From owner-chemistry@ccl.net Fri Jun 1 06:14:02 2007 From: "CARLO GATTI c.gatti:+:istm.cnr.it" To: CCL Subject: CCL: GRC on Electron Distribution and Chemical Bonding 1-6 July 2007 Message-Id: <-34388-070601041045-3717-Rxiz1FCJZOEgmbCqW6mPKQ-$-server.ccl.net> X-Original-From: "CARLO GATTI" Date: Fri, 1 Jun 2007 04:10:41 -0400 Sent to CCL by: "CARLO GATTI" [c.gatti]_[istm.cnr.it] ONLY 10 DAYS left (deadline 10 June 2007) to APPLY to the 2007 GORDON RESEARCH CONFERENCE ON ELECTRON DISTRIBUTION AND CHEMICAL BONDING: DYNAMICS AND DENSITIES 1-6 July 2007, Mount Holyoke College , South Hadley, MA, USA http://www.grc.org/programs.aspx?year=2007&program=elecdist Bring your poster! No other conference will ensure your poster the same visibility! All posters will be displayed for at least 2 full days, each poster being discussed in 4 sessions of 2 hours each (a total of at least 8 hrs per poster!), in addition to the free time for discussing and visiting posters in the early afternoons from Monday to Thursday. Dear colleague, Dylan Jayatilaka and I are pleased to draw your attention to the next 2007 GORDON RESEARCH CONFERENCE (GRC) ON ELECTRON DISTRIBUTION AND CHEMICAL BONDING: DYNAMICS AND DENSITIES. The conference will be held in Mount Holyoke College, South Hadley, MA (USA), during the week of 1-6 July 2007. Details on the conference, on the application and registration procedures along with a full conference program can be find at the conference web location : http://www.grc.org/programs.aspx?year=2007&program=elecdist The aim of the conference, the scientific program, the information on IUCr scholarship are detailed below. As you may know, Gordon Research Conferences (GRCs) are the leading international conferences in each field. They attract the top international scientists in each field in a relaxed atmosphere with plenty of time to encourage communication and discussion of ideas at the Frontiers of Science. As chair of the conference, I have put together with Dylan Jayatilaka (University of Western Australia, Perth) a conference program that will hopefully fulfill this goal with an outstanding collection of speakers and discussion leaders. AIMS OF THE CONFERENCE This research conference is traditionally aimed at presenting a forum for discussion on the interplay between theory and experiment when measuring and calculating properties related to electron distribution and the making/breaking of chemical bonds. However, time resolved studies are becoming more and more important and will be the hot topic of the future. This conference thus have a look at the present forefront research in the charge density field, but at the same time is shaped as to keep the eye towards the coming new directions, those that will be promoted by the advent of the X-ray Free Electron Laser facilities and the exciting opportunities and challenging problems of single-particle X-ray diffraction imaging. Indeed, these instrumental and basic science progresses are increasingly opening the traditional field of this conference towards life sciences and the "movie-view" of electron distributions and chemical bonding. The conference will also discuss the impact of charge density databases towards structural determination and charge density reconstruction in proteins, and will debate on the relative importance of "fast" versus "good" X-ray data and on the quality of properties derived thereof. It will also deal with the most recent progresses in electron diffraction, it will discuss as well the "chemical concepts" one may obtain from experimental and theoretical electron densities or wavefunctions and it will afford the problem of density, density matrices and wavefunction reconstruction. Looking forward to seeing you next July in Mount Holyoke, With very best regards, Carlo Gatti SCIENTIFIC PROGRAM for a complete program, with timetable, see http://www.grc.org/programs.aspx?year=2007&program=elecdist Sessions, Discussion Leaders, Speakers and Title of the talks 1. WHERE ARE WE NOW, WHERE ARE WE GOING Discussion Leader: Robert F. Stewart (CMU, Pittsburgh, USA) W.H. Eugen Schwarz (AG Theoretische Chemie, Siegen, Germany) Synergic symbiosis of experimental electron density determinations and quantum theoretical calculations Mark A. Spackman (University Western Australia, Perth, Australia) Charge densities from X-ray diffraction data: Looking back, looking forward" 2. TIME RESOLVED SPECTROSCOPY, STRUCTURE AND BONDING : THE PRESENT Discussion Leader: Claude Lecomte (LCM3B, Nancy, France) Philip Coppens (SUNY, Buffalo, NY, USA) What is next in excited state diffraction? R.J. Dwayne Miller (Physics Dept., University of Toronto, Toronto, Canada) Femtosecond Electron Diffraction: Making the Molecular Movie Majed Chergui (LSU, ISIC, Lausanne, Switzerland) Photoinduced electronic and structural changes in liquids probed by picosecond X-ray absorption spectroscopy 3. TIME RESOLVED SPECTROSCOPY, STRUCTURE AND BONDING : THE FUTURE Discussion Leader: Jochen R. Schneider (DESY, Hamburg, Germany) Massimo Altarelli (European XFEL Project team, DESY, Hamburg, Germany) Planning for time resolved experiments at the European XFEL Jerome Hastings (SLAC, Menlo Park, California, USA) Opportunities and Challenges Presented by the LCLS Henry Chapman (LLNL, Livermore, CA, USA) Ultrafast Coherent X-ray Imaging with Free- Electron Lasers 4. HIGH THROUGHPUT OR QUALITY: ALTERNATIVE PATHS FOR X-RAY DIFFRACTION Discussion Leader: Bo B. Iversen (iNANO, University of Aarhus, Aarhus, Denmark) Mike Probert (Durham University, Durham, UK) Spend time collecting, or wishing you had Alan Pinkerton (University of Toledo, Toledo, OH, USA) Optimization and evaluation of data quality for charge density studies Hans-Beat Brgi (University of Bern, Bern, Switzerland) Vibrational dynamics of molecules in crystals from the temperature dependence of high quality Bragg data 5. NEW TECHNIQUES AND TOOLS FOR STRUCTURE, BONDING AND PROPERTIES IN BIOLOGY Discussion Leader: Sine Larsen (ESRF, Grenoble, France and Univ. Copenhaghen, DK) Pieter Glatzel (ESRF, Grenoble, France) Electron distribution and inner-shell spectroscopy: Can we measure oxidation states? Cherif Matta (Mount Saint Vincent University, Halifax, Nova Scotia, Canada) Bond dissociation in biological molecules: Insight from the Theory of Atoms in Molecules 6. TOWARD CHARGE DENSITIES FOR PROTEINS: WHICH DATABASE TO USE? WILL BIOLOGISTS CARE? Discussion Leader: Paul L.A. Popelier (University of Manchester, Manchester, UK) Alberto Podjarny (CNRS, Strasbourg, France) Quantum modeling of the catalytic mechanism of Aldose Reductase based on proton mobility revealed by neutron and subatomic resolution X-Ray crystallography". Christian Jelsch (LCM3B, Nancy, France) On the application of an experimental multipolar atoms library for accurate refinement of small-molecule and protein crystal structures Pauline Dominiak (SUNY, Buffalo, NY, USA and University of Warsaw, Warsaw, Poland) The UBDB Aspherical-Atom Databank Designed for Charge Density Analysis of Low-Resolution Structures and Electrostatic Evaluation of Macromolecular Complexes Birger Dittrich (University Western Australia, Perth, Australia) Invariom modeling: past achievements and future developments 7. PROGRESSES IN ELECTRON DIFFRACTION Discussion Leader: Kenji Tsuda (Tohoku University, Sendai, Japan) Chong-Yu Ruan (Michigan State University, East Lansing, MI, USA) Ultrafast meets ultrasmall: the development of ultrafast electron nanocrystallography Jesper Friis (NTNU, Trondheim, Norway) Charge density studies using convergent beam electron diffraction 8. CHEMICAL CONCEPTS FROM ELECTRON DENSITY: THEORY VS EXPERIMENT Discussion Leader: Richard F.W. Bader (McMaster Univ., Hamilton, Ontario, Canada) Miguel A. Blanco (Universidad de Oviedo, Oviedo, Spain) Electron number distributions, interacting quantum atoms, and chemical bonds in real space Wolfgang Scherer (University of Augsburg, Augsburg, Germany) On the nature and consequences of ligand-induced charge concentrations in transition metal oxides, carbides and alkyls Louis J. Farrugia (University of Glasgow, Glasgow, Scotland) Topological characterisation of the transition metal-metal bond in ligand bridged systems 9. DENSITIES, DENSITY MATRICES AND WAVEFUNCTIONS (in honor of Prof. Vedene H. Smith, Jr) Discussion Leader: AJIT THAKKAR (Univ. of New Brunswick, Fredericton, Canada) David A Mazziotti (University of Chicago, Chicago, IL, USA) Reduced-density-matrix mechanics with application to many-electron molecules Wolf Weyrich (University of Konstanz, Konstanz, Germany) Title : To be announced SCHOLARSHIPS: A limited number of SCHOLARSHIPS, in the form of IUCr Young Scientists Awards are available for graduate students and post-docs under 35. Applications for this financial contribution toward accommodation and/or travel should be made to the chair and include a recent CV and full mailing and email address. Funding from NIH (National Institute of Health) is also available. From owner-chemistry@ccl.net Fri Jun 1 06:39:01 2007 From: "Herbert Fruchtl herbert.fruchtl ~ st-andrews.ac.uk" To: CCL Subject: CCL: Book on solid state / surface simulations Message-Id: <-34389-070601063156-31977-m/tnUWX/mB+LPLbghNs37g(~)server.ccl.net> X-Original-From: Herbert Fruchtl Content-Transfer-Encoding: 7bit Content-Type: text/plain; charset=ISO-8859-1; format=flowed Date: Fri, 01 Jun 2007 11:31:37 +0100 MIME-Version: 1.0 Sent to CCL by: Herbert Fruchtl [herbert.fruchtl%x%st-andrews.ac.uk] While we are discussing books: Can somebody recommend a book or review article on computational chemistry of periodic systems? What I am interested in is a comparison of (mainly DFT) methods (plane waves, LAPW, periodic LCAO, different kinds of pseudopotentials, etc.). While an understanding of the underlying theory is of course necessary, I am more interested in practical aspects (What systems are these methods good for? What are they NOT good for? How large a unit cell can be treated?). Any recommendations? Herbert -- Herbert Fruchtl EaStCHEM Fellow School of Chemistry University of St Andrews From owner-chemistry@ccl.net Fri Jun 1 07:42:00 2007 From: "Taye Beyene Demisse sene3095]~[yahoo.com" To: CCL Subject: CCL:G: Symmetry Message-Id: <-34390-070601073802-14116-x0kS9c/TtOZFzZzfu5sQeg#server.ccl.net> X-Original-From: "Taye Beyene Demisse" Date: Fri, 1 Jun 2007 07:37:59 -0400 Sent to CCL by: "Taye Beyene Demisse" [sene3095^yahoo.com] Dear CCL'rs,peace first. Any suggestion about symmetry of molecules in DFT calculation? Aditionally, how the symmetry is changed in the G03 package? Any help is appreciated. Taye. From owner-chemistry@ccl.net Fri Jun 1 09:06:00 2007 From: "Andrew Ryzhkov andrew-,-meteo.mcgill.ca" To: CCL Subject: CCL: Running GAMESS on Windows Message-Id: <-34391-070531142930-19759-mx7/zdeHAjw+cfpaSTCQpQ++server.ccl.net> X-Original-From: Andrew Ryzhkov Content-Transfer-Encoding: 7bit Content-Type: text/plain; charset=us-ascii Date: Thu, 31 May 2007 13:49:56 -0400 MIME-Version: 1.0 Sent to CCL by: Andrew Ryzhkov [andrew#,#meteo.mcgill.ca] Dear Alex, >> manual. However for future production work, make sure to learn what is >> *nix, and you can eat it :^) AAGgccms> What's the reason for this statement? PC GAMESS AAGgccms> runs equally fast under Windows and Linux, AAGgccms> and there are many cases when Windows version is AAGgccms> somewhat faster (e.g., jobs which require AAGgccms> lots of memory and lots of disk I/O at the same time). IMHO, to learn *nix makes sense because almost all quantum chemical programs are developed for this system and only few of them are able to work under the Windows. And I would say the PC GAMESS is a pretty rare example of such program, which works even better in Windows version. AAGgccms> ----- Original Message ----- >> From: "Alexandr Isayev alex(_)ccmsi.us" AAGgccms> To: "Granovsky, Alex, A. " AAGgccms> Sent: Thursday, May 31, 2007 4:27 AM AAGgccms> Subject: CCL: Running GAMESS on Windows >> >> Sent to CCL by: Alexandr Isayev [alex*_*ccmsi.us] >> Mustafa, >> >> Get a PC GAMESS from Alexandr Granovsky >> http://classic.chem.msu.su/gran/gamess/ >> It natively runs under windows environment and has comprehensive >> manual. However for future production work, make sure to learn what is >> *nix, and you can eat it :^) >> >> hope this will help, >> Alexandr >> >> Wednesday, May 30, 2007, 5:25:00 PM, you wrote: >> >> MHmhyc> Sent to CCL by: "Mustafa Hussein" [mustafa.hussein86,yahoo.com] >> MHmhyc> Hi, >> MHmhyc> I have got a copy of GAMESS. I need to run it on Windows; is >> MHmhyc> it possible? If it is, I appreciate if you tell me how. >> >> MHmhyc> Thanks >> >> MHmhyc> Mustafa >> >> >> >> MHmhycMHmhycMHmhycMHmhycMHmhycMHmhycMHmhycMHmhycMHmhycMHmhycMHmhycMHmhycMHmhyc> Conferences: >> MHmhyc> http://server.ccl.net/chemistry/announcements/conferences/ >> >> MHmhycMHmhycMHmhycMHmhycMHmhyc------------------------------------------------------- >> Alexandr Isayev, >> Graduate Research Assistant, and System Administrator >> [A] Computational Center for Molecular Structure >> and Interactions (CCMSI), >> Jackson State University, >> Jackson, MS USA >> Tel: +(601) 979-1134 >> e-mail: alex(at)ccmsi.us >> Web: http://www.ccmsi.us >> --------------------------------------------------------> >> >> >> AAGgccmsAAGgccmsAAGgccmsAAGgccmsAAGgccmsAAGgccmsAAGgccmsAAGgccmsAAGgccmsAAGgccmsAAGgccmsAAGgccmsAAGgccms> Conferences: AAGgccms> http://server.ccl.net/chemistry/announcements/conferences/ AAGgccms> Search Messages: http://www.ccl.net/htdig AAGgccms> (login: ccl, Password: search) AAGgccmsAAGgccmsAAGgccmsAAGgccmsBest regards, Andrew Dr. Andrei Ryjkov Departments of Atmospheric and Oceanic Sciences, McGill University, 805 Sherbrooke St. West Montreal, Quebec, CANADA, H3A 2K6 -------------------------------------- Phone: +1(514)398-8867 Fax: +1(514)398-6115 -------------------------------------- E-mail : andrew^^meteo.mcgill.ca Internet: http://www.meteo.mcgill.ca/andrew From owner-chemistry@ccl.net Fri Jun 1 09:41:00 2007 From: "Jeff Hammond jeff.science]*[gmail.com" To: CCL Subject: CCL: Book on solid state / surface simulations Message-Id: <-34392-070601085745-17372-eFNcstYRmfpuOYgahVEmUA]~[server.ccl.net> X-Original-From: Jeff Hammond Content-Transfer-Encoding: 8bit Content-Type: text/plain; charset=windows-1252; format=flowed Date: Fri, 01 Jun 2007 07:57:37 -0500 MIME-Version: 1.0 Sent to CCL by: Jeff Hammond [jeff.science/./gmail.com] Herbert, Four articles from low to high level: "Computational Nanoscience: Do It Yourself!" (available online) http://www.fz-juelich.de/nic-series/volume31/ has at least three review/tutorial articles of interest Solid State Physics 54, 1-218 (2000) (available online) "Quasiparticle calculations in solids" by Aulbur, Jonsson, Wilkins, http://www.physics.ohio-state.edu/~wilkins/vita/gw_review.ps Rev. Mod. Phys. 64, 1045 (1992) M. C. Payne, M. P. Teter, D. C. Allan, T. A. Arias, and J. D. Joannopoulo "Iterative minimization techniques for ab initio total-energy calculations: molecular dynamics and conjugate gradients" Rev. Mod. Phys. 74, 601 - 659 (2002) Giovanni Onida, Lucia Reining, and Angel Rubio. "Electronic excitations: density-functional versus many-body Green’s-function approaches" Textbooks rarely contain practical information, but these are two good ones nonetheless: Atomic and Electronic Structure of Solids by Efthimios Kaxiras Electronic Structure: Basic Theory and Practical Methods by Richard M. Martin Although you will probably use another program, this may still be useful: http://dft.physics.cornell.edu/minicourse/ Best, Jeff Herbert Fruchtl herbert.fruchtl ~ st-andrews.ac.uk wrote: > > Sent to CCL by: Herbert Fruchtl [herbert.fruchtl%x%st-andrews.ac.uk] > While we are discussing books: Can somebody recommend a book or review > article on computational chemistry of periodic systems? What I am > interested in is a comparison of (mainly DFT) methods (plane waves, > LAPW, periodic LCAO, different kinds of pseudopotentials, etc.). > > While an understanding of the underlying theory is of course necessary, > I am more interested in practical aspects (What systems are these > methods good for? What are they NOT good for? How large a unit cell can > be treated?). Any recommendations? > > Herbert From owner-chemistry@ccl.net Fri Jun 1 11:10:00 2007 From: "David Santos Carballal spectrum_dav.:.operamail.com" To: CCL Subject: CCL:G: Gaussian/NBO/zero and first order perturbational energies Message-Id: <-34393-070601110256-12550-3RpsV2yi+fftzOctASjPbg a server.ccl.net> X-Original-From: "David Santos Carballal" Content-Disposition: inline Content-Transfer-Encoding: 8bit Content-Type: text/plain; charset="iso-8859-1" Date: Fri, 1 Jun 2007 09:35:06 -0500 MIME-Version: 1.0 Sent to CCL by: "David Santos Carballal" [spectrum_dav##operamail.com] Dear CCL'rs: The Gaussian output of the NBO's (3.1) just gives the second order perturbational energies. These energies can be used to quantify conjugative effects of the molecular systems. I want to estimate steric repulsions on molecular systems using zero and first order perturbational energies. Is this idea correct? Any suggest to obtain the zero and first order contributions to the energy in Gaussian are welcome. David Santos -- _______________________________________________ Surf the Web in a faster, safer and easier way: Download Opera 9 at http://www.opera.com Powered by Outblaze From owner-chemistry@ccl.net Fri Jun 1 11:44:00 2007 From: "David Santos Carballal spectrum_dav_-_operamail.com" To: CCL Subject: CCL: Gaussian/PCM/chemical shifts Message-Id: <-34394-070601110430-12664-TKJUA1UeCFFtb7agft0p7g*|*server.ccl.net> X-Original-From: "David Santos Carballal" Content-Disposition: inline Content-Transfer-Encoding: 8bit Content-Type: text/plain; charset="iso-8859-1" Date: Fri, 1 Jun 2007 10:05:00 -0500 MIME-Version: 1.0 Sent to CCL by: "David Santos Carballal" [spectrum_dav]![operamail.com] Dear CCL'rs: I want to estimate the solvent effect on shielding constants. I calculated shielding constants with DFT/PCM using optimized structures with DFT/PCM. However, the calculated shielding constants don't agree to experimental chemical shifts. I repeated the calculation of shielding constants (without PCM) using the same optimized structures (with DFT/PCM). This time, the calculated chemical shifts agree to experimental data. Is the correct methodology to estimate the solvent effect on shielding constants: -to optimize geometry and to calculate shielding constants using DFT/PCM on both, or -to optimize geometry using DFT/PCM and to calculate shielding constants using DFT (without PCM)? Any suggest about the correct procedure to estimate the solvent effect on shielding constants will be appreciated. David Santos -- _______________________________________________ Surf the Web in a faster, safer and easier way: Download Opera 9 at http://www.opera.com Powered by Outblaze From owner-chemistry@ccl.net Fri Jun 1 12:19:00 2007 From: "chupvl chupvl:-:gmail.com" To: CCL Subject: CCL: Pharmacophore modeling Message-Id: <-34395-070601063614-1797-fmzZuN+0ToVi1dYFAsVp/A##server.ccl.net> X-Original-From: chupvl Content-Transfer-Encoding: 7bit Content-Type: text/plain; charset=ISO-8859-1; format=flowed Date: Fri, 01 Jun 2007 13:31:47 +0400 MIME-Version: 1.0 Sent to CCL by: chupvl [chupvl(_)gmail.com] LigandScout is not for constructing pharmacophore but for visualization and saving only. The pharmacophore modeling takes a lot of time and various techniques can be applied. Free software for visualization is LIQUID http://gecco.org.chemie.uni-frankfurt.de/liquid/index.html as a PYMOL plugin. Vladimir Chupakhin Jian computationalboy-#-gmail.com wrote: > I think you can try Ligandscout, You can get a free evaluation for 1 > month. > Furthermore, one-year license is very cheap, about 10 US dollars. > It can run under windows, linux and sgi, with the aid of java > environment. > Regards! > > On 5/25/07, *Richard L Wood rwoodphd[A]msn.com* -ccl.net > wrote: > > > Sent to CCL by: "Richard L Wood" [rwoodphd=msn.com ] > Hi all, > > Do any of you know of any FREE programs to do pharmacophore > modeling that wil run under Windows? I'm currently using Sybyl > under Linux, but I'd like to try something else. If not Windows, > Linux would be alright, but I'd prefer that it run under Windows. > > The bottom line is that it must be free. > > Richard > > > > > > > > > E-mail to subscribers: CHEMISTRY- -ccl.net > or use:> > E-mail to administrators: CHEMISTRY-REQUEST- -ccl.net > or use> Conferences: > http://server.ccl.net/chemistry/announcements/conferences/ > > Search Messages: http://www.ccl.net/htdig > (login: ccl, Password: search)> > > > > > From owner-chemistry@ccl.net Fri Jun 1 15:13:00 2007 From: "Christopher Cramer cramer:_:chem.umn.edu" To: CCL Subject: CCL: Gaussian/PCM/chemical shifts Message-Id: <-34396-070601150520-9863-lAYADWMKX57yRq13EUle9A+*+server.ccl.net> X-Original-From: Christopher Cramer Content-Type: multipart/alternative; boundary=Apple-Mail-23-552220667 Date: Fri, 1 Jun 2007 13:34:43 -0500 Mime-Version: 1.0 (Apple Message framework v752.2) Sent to CCL by: Christopher Cramer [cramer|-|chem.umn.edu] --Apple-Mail-23-552220667 Content-Transfer-Encoding: 7bit Content-Type: text/plain; charset=US-ASCII; delsp=yes; format=flowed In Wiitala et al., JCTC 2 (2006) 1085, for a test set of 43 molecules with 141 and 255 unique 13C and 1H chemical shifts, it was found that mean unsigned errors for 13C shifts were 3.3, 3.2, and 3.1 ppm for gas//gas, solvated//gas, and solvated//solvated calculations with a good functional/basis set (where "gas" or "solvated" before the double solidus refers to the density, and after refers to the geometry optimization). For 1H the corresponding MUEs were 0.14, 0.14, and 0.10 ppm. Thus, continuum chloroform solvation (the method used here) had relatively little impact. However, the test set molecules were relatively rigid. It is possible that a molecule having one or more very floppy degrees of freedom might have a sufficiently different solvated structured compared to the gas phase that larger effects might be seen. In addition, specific interactions with first-shell solvent molecules (not present by default in a continuum treatment) can be important (see, for instance, Klein et al. JPC A 108 (2004) 5851). The observation that gas-phase chemical shifts computed at solvated geometries seem to agree better than solvated shifts at solvated geometries would seem to me a random manifestation of the many possible errors in the model (one-particle basis set size, functional, continuum approximation, etc.) and by no means representative of a preferred protocol. Chris On Jun 1, 2007, at 10:05 AM, David Santos Carballal spectrum_dav_- _operamail.com wrote: > > Sent to CCL by: "David Santos Carballal" [spectrum_dav]! > [operamail.com] > Dear CCL'rs: > I want to estimate the solvent effect on shielding constants. > I calculated shielding constants with DFT/PCM using optimized > structures with DFT/PCM. However, the calculated shielding constants > don't agree to experimental chemical shifts. > > I repeated the calculation of shielding constants (without PCM) using > the same optimized structures (with DFT/PCM). This time, the > calculated chemical shifts agree to experimental data. > > Is the correct methodology to estimate the solvent effect on > shielding constants: > -to optimize geometry and to calculate shielding constants using > DFT/PCM on both, or > -to optimize geometry using DFT/PCM and to calculate shielding > constants using DFT (without PCM)? > > Any suggest about the correct procedure to estimate the solvent > effect on shielding constants will be appreciated. > David Santos > > -- > _______________________________________________ > Surf the Web in a faster, safer and easier way: > Download Opera 9 at http://www.opera.com > > Powered by Outblaze > > > > -= 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)> > -+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+- > +-+-+ > > > -- Christopher J. Cramer University of Minnesota Department of Chemistry 207 Pleasant St. SE Minneapolis, MN 55455-0431 -------------------------- Phone: (612) 624-0859 || FAX: (612) 626-2006 Mobile: (952) 297-2575 cramer(-)pollux.chem.umn.edu http://pollux.chem.umn.edu/~cramer (website includes information about the textbook "Essentials of Computational Chemistry: Theories and Models, 2nd Edition") --Apple-Mail-23-552220667 Content-Transfer-Encoding: quoted-printable Content-Type: text/html; charset=ISO-8859-1 In Wiitala et al., JCTC 2 (2006) = 1085, for a test set of 43 molecules with 141 and 255 unique 13C and 1H = chemical shifts, it was found that mean unsigned errors for 13C shifts = were 3.3, 3.2, and 3.1 ppm for gas//gas, solvated//gas, and = solvated//solvated calculations with a good functional/basis set (where = "gas" or "solvated" before the double solidus refers to the density, and = after refers to the geometry optimization). For 1H the corresponding = MUEs were 0.14, 0.14, and 0.10 ppm. Thus, continuum chloroform solvation = (the method used here) had relatively little impact.

However, the test set = molecules were relatively rigid. It is possible that a molecule having = one or more very floppy degrees of freedom might have a sufficiently = different solvated structured compared to the gas phase that larger = effects might be seen. In addition, specific interactions with = first-shell solvent molecules (not present by default in a continuum = treatment) can be important (see, for instance, Klein et al. JPC A 108 = (2004) 5851).

The observation that = gas-phase chemical shifts computed at solvated geometries seem to agree = better than solvated shifts at solvated geometries would seem to me a = random manifestation of the many possible errors in the model = (one-particle basis set size, functional, continuum approximation, etc.) = and by no means representative of a preferred protocol.

Chris

On Jun 1, 2007, at 10:05 AM, David Santos Carballal = spectrum_dav_-_operamail.com wrote:


Sent to = CCL by: "David Santos Carballal" = [spectrum_dav]![operamail.com]
Dear = CCL'rs:
I want to estimate the solvent = effect on shielding constants.
I calculated = shielding constants with DFT/PCM using optimized
structures with DFT/PCM. However, the calculated = shielding constants
don't agree to experimental = chemical shifts.

I repeated the calculation of shielding constants = (without PCM) using
the same optimized = structures (with DFT/PCM). This time, the

Is the = correct methodology to estimate the solvent effect on
shielding constants:
-to = optimize geometry and to calculate shielding constants using
DFT/PCM on both, or
-to = optimize geometry using DFT/PCM and to calculate shielding
constants using DFT (without PCM)?

Any = suggest about the correct procedure to estimate the solvent
effect on shielding constants will be = appreciated.
David Santos

--=A0
Surf the Web in a faster, safer and easier = way:
Download Opera 9 at http://www.opera.com

Powered = by Outblaze



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If your mail bounces from CCL with 5.7.1 error, = check:






--


Christopher J. Cramer

University of Minnesota

Department of Chemistry

207 Pleasant St. = SE

Minneapolis, MN 55455-0431

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

=

Phone:=A0 (612) 624-0859 || FAX:=A0 (612) 626-2006

Mobile: (952) = 297-2575

cramer(-)pollux.chem.umn.edu<= /FONT>

http://pollux.chem.umn.edu/~cr= amer

(website = includes information about the textbook "Essentials

=A0 =A0 of Computational = Chemistry:=A0 Theories and = Models, 2nd Edition")


= --Apple-Mail-23-552220667-- From owner-chemistry@ccl.net Fri Jun 1 15:47:00 2007 From: "David Hose anthrax_brothers]![hotmail.com" To: CCL Subject: CCL: CHARMM: SCCDFTB GHO Message-Id: <-34397-070601153315-19528-o80D67vVBtiLxWnyey+vTg]^[server.ccl.net> X-Original-From: "David Hose" Date: Fri, 1 Jun 2007 15:33:12 -0400 Sent to CCL by: "David Hose" [anthrax_brothers:hotmail.com] Per, You might find the CHARMM forum a useful place to start. http://www.charmm.org/ubbthreads/ubbthreads.php?Cat=0&C=1 Dave. From owner-chemistry@ccl.net Fri Jun 1 18:56:00 2007 From: "GUERMOUNE ABDELADIM lguermoune]_[hotmail.com" To: CCL Subject: CCL:G: about AIM calculation Message-Id: <-34398-070601180905-6415-XRBWfHmxKzbjvreLx3L6ZQ-x-server.ccl.net> X-Original-From: "GUERMOUNE ABDELADIM" Date: Fri, 1 Jun 2007 18:09:02 -0400 Sent to CCL by: "GUERMOUNE ABDELADIM" [lguermoune..hotmail.com] Hello, I am beginner with the program of AIM2000 analysis. First I have create file wfn from the Gaussian98 using words key P B3LYP/6-311+G** output=wfn density=current then I treated file wfn by the AIM2000 program to localize the critical points, the density and laplacian. But the results don't seem to me coherent, for example when the density increases laplacian can take a positive value, and it can take a negative value when the density decrease. In my structure I have specially a metallic center: iron, and two borons with hydrogens in bridged position. I wish to know if there is another manner to improve my file result wfn or any others suggestions. Thanks. From owner-chemistry@ccl.net Fri Jun 1 19:35:00 2007 From: "Guermoune Abdeladim lguermoune- -hotmail.com" To: CCL Subject: CCL:G: AIM information Message-Id: <-34399-070601171103-1523-cPHtuNqf+Opiw+0j+Sy6nw .. server.ccl.net> X-Original-From: "Guermoune Abdeladim" Date: Fri, 1 Jun 2007 17:10:59 -0400 Sent to CCL by: "Guermoune Abdeladim" [lguermoune]|[hotmail.com] Hello, I am beginner with the program of AIM2000 analysis. First I have create file wfn from the Gaussian98 using words key P B3LYP/6-311+G** output=wfn density=current, then I treated file wfn by the AIM2000 program to localize the critical points, the density and laplacian. But the results don't seem to me coherent, for example when the density increases laplacian can take a positive value, and it can take a negative value when the density decrease. In my structure I have specially a metallic center: iron, and two borons with hydrogens in bridged position. I wish to know if there is another manner to improve my file result wfn or any others suggestions. Thanks.