rather unimportant for the H atom) from Schroedinger (this gives numbers and types of orbitals) and Pauli tells us how many electrons and orbital can "hold". I then tell my students that we're going to use the H atom solutions (the only ones we have in closed form) and hope that they will be approximately correct for all of the other atoms with the "minor" correction that orbital energies depend on l as well as n for multi-electron atoms! This approximation is drastic (those few who come back in a few years to take a year of pchem learn just how drastic), and it is rather remarkable that it does lead to correct ground state configurations for neutral atoms most of the time. Given an atom's location on the periodic table and these ideas we can usually get the correct ground state configuration. I do emphasize that due to the approximate nature of this process it should be regarded as a rationalization, and not a prediction. This topic reminds me of a naive question that I used to ask nuclear physicists whenever I got the chance: "Why does Tc have no stable isotopes when it is surrounded by elements that do have stable isotopes?" I usually got wrong answers about odd-odd nuclei (there are stable odd-odd nuclei heavier then Tc),or none at all. I learned a better way to ask: "Is there a simple explanation, without resorting to detailed quantum mechanics computation, for the lack of stable isotopes of Tc?" The answer it seems is no.... Detailed nuclear structure computations do show that there are no neutron numbers for 43 protons that are stable, but you must do the computations to get this result. Similarly, we can use the whole arsenal of computational quantum chemistry (Hartree-Fock theory, CC methods, CI, Dirac-Fock theory, etc.) to do the detailed computations to correctly predict the ground configurations of all the atoms, including Cu, the lanthanides and actinides, etc. I doubt that any of us would try teach these methods in an introductory chemistry course as "simple explanations." So I am content in such courses to teach that this aufbau is an approximation and it cannot work correctly in all cases, and that we should be pleased that it does work as well as it does, including for almost all of the elements important for life. Steve williams ----- Original Message ----- > From: "Eric Scerri scerri_-_chem.ucla.edu" Date: Monday, June 25, 2012 6:52 pm Subject: CCL:G: The aufbau principle in teaching chemistry To: "Williams, Steve " > > > Dear Colleagues, > > > > I have a blog on the question of using the aufbau to 'predict' > and teach electronic configurations of atoms at, > > > > http://ericscerri.blogspot.com/ > > > > and would be interested in hearing comments on it. > > > > all the best > > eric scerri > > UCLA > > > > ______________________________________________________ > > > > > > ericscerri.com > > On Twitter: > https://twitter.com/#!/ericscerri > > > > > > > > > > > From owner-chemistry@ccl.net Tue Jun 26 10:38:00 2012 From: "Markus Dittrich dittrich^_^psc.edu" To: CCL Subject: CCL: Request for proposals for simulation time on Anton at NRBSC/PSC Message-Id: <-47138-120626093426-12160-Z+govhv+cFrGMa6Et5GKfg=-=server.ccl.net> X-Original-From: "Markus Dittrich" Date: Tue, 26 Jun 2012 09:34:24 -0400 Sent to CCL by: "Markus Dittrich" [dittrich(!)psc.edu] Dear Colleagues, The National Resource for Biomedical Supercomputing at the Pittsburgh Supercomputing Center is soliciting proposals for computer time on Anton, a special-purpose supercomputer for molecular dynamics (MD) simulation designed by D.E. Shaw Research. Anton allows MD simulations of biomolecular systems nearly two orders of magnitude faster than possible on current state of the art general purpose supercomputing resources. For more details and instructions on how to apply please go to The deadline for applications is 11:59 p.m., EDT, Monday, July 9, 2012. Best regards, Markus Dittrich From owner-chemistry@ccl.net Tue Jun 26 11:58:00 2012 From: "mena niihi stojanovicmljiljana ~ gmail.com" To: CCL Subject: CCL:G: Format of the Gaussian CUBE file Message-Id: <-47139-120626103838-24476-7/BvtmUMduWwQW4IAfxbQg%a%server.ccl.net> X-Original-From: "mena niihi" Date: Tue, 26 Jun 2012 10:38:30 -0400 Sent to CCL by: "mena niihi" [stojanovicmljiljana__gmail.com] Dear all, does anyone know if the format of values in Gaussian CUBE file can be changed and how? The default format is 6e13.5, but I need more significant digits. Thanks in advance. Best regards Liljana From owner-chemistry@ccl.net Tue Jun 26 12:33:00 2012 From: "Prof. Dr. N. Sekar nethi.sekar]=[gmail.com" To: CCL Subject: CCL:G: The aufbau principle in teaching chemistry Message-Id: <-47140-120626115746-30785-OBnt2Fw7uvPLE7KS5Zua5Q^-^server.ccl.net> X-Original-From: "Prof. Dr. N. Sekar" Content-Type: multipart/related; boundary=f46d04479f9178e9f704c3622865 Date: Tue, 26 Jun 2012 21:27:39 +0530 MIME-Version: 1.0 Sent to CCL by: "Prof. Dr. N. Sekar" [nethi.sekar^gmail.com] --f46d04479f9178e9f704c3622865 Content-Type: multipart/alternative; boundary=f46d04479f9178e9ef04c3622864 --f46d04479f9178e9ef04c3622864 Content-Type: text/plain; charset=ISO-8859-1 Dear Prof Eric Scerri, Really commendable. I was wondering whether such similar principles are available for filling up electrons in molecules containing pi-conjugated electrons. We also observe in reconciling the observation with DFT and TDDFT computations it is not always HOMO is the orbital involved in absorption. Many a times a orbital lower than HOMO absorbs energy in bringing out verical excitatios. So also it is not always a LUMO which is the excited state. Sometimes a state higher than the LUMO. On Mon, Jun 25, 2012 at 8:38 PM, Eric Scerri scerri_-_chem.ucla.edu < owner-chemistry#,#ccl.net> wrote: > > Dear Colleagues, > > I have a blog on the question of using the aufbau to 'predict' and teach > electronic configurations of atoms at, > > http://ericscerri.blogspot.com/ > > and would be interested in hearing comments on it. > > all the best > eric scerri > UCLA > > ______________________________________________________ > > > > > ericscerri.com > > On Twitter: > https://twitter.com/#!/ericscerri > > > > > > > > > > > -- Thanks and regards Prof. Dr. N. Sekar CCol FSDC Co-ordinator, UGC-CAS and Professor in Tinctorial Chemistry Dyestuff Technology Department Institute of Chemical Technology (formerly UDCT) Matunga, Mumbai-400019 Mob +91-9867958452 n.sekar#,#ictmumbai.edu.in sekarnm#,#rediffmail.com drnsekar4562000#,#yahoo.co.in website: http://ictmumbai.edu.in/Fac_FacDetails.aspx?fidno=116 --f46d04479f9178e9ef04c3622864 Content-Type: text/html; charset=ISO-8859-1 Content-Transfer-Encoding: quoted-printable
Dear Prof Eric Scerri,
=A0
Really commendable.=A0 =
I was wondering whether such similar principles are available fo= r filling up electrons in molecules containing pi-conjugated electrons.=A0 = We also observe in reconciling the observation with DFT and TDDFT computati= ons it is not always HOMO is the orbital involved in absorption.=A0 Many a = times a orbital lower than HOMO absorbs energy in bringing out verical exci= tatios.=A0 So also it is not always a LUMO which is the excited state.=A0 S= ometimes a state higher than the LUMO.=A0

On Mon, Jun 25, 2012 at 8:38 PM, Eric = Scerri scerri_-_chem.ucla.edu= <owner-chemistry#,#ccl.net> wrote:

Dear Colleagues,

I have a blog on the question of using the aufbau to 'p= redict' and teach electronic configurations of atoms at,


and would be i= nterested in hearing comments on it.

all the best
eric s= cerri
UCLA

_____________________________________= _________________
=


=A0= =A0 =A0 =A0=A0 ericsce= rri.com




--
Thanks and regards

Prof. Dr.= N. Sekar=A0=A0 CCol FSDC
Co-ordinator, UGC-CAS and Professor in Tinctor= ial Chemistry
Dyestuff Technology Department
Institute of Chemical Technology (formerl= y UDCT)
Matunga, Mumbai-400019

Mob +91-9867958452
n.sekar#,#ictmumbai.edu.in<= /a>
sekarnm#,#rediffm= ail.com
drnsekar4562000#,#yahoo.co.in
=A0

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Sekar nethi.sekar[*]gmail.com" To: CCL Subject: CCL:G: The aufbau principle in teaching chemistry Message-Id: <-47141-120626120229-970-QcsTeLLjk8HzXaunxy51Jg[A]server.ccl.net> X-Original-From: "Prof. Dr. N. Sekar" Content-Type: multipart/related; boundary=f46d04479f91572b0804c3623955 Date: Tue, 26 Jun 2012 21:32:22 +0530 MIME-Version: 1.0 Sent to CCL by: "Prof. Dr. N. Sekar" [nethi.sekar/./gmail.com] --f46d04479f91572b0804c3623955 Content-Type: multipart/alternative; boundary=f46d04479f91572b0104c3623954 --f46d04479f91572b0104c3623954 Content-Type: text/plain; charset=ISO-8859-1 Dear Prof Eric Scerri, Really commendable. I was wondering whether such similar principles are available for filling up electrons in molecules containing pi-conjugated electrons. We also observe in reconciling the observation with DFT and TDDFT computations it is not always HOMO which is the orbital involved in absorption. Many a times a orbital lower than HOMO absorbs energy in bringing out verical excitatios. So also it is not always a LUMO which is the excited state. Sometimes a state higher than the LUMO. On Mon, Jun 25, 2012 at 8:38 PM, Eric Scerri scerri_-_chem.ucla.edu < owner-chemistry::ccl.net> wrote: > > Dear Colleagues, > > I have a blog on the question of using the aufbau to 'predict' and teach > electronic configurations of atoms at, > > http://ericscerri.blogspot.com/ > > and would be interested in hearing comments on it. > > all the best > eric scerri > UCLA > > ______________________________________________________ > > > > > ericscerri.com > > On Twitter: > https://twitter.com/#!/ericscerri > > > > > > > > > > > -- Thanks and regards Prof. Dr. N. Sekar CCol FSDC Co-ordinator, UGC-CAS and Professor in Tinctorial Chemistry Dyestuff Technology Department Institute of Chemical Technology (formerly UDCT) Matunga, Mumbai-400019 Mob +91-9867958452 n.sekar::ictmumbai.edu.in sekarnm::rediffmail.com drnsekar4562000::yahoo.co.in website: http://ictmumbai.edu.in/Fac_FacDetails.aspx?fidno=116 --f46d04479f91572b0104c3623954 Content-Type: text/html; charset=ISO-8859-1 Content-Transfer-Encoding: quoted-printable

Dear Prof Eric Scerri,

=A0

Really commendable.=A0

I w= as wondering whether such similar principles are available for filling up e= lectrons in molecules containing pi-conjugated electrons.=A0 We also observ= e in reconciling the observation with DFT and TDDFT computations it is not = always HOMO which is the orbital involved in absorption.=A0 Many a times a = orbital lower than HOMO absorbs energy in bringing out verical excitatios.= =A0 So also it is not always a LUMO which is the excited state.=A0 Sometime= s a state higher than the LUMO.=A0

On Mon, Jun 25, 2012 at 8:38 PM, Eric Sc= erri scerri_-_chem.ucla.edu <= span dir=3D"ltr"><owner-chemistry::ccl.net> wrote:

Dear Colleagues,

I have a blog on the question of using the aufbau to 'p= redict' and teach electronic configurations of atoms at,


and would be i= nterested in hearing comments on it.

all the best
eric s= cerri
UCLA

_____________________________________= _________________
=


=A0= =A0 =A0 =A0=A0 ericsce= rri.com




--
Thanks and regards

Prof. Dr.= N. Sekar=A0=A0 CCol FSDC
Co-ordinator, UGC-CAS and Professor in Tinctor= ial Chemistry
Dyestuff Technology Department
Institute of Chemical Technology (formerl= y UDCT)
Matunga, Mumbai-400019

Mob +91-9867958452
n.sekar::ictmumbai.edu.in<= /a>
sekarnm::rediffm= ail.com
drnsekar4562000::yahoo.co.in
=A0

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-0400 Sent to CCL by: "Ronald Bakus" [rbakus]-[chem.ucsb.edu] I'm attempting to tease out whether there is an interaction between a nitrogen and sulfur in a small molecule that I'm studying in Gaussian 09. After having read the gaussian manual on the pop keyword, and the NBO manual, I'm completely and utterly confused as to how to go about the analysis. As such I'm hoping that someone here will have some suggestions. I was thinking of something along the lines of 'pop=nbo' (or something related), but given that the molecule isn't exactly small, if there is a keycard I can throw in to limit the output to a sane level (ie, only look at N-S interactions), Id appreciate that as well. I also expect this interaction, if it exists, to be fairly weak (~6kJ/mol). In essence, any suggestions that you may have are appreciated. Thanks, Ron From owner-chemistry@ccl.net Tue Jun 26 15:55:00 2012 From: "John Keller jwkeller^^alaska.edu" To: CCL Subject: CCL:G: Looking at weak N-S interactions Message-Id: <-47143-120626154431-12503-OH3oD4NwFSmlcnXP0Y2nxQ(!)server.ccl.net> X-Original-From: John Keller Content-Transfer-Encoding: 8bit Content-Type: text/plain; charset=ISO-8859-1 Date: Tue, 26 Jun 2012 11:44:19 -0800 Mime-Version: 1.0 (1.0) Sent to CCL by: John Keller [jwkeller+/-alaska.edu] Go to the NBO website at univ of wisconsin. Excellent tutorial. John Keller Sent from my iPhone On Jun 26, 2012, at 10:21 AM, "Ronald Bakus rbakus-,-chem.ucsb.edu" wrote: > > Sent to CCL by: "Ronald Bakus" [rbakus]-[chem.ucsb.edu] > I'm attempting to tease out whether there is an interaction between a nitrogen and sulfur in a small molecule that I'm studying in Gaussian 09. After having read the gaussian manual on the pop keyword, and the NBO manual, I'm completely and utterly confused as to how to go about the analysis. As such I'm hoping that someone here will have some suggestions. I was thinking of something along the lines of 'pop=nbo' (or something related), but given that the molecule isn't exactly small, if there is a keycard I can throw in to limit the output to a sane level (ie, only look at N-S interactions), Id appreciate that as well. I also expect this interaction, if it exists, to be fairly weak (~6kJ/mol). In essence, any suggestions that you may have are appreciated. > > Thanks, > Ron> > From owner-chemistry@ccl.net Tue Jun 26 17:04:00 2012 From: "Sten Nilsson Lill stenil]~[chalmers.se" To: CCL Subject: CCL:G: Looking at weak N-S interactions Message-Id: <-47144-120626160621-31907-uUTIwfHHz+mWAaeW8BGycg(_)server.ccl.net> X-Original-From: Sten Nilsson Lill Content-Language: en-US Content-Transfer-Encoding: 8bit Content-Type: text/plain; charset="us-ascii" Date: Tue, 26 Jun 2012 20:06:11 +0000 MIME-Version: 1.0 Sent to CCL by: Sten Nilsson Lill [stenil]~[chalmers.se] Dear Ron, maybe you can try NCI-plot for detecting/visualizing any interaction between N-S. Have a look at work by Erin Johnson and Weitao Yang for example at: http://faculty1.ucmerced.edu/ejohnson29/2.cfm?pm=432&lvl=2&menuid=562 and the key references cited there. Hope that helps! /Sten Ph.D. Sten Nilsson Lill Dep. of Chemistry University of Gothenburg SE-412 96 Gothenburg, Sweden e-mail: stenil%x%chem.gu.se Phone: +46-31 786 9103 Fax: +46-31-772 3840 ________________________________________ > From: owner-chemistry+stenil==chem.gu.se%x%ccl.net [owner-chemistry+stenil==chem.gu.se%x%ccl.net] on behalf of Ronald Bakus rbakus-,-chem.ucsb.edu [owner-chemistry%x%ccl.net] Sent: Tuesday, June 26, 2012 7:44 PM To: Nilsson Lill, Sten Subject: CCL:G: Looking at weak N-S interactions Sent to CCL by: "Ronald Bakus" [rbakus]-[chem.ucsb.edu] I'm attempting to tease out whether there is an interaction between a nitrogen and sulfur in a small molecule that I'm studying in Gaussian 09. After having read the gaussian manual on the pop keyword, and the NBO manual, I'm completely and utterly confused as to how to go about the analysis. As such I'm hoping that someone here will have some suggestions. I was thinking of something along the lines of 'pop=nbo' (or something related), but given that the molecule isn't exactly small, if there is a keycard I can throw in to limit the output to a sane level (ie, only look at N-S interactions), Id appreciate that as well. I also expect this interaction, if it exists, to be fairly weak (~6kJ/mol). In essence, any suggestions that you may have are appreciated. Thanks, Ronhttp://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 Tue Jun 26 23:36:00 2012 From: "Dr. Robert C. Mawhinney dr.robert.mawhinney[#]gmail.com" To: CCL Subject: CCL:G: The aufbau principle in teaching chemistry Message-Id: <-47145-120626141228-8451-DTdKt0mul30I2lpRF2Bdmg|,|server.ccl.net> X-Original-From: "Dr. Robert C. Mawhinney" Content-Type: multipart/related; boundary=00151747b004ad1b2b04c3640949 Date: Tue, 26 Jun 2012 14:12:12 -0400 MIME-Version: 1.0 Sent to CCL by: "Dr. Robert C. Mawhinney" [dr.robert.mawhinney#,#gmail.com] --00151747b004ad1b2b04c3640949 Content-Type: multipart/alternative; boundary=00151747b004ad1b2604c3640948 --00151747b004ad1b2604c3640948 Content-Type: text/plain; charset=ISO-8859-1 Hi Eric, The aufbau principle is an interesting pedagogical tool for beginning to understand electronic structure and a stepping stone to quantum theory. One point I feel you left out is the fact that it is the electronic state, as given by the term symbol, that is being described by the electron configuration (which corresponds to a single determinant in the Hartree-Fock (or Khon-Sham) approximation. For any atom (or molecule) with more than one electron, the more accurate description employs a weighted linear combination of several determinants, each of which is an electron configuration. This is the point I try to get my PCHEM students to understand. Sincerely, Rob Mawhinney On Mon, Jun 25, 2012 at 11:08 AM, Eric Scerri scerri_-_chem.ucla.edu < owner-chemistry%a%ccl.net> wrote: > > Dear Colleagues, > > I have a blog on the question of using the aufbau to 'predict' and teach > electronic configurations of atoms at, > > http://ericscerri.blogspot.com/ > > and would be interested in hearing comments on it. > > all the best > eric scerri > UCLA > > ______________________________________________________ > > > > > ericscerri.com > > On Twitter: > https://twitter.com/#!/ericscerri > > > > > > > > > > > --00151747b004ad1b2604c3640948 Content-Type: text/html; charset=ISO-8859-1 Content-Transfer-Encoding: quoted-printable Hi Eric,

The aufbau principle is an interesting pedagogical tool for= beginning to understand electronic structure and a stepping stone to quant= um theory.=A0 One point I feel you left out is the fact that it is the elec= tronic state, as given by the term symbol, that is being described by the e= lectron configuration (which corresponds to a single determinant in the Har= tree-Fock (or Khon-Sham) approximation.=A0 For any atom (or molecule) with = more than one electron, the more accurate description employs a weighted li= near combination of several determinants, each of which is an electron conf= iguration.=A0 This is the point I try to get my PCHEM students to understan= d.

Sincerely,

Rob Mawhinney


O= n Mon, Jun 25, 2012 at 11:08 AM, Eric Scerri scerri_-_chem.ucla.edu <owner-chemistry%a%ccl.net&= gt; wrote:
Dear Colleagues,

I have a blog on the question of using the aufbau to 'p= redict' and teach electronic configurations of atoms at,


and would be i= nterested in hearing comments on it.

all the best
eric s= cerri
UCLA

_____________________________________= _________________

=

=A0=A0 =A0 =A0=A0

On Twitter: =A0





=



=
=


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