From owner-chemistry@ccl.net Wed Aug 30 07:27:00 2006 From: "Arvydas Tamulis tamulis.!=!.mserv.itpa.lt" To: CCL Subject: CCL: Summary: Experimental stacking and hydrogen bonding energies between natural nucleobases in water environment Message-Id: <-32452-060830072518-2320-Yg9fpY1MJl5eta30SqNE9g!=!server.ccl.net> X-Original-From: Arvydas Tamulis Content-Type: TEXT/PLAIN; charset=US-ASCII; format=flowed Date: Wed, 30 Aug 2006 14:24:44 +0300 (EEST) MIME-Version: 1.0 Sent to CCL by: Arvydas Tamulis [tamulis]*[mserv.itpa.lt] Dear Tomasz and other Colleagues, I have received many references experimental and theoretical papers about stacking and hydrogen bonding energies between natural nucleobases but almost all of these references concerns DNA and RNA. I would like to pay attention that the stacking distances between G::C and A::T are significantly larger in DNA and RNA in comparison with our investigated free nucleobases stacked in water environment therefore our calculated stacking interactions should be significantly larger in comparison with stacking interactions in DNA. I have received only one indirect experimental paper [1] and one unpublished indirect experimental result and now we are additionally recalculating some values in stacked G::C in order to fit this experiment. [1] Molecular recognition of cytosine- and guanine-functionalized nucleolipids in the mixed monolayers at the air-water interface and Langmuir-Blodgett films Wang, YC; Du, XZ; Miao, WG; Liang, YQ Source: Journal of Physical Chemistry B; Mar 16 2006; v.110, no.10, p.4914-4923 Would you please again send me your known direct experiments of stacking and hydrogen bonding energies between natural nucleobases in water environment. With best regards, Arvydas Tamulis ************************************* On Tue, 29 Aug 2006, Tomasz Grabarkiewicz wrote: > Dear Dr Tamulis, > A few days ago you've posted a question to the CCL about the experimental stacking energy values. > Since there were no reasonable answer to your question, I'm wondering if you received any "private" responses concerning this subject or perhaps managed to find these values by your own. > I would be really grateful if you could eventually share them with me. > > Regards, > Tomasz Grabarkiewicz > > ------------------------------------------------------------------------------ > A. Mickiewicz University, Faculty of Chemistry > Quantum Chemistry Group > Grunwaldzka 6, 60-780 Poznan, Poland > phone: (+4861)8291289 > e-mail: grabar]-[man.poznan.pl > ------------------------------------------------------------------------------ > > From owner-chemistry@ccl.net Wed Aug 30 09:06:01 2006 From: "Maria Cristina Menziani menziani-$-unimo.it" To: CCL Subject: CCL: School of Graduate studies: call for applications 2007 Message-Id: <-32453-060830090142-1972-a1pVawvH7YU+CIl96GLa3A]^[server.ccl.net> X-Original-From: "Maria Cristina Menziani" Date: Wed, 30 Aug 2006 09:01:41 -0400 Sent to CCL by: "Maria Cristina Menziani" [menziani],[unimo.it] Universit degli Studi di Modena e Reggio Emilia School of graduate studies Multiscale Modelling, Computational Simulations and Characterization in Material and Life Sciences http://multiscale-school.unimore.it Call for applications 2007: deadline October, 9 2006 The School is aimed at providing students with a sound working knowledge of modern mathematical, computational and statistical modelling methods and algorithms as well as innovative experimental techniques for the characterization of complex systems at a multiscale level. The students will learn to apply this knowledge both in the field of material and life sciences working in multi-disciplinary well-integrated teams that emphasize the benefit of coordinated, iterative interactions between specialists in modelling/simulation and experimentalists. Topics in material and life sciences. Combinatorial and Numerical Algorithms, Computer Graphics, Chemo- and Bio-informatics, Experimental characterization of structures and properties, Human Computer Interface, Mathematical and computational Modelling, Neuroimaging, Statistical Modelling and Chemometrics. Doctoral Program This is a 3 years full-time course that includes introductory, basic and elective courses, seminars, tutorials, computer and experimental laboratory sessions and project work to produce a final dissertation on original themes of high standard in the international scientific framework. Stages in qualified research institutes in Italy and abroad are part of the student preparation as well. Possible positions achieved by graduated doctors. Students following this multi-disciplinary training will acquire the mathematical skills, chemical, engineering and biological insight, computational and experimental know-how necessary for tackling real-world problems. They will therefore be highly adaptable, with great employment prospects. Entry requirements. A second class honours degree or equivalent in a science, biotechnology, medicinal chemistry, medical or engineering subject. Admission is granted on a competitive basis. A Commission examines the CVs of the candidates and evaluates, in an interview (in Italian or English), their abilities to carry out research. Please refer to the Announcement published in the web site http://multiscale-school.unimore.it Scholarships The School awards 6 scholarships on a merit basis, two of which are reserved for candidates from universities other than the funding institution. Each scholarship is for about Euro 10.500 per year plus School tuition fees. The study grant is increased by 50% per month (for a maximum of 18 months) for time spent by the student at institutions abroad. For students who do not hold a scholarship, the tuition and registration fees amount to about Euro 1000 per year, depending on the income. Deadlines for application The notice of the competitive examination for the Doctoral Programs is available http://www.unimo.it/OffertaFormativa/CSdottorato.html?id=7&lang=ita. The application for admission must be submitted before October, 9, 2006. More info? scmamat]-[unimore.it Prof. Maria Cristina Menziani University of Modena and Reggio E. Department of Chemistry Via Campi 183 41100 Modena -Italy Tel: +39-059-2055091 Fax: +39-059-373543 E-mail: menziani]-[unimo.it From owner-chemistry@ccl.net Wed Aug 30 11:56:01 2006 From: "Gustavo L.C. Moura gustavo%%mercury.chem.pitt.edu" To: CCL Subject: CCL: Database with Dipole Moments and Ionization Potentials Message-Id: <-32454-060830114538-13169-6EjN11qAwBmu2aob/t292A/a\server.ccl.net> X-Original-From: "Gustavo L.C. Moura" Date: Wed, 30 Aug 2006 11:45:38 -0400 Sent to CCL by: "Gustavo L.C. Moura" [gustavo/a\mercury.chem.pitt.edu] Dear CCL Readers, I am looking for databases containing dipole moments and ionization potentials of molecules (organic or inorganic). Does anybody knows of any such database? Thank you very much in advance for any kind of help. Sincerely yours, Gustavo L.C. Moura gustavo- -mercuey.chem.pitt.edu From owner-chemistry@ccl.net Wed Aug 30 15:05:03 2006 From: "Steve Williams willsd-,-appstate.edu" To: CCL Subject: CCL: Database with Dipole Moments and Ionization Potentials Message-Id: <-32455-060830143133-16960-TNnFDgQi2k9KpBXwgExo1A_+_server.ccl.net> X-Original-From: Steve Williams Content-transfer-encoding: 7bit Content-type: text/plain; format=flowed; charset=ISO-8859-1 Date: Wed, 30 Aug 2006 12:31:28 -0400 MIME-version: 1.0 Sent to CCL by: Steve Williams [willsd~~appstate.edu] NIST has an extensive collection of well referenced ionization potentials, in many cases both verical and adiabatic values are available, but I do not think dipole moments are also listed. Steve Williams Gustavo L.C. Moura gustavo%%mercury.chem.pitt.edu wrote: > Sent to CCL by: "Gustavo L.C. Moura" [gustavo/a\mercury.chem.pitt.edu] > Dear CCL Readers, > I am looking for databases containing dipole moments and ionization potentials of molecules (organic or inorganic). Does anybody knows of any such database? > Thank you very much in advance for any kind of help. > Sincerely yours, > Gustavo L.C. Moura > gustavo*|*mercuey.chem.pitt.edu> > > > From owner-chemistry@ccl.net Wed Aug 30 18:13:01 2006 From: "Jeff Hammond jhammond{=}uchicago.edu" To: CCL Subject: CCL: Database with Dipole Moments and Ionization Potentials Message-Id: <-32456-060830181218-25601-rXdqdtMnKkLZzJg9IdbP4A..server.ccl.net> X-Original-From: Jeff Hammond Content-Transfer-Encoding: 7bit Content-Type: text/plain; charset=us-ascii Date: Wed, 30 Aug 2006 17:11:38 -0500 (CDT) MIME-Version: 1.0 Sent to CCL by: Jeff Hammond [jhammond_+_uchicago.edu] The CCCBDB (http://srdata.nist.gov/cccbdb/) has experimental data for ionization potentials and dipole moments, among many other things, for a variety of molecules, mostly organic. ---- Original message ---- >Dear CCL Readers, > I am looking for databases containing dipole moments and ionization potentials of molecules (organic or inorganic). Does anybody knows of any such database? > Thank you very much in advance for any kind of help. > Sincerely yours, > Gustavo L.C. Moura > gustavo*|*mercuey.chem.pitt.edu From owner-chemistry@ccl.net Wed Aug 30 20:12:00 2006 From: "Sengen Sun sengensun(_)yahoo.com" To: CCL Subject: CCL: Comment on A Critique of Chemical Language Message-Id: <-32457-060830200104-32473-egwgCZ/pR/E8FixrjwB8BA{=}server.ccl.net> X-Original-From: Sengen Sun Content-Transfer-Encoding: 8bit Content-Type: text/plain; charset=iso-8859-1 Date: Wed, 30 Aug 2006 16:01:00 -0700 (PDT) MIME-Version: 1.0 Sent to CCL by: Sengen Sun [sengensun() yahoo.com] > > > > 1. most viewed > > > Date: Sun, 27 Aug 2006 17:50:31 -0700 > > From: Eric Scerri > > Subject: most viewed > > > > Most viewed articles from "Foundations of > Chemistry" > > > > Most viewed articles are the full-text articles > from > > this journal > > that have been accessed most frequently within the > > last 90 days. The > > collection of most viewed articles below is > updated > > weekly. > > 1. Green Chemistry: An Innovative Technology > > Kidwai, M., Mohan, R. > > Published Print: October 2005 > > 2. The Role of Observables and Non-observables in > > Chemistry: A > > Critique of Chemical Language > > Shahbazian, S., Zahedi, M. > > Published Print: February 2006 > > 3. SOME PRESUPPOSITIONS IN THE METAPHYSICS OF > > CHEMICAL REACTIONS > > HARRÉ, R. > > Published online: 04 April 2006 > > 4. Lavoisier and Mendeleev on the Elements > > Hendry, R. > > Published Print: January 2005 > By titles, I was keenly interested in No 2 article above by Shahbazian and Zahedi. I was curious to see which particular sentences in chemical language they really criticize and why they think there is a "need to develop a clear chemical language". I feel very disappointed after I read the whole paper of 15 writing pages, I absolutely have no idea about what they are criticizing and why there is the "need". They probably criticized Gillespie's work, as shown at the end of Page 38: "His (Gillespie's) concluding remarks were: 'Unlike an orbital, the electron density of a molecule is a physical observable that can be obtained by experiment...'. This leads to the question of why electron charge densities and other mathematical functions derived from charge densities are observables and if it is possible to replace orbitals with charge density". This doubly quoted statement probably mean that Shahbazian and Zahedi don't agree with Gillespie's remarks. It is strange that Shahbazian and Zahedi do not make their opinion clear while they are calling to clarify the chemcial languange. Shahbazian and Zahedi attempt to discuss "how can chemists' use of orbitals be justified?". For example: "A well-known example found in general chemistry texts is a sentence such as: "The sp3 hybridization of the carbon atom in methane causes its tetrahedral geometry". Although, at first glance, it seems that we are faced with a causal sentence, this is not the case. If we ask a chemist how we can be sure that the carbon atom has sp3 hybridization in the methane molecule, the carbon tetrahedral shape will be offered as the main reason! It seems that tetrahedral geometry and sp3 hybridization confirm each other in a circular manner, like a logical loop. Here, tetrahedral geometry and sp3 hybridization have the same logical depth." What do they really mean here? Do they mean that it is perfectly fine to say "The sp3 hybridization of the carbon atom in methane causes its tetrahedral geometry"? To me, they are saying that "something causes something" is equavalent to "something does not cause something". It seems to me that the logic is made up-side-down. Any one can say anything one wants. YES means NO and NO means YES. Could some one please kindly come forward to explain more about what they really want to criticize particularly? Thanks. Sengen __________________________________________________ Do You Yahoo!? Tired of spam? Yahoo! Mail has the best spam protection around http://mail.yahoo.com From owner-chemistry@ccl.net Wed Aug 30 22:21:00 2006 From: "Abrash, Samuel sabrash * richmond.edu" To: CCL Subject: CCL: Mulliken Charges and Augmented Functions Message-Id: <-32458-060830205143-29580-D17Jhkc9Fapu5WJD53dxtQ],[server.ccl.net> X-Original-From: "Abrash, Samuel" Content-class: urn:content-classes:message Content-Transfer-Encoding: 8bit Content-Type: text/plain; charset="us-ascii" Date: Wed, 30 Aug 2006 15:41:57 -0400 MIME-Version: 1.0 Sent to CCL by: "Abrash, Samuel" [sabrash _ richmond.edu] Hi to All CCLers, Recently there was a discussion on how adding augmented functions to a basis set made Mulliken charge distributions (even) less accurate. Can anyone point me to a reference, either a book or an article, that discusses this problem? Thank you. Samuel A. Abrash Department of Chemistry University of Richmond Richmond, VA 23173 Phone: 804-289-8248 Fax: 804-287-1897 E-mail: sabrash*_*richmond.edu Web-page: http://oncampus.richmond.edu/~sabrash "The time it takes to do a scientific project is given by the equation t = 2a + b, where a is the original estimate of the length of the project, 2 is a correction factor, and b is a number large compared to 2a."