From chemistry-request@server.ccl.net Fri Jul 6 15:53:03 2001 Received: from phobos.email.Arizona.EDU (IDENT:root@[128.196.133.165]) by server.ccl.net (8.11.0/8.11.0) with ESMTP id f66Jr2518956 for ; Fri, 6 Jul 2001 15:53:03 -0400 Received: from demetrio.u.arizona.edu (128.196.86.129) by phobos.email.Arizona.EDU (5.1.056) id 3B1F829C001EC0F9 for CHEMISTRY@ccl.net; Fri, 6 Jul 2001 12:53:01 -0700 Message-Id: <5.1.0.14.0.20010706124722.024390a0@deimos.email.arizona.edu> X-Sender: dasf@deimos.email.arizona.edu X-Mailer: QUALCOMM Windows Eudora Version 5.1 Date: Fri, 06 Jul 2001 12:52:21 -0700 To: CHEMISTRY@ccl.net From: Demetrio Antonio da Silva Filho Subject: BSSE on Dimers Mime-Version: 1.0 Content-Type: text/plain; charset="us-ascii"; format=flowed Dear CCL'ers, I am doing some MP2/6-311G(2d,2p) canculation on anthracene dimers (using Gaussian'98) and I want to know how I can eliminate the BSSE (basis set superposition error) using the counterpoise method for that system of two equal molecules. I wonder if someone can point me to articles or a scheme in order to do that using Gaussian'98. Thanks in advance, Demetrio Filho From chemistry-request@server.ccl.net Thu Jul 5 21:26:55 2001 Received: from web10106.mail.yahoo.com ([216.136.130.56]) by server.ccl.net (8.11.0/8.11.0) with SMTP id f661Qt520648 for ; Thu, 5 Jul 2001 21:26:55 -0400 Message-ID: <20010706012651.44748.qmail@web10106.mail.yahoo.com> Received: from [161.142.10.11] by web10106.mail.yahoo.com via HTTP; Thu, 05 Jul 2001 18:26:51 PDT Date: Thu, 5 Jul 2001 18:26:51 -0700 (PDT) From: ng ling Subject: Free Energy Pertubation (Amber) To: chemistry@ccl.net MIME-Version: 1.0 Content-Type: text/plain; charset=us-ascii Dear friends : I'm using Free Energy Pertubation (FEP) method (Amber)in my master project in Penang. Can anyboy send me references about FEP method (Amber)? __________________________________________________ Do You Yahoo!? Get personalized email addresses from Yahoo! Mail http://personal.mail.yahoo.com/ From chemistry-request@server.ccl.net Thu Jul 5 16:57:53 2001 Received: from web13205.mail.yahoo.com ([216.136.174.190]) by server.ccl.net (8.11.0/8.11.0) with SMTP id f65Kvr517431 for ; Thu, 5 Jul 2001 16:57:53 -0400 Message-ID: <20010705205752.48785.qmail@web13205.mail.yahoo.com> Received: from [129.105.55.29] by web13205.mail.yahoo.com; Thu, 05 Jul 2001 13:57:52 PDT Date: Thu, 5 Jul 2001 13:57:52 -0700 (PDT) From: mike smith Subject: short summary of my post on June 29 << CCL:Short-term certificate on drug design or bioinformatics To: ccl MIME-Version: 1.0 Content-Type: multipart/mixed; boundary="0-1804289383-994366672=:48740" --0-1804289383-994366672=:48740 Content-Type: text/plain; charset=us-ascii Content-Disposition: inline Dear listers, As the requests of more than 3 people on the topic, I am attaching the summary. Hope this may be a little helpful for them, and those who may want to know it but did not ask for. Many thanks to all of those who replied to my message. Best wishes to all of you. --Mike __________________________________________________ Do You Yahoo!? Get personalized email addresses from Yahoo! Mail http://personal.mail.yahoo.com/ --0-1804289383-994366672=:48740 Content-Type: text/html; name="ccl.html" Content-Description: ccl.html Content-Disposition: inline; filename="ccl.html" (1)
I had a similar background--grad degree in theoretical chemistry,
but I didn't have any trouble finding a post-doc in bio-simulation (3 years
ago) I know of at least 2 other people who also found a post-doc in a
bio-simulation group with a very theoretical grad school experience. Have you tried
applying for a NRC Postdoctoral Research Associate position? They fund
positions at a lot of the national labs (NIST/Naval/etc) and seem to be a good route
for making the transition. I think you need to keep trying for a post-doc
position.

good luck,
---------------------------------------------------

(2)
Workshop attendees,

Here is a webpage with links to Prof. Vaisman's PPT
lectures, the main workshop page, the in-class exer-
cises, and solutions to the exercises:

http://www.ib3.gmu.edu/taylor/PROTWORKSHOPSUM01/workshop.html

-----------------------------------------------------

(3)
I'm no expert on this, but here's one man's opinion.

First, lean on your Ph.D. advisor for help. He/She has a
responsibility to help you build a rewarding career. If you are not
a recent graduate, then you might ask for some help from supervisors
at your subsequent jobs.

It also sounds like you have pretty specific ideas about the kind of
job you want. This suggests: (1) Talk to experienced people in that
industry. Ask them directly what kind of training, which postdoc
advisers (if any), etc., are the best for obtaining the job you
want. (2) If you can't get that job, be flexible and start with
something else. You may find that you like if very much, but if your
goals are unaffected you at least have a richer career/resume to help
you.

Also keep in mind that obtaining (and holding) a job takes more than
technical skills. There are many "soft skills" required, and which
are difficult to learn. They can be evaluated in an interview, in
letters of reference, etc.

Industrial jobs usually require great flexibility, since projects
(and job descriptions) may change every quarter. If you've been in
one area a long time, flexibility may be an important concern to
potential employers.

It's unrealistic to expect to master any of those research areas in a
couple of months. A Ph.D. alone takes 5-6 years. The fastest I've
heard of was less than four years, but that was an unusually good
student (now a HHMI at a top-tier research university). However, you
can train yourself to some extent by attending meetings (for
technical content but especially to build your interpersonal network)
and by studying (textbooks, journals, software).

My last comment--be sure that your resume and cover letter are
linguistically polished, as appropriate when seeking a professional
position. I realize it's "just" an e-mail message, but you have
several grammatical errors (below).

Good luck to you! I hope my comments are helpful; use the useful and
discard the rest.

Sincerely,
........
----------------------------------------------

(4)
Where did you get your degree? What, if anything, did your university
have for a placement office? Do they offer resume critiquing? & if so, did
you participate? To what professional organizations do you belong? [ACS?]
ACS has a LOT of job stuff for members - placement at meetings, though you
have to scrape up the funds to get there. If you're unemployed, tell them &
they waive the registration - members, of course. Do you follow C&E News'
employment sections, Science, Nature, & respond to ads there?

What is your relationship with your degree preceptor? What does he
usually do to help his students find jobs? [Writing letters of recommendation
only is not really enough, but too many of them think along those lines].
If that's usually all he does, ask him to what groups he thinks you should
be applying for post-docs. Post-docs are often passed to friends &
acquaintances, then an ad is written so specifically only the person
already in mind will fit the criteria.

Next: please don't take this personally, but if the grammar of your
posting [below] is the way you normally write, you need to pay a lot more
attention to it. There are numerous errors. Paradoxically, scientists have by
default become the custodians of written English- the literary types
are all into anything goes, but most scientists still think poor grammar &
spelling are hallmarks of sloppy thinking.
Your grammar is such that, in fact, were it not for your All-American
user ID, I'd think English is not your first language. So much so, that I
suspect many who might otherwise have replied think you may be someone
not using their real name as their user id. A lot of people tend to think
replying to someone who won't tell you who they really are is a waste
of time.

SO, if your posting is your normal grammar, you need to take some
courses. Since you obviously also need a job, you need to get someone to correct
any letters you intend to mail before you send them out. If you have a
learning disability that prevents you from using standard grammar, forget what I
said about more courses, but DO have someone check your outgoing letters.
By all means use a computer grammar checker, but still have a person it
afterward. I am not impressed by computer grammar checkers. The one with MS Word
gets upset at many proper constructions & overlooks egregious errors such as
incorrectly typing form instead of from.

Hope this is somewhat helpful. I'm going away until after the 4th, so
if I don't reply, that's why.

-----------
(5)
I think whether you do some research work in your known area during a short-term?
if it is not suitable for publication, may you directly see
employer with your manuscript to prove you eligible to work in this area?

with a best wish,

------------

--0-1804289383-994366672=:48740-- From chemistry-request@server.ccl.net Fri Jul 6 12:08:44 2001 Received: from ucidoor.unitedcatalysts.com ([208.23.162.2]) by server.ccl.net (8.11.0/8.11.0) with ESMTP id f66G8h516452 for ; Fri, 6 Jul 2001 12:08:43 -0400 Received: by ucidoor.unitedcatalysts.com; (8.8.8/1.3/10May95) id MAA18770; Fri, 6 Jul 2001 12:08:43 -0400 (EDT) Received: from 10.1.0.50 by ucismtp02.unitedcatalysts.com (InterScan E-Mail VirusWall NT); Fri, 06 Jul 2001 12:09:38 -0400 (Eastern Daylight Time) Received: from lvlxch01.unitedcatalysts.com ([10.16.100.88]) by lvlmail.unitedcatalysts.com (PMDF V6.0-24 #41777) with ESMTP id <0GG2002287AX5Y@lvlmail.unitedcatalysts.com> for chemistry@ccl.net; Fri, 06 Jul 2001 12:04:09 -0400 (EDT) Received: by lvlxch01.unitedcatalysts.com with Internet Mail Service (5.5.2650.21) id ; Fri, 06 Jul 2001 12:09:00 -0400 Content-return: allowed Date: Fri, 06 Jul 2001 12:08:59 -0400 From: "Shobe, Dave" Subject: aromaticity w/o orbitals To: "'CCL'" Message-id: <157A51F55AAAD3119CD70008C7B1629DDAB043@lvlxch01.unitedcatalysts.com> MIME-version: 1.0 X-Mailer: Internet Mail Service (5.5.2650.21) Content-type: text/plain; charset=iso-8859-1 Content-Transfer-Encoding: 8bit X-MIME-Autoconverted: from quoted-printable to 8bit by server.ccl.net id f66G8i516453 Another question in the philosophical debate about orbitals. The explanation of aromaticity and the 4n+2 rule that I was taught was very dependent on the idea of orbitals. In fact, it was usually presented in terms of the Huckel orbitals derived from the molecular graph of the pi system. My question is, is it possible to explain the Huckel 4n+2 rule without appealing to orbitals? How does one do it? --David Shobe Süd-Chemie Inc. phone (502) 634-7409 fax (502) 634-7724 email dshobe@sud-chemieinc.com Don't bother flaming me: I'm behind a firewall. From chemistry-request@server.ccl.net Thu Jul 5 16:53:24 2001 Received: from hotmail.com ([216.33.240.134]) by server.ccl.net (8.11.0/8.11.0) with ESMTP id f65KrO517233 for ; Thu, 5 Jul 2001 16:53:24 -0400 Received: from mail pickup service by hotmail.com with Microsoft SMTPSVC; Thu, 5 Jul 2001 13:52:55 -0700 Received: from 149.169.26.114 by lw8fd.law8.hotmail.msn.com with HTTP; Thu, 05 Jul 2001 20:52:55 GMT X-Originating-IP: [149.169.26.114] From: "Jayalakshmi Rajaraman" To: chemistry@ccl.net Subject: Help in Gaussian Date: Thu, 05 Jul 2001 20:52:55 -0000 Mime-Version: 1.0 Content-Type: text/html Message-ID: X-OriginalArrivalTime: 05 Jul 2001 20:52:55.0549 (UTC) FILETIME=[7727F2D0:01C10594]

Hello!!

I am a new user of Gaussian 98 and am trying to run some geometry optimization and frequency calculations of adsorbed species on copper.. I am having some problems in using the commands of gaussian98 and a friend of mine referred me to you.. I would appreciate if you could help me out with my problem..

Here is the description of the problem:

I was originally using the command,

# UHF/3-21G* opt(maxcycle=70) freq=noraman scf=maxcycle=300 gfprint pop=full

to run my geo. optimization and freq calculations.. There were some non-convergence and I was suggested that i should use command stable=opt in the SCF calculations to alleviate this problem. I do not know how to incorporate the above command into my existing commands.. I tried a couple of things like removing scf=maxcycle= and replacing it with stable=opt but I got Illegal Iparse error in my calculations.. Could someone please let me know how stable=opt keyword could be used?

I would very much appreciate your help..

Thanks!

Jaya

Get Your Private, Free E-mail from MSN Hotmail at http://www.hotmail.com.

From chemistry-request@server.ccl.net Fri Jul 6 23:07:42 2001 Received: from sirius.chem.vt.edu (IDENT:root@[128.173.181.42]) by server.ccl.net (8.11.0/8.11.0) with ESMTP id f6737g524790 for ; Fri, 6 Jul 2001 23:07:42 -0400 Received: from localhost (crawdad@localhost) by sirius.chem.vt.edu (8.11.0/8.11.0) with ESMTP id f6737f210064; Fri, 6 Jul 2001 23:07:41 -0400 X-Authentication-Warning: sirius.chem.vt.edu: crawdad owned process doing -bs Date: Fri, 6 Jul 2001 23:07:41 -0400 (EDT) From: "T. Daniel Crawford" X-Sender: To: "Shobe, Dave" cc: "'CCL'" Subject: Re: CCL:aromaticity w/o orbitals In-Reply-To: <157A51F55AAAD3119CD70008C7B1629DDAB043@lvlxch01.unitedcatalysts.com> Message-ID: MIME-Version: 1.0 Content-Type: TEXT/PLAIN; charset=US-ASCII On Fri, 6 Jul 2001, Shobe, Dave wrote: > Another question in the philosophical debate about orbitals. > > The explanation of aromaticity and the 4n+2 rule that I was taught was very > dependent on the idea of orbitals. In fact, it was usually presented in > terms of the Huckel orbitals derived from the molecular graph of the pi > system. My question is, is it possible to explain the Huckel 4n+2 rule > without appealing to orbitals? How does one do it? > > --David Shobe > The recent issue of Chemical Reviews dedicated entirely to the topic of aromaticity may be useful to you. See issue five of the current volume. Prof. Paul Schleyer, whose recent work in alternative definitions of aromaticity based on magnetic susceptibilities is well known, is the guest editor. -Daniel -- T. Daniel Crawford Department of Chemistry crawdad@vt.edu Virginia Tech www.chem.vt.edu/chem-dept/crawford Voice: 540-231-7760 FAX: 540-231-3255 -------------------- PGP Public Key at: http://www.chem.vt.edu/chem-dept/crawford/publickey.txt