From chemistry-request@www.ccl.net Fri Mar 19 05:12:48 1999 Received: from comsig.nibsc.ac.uk (comsig.nibsc.ac.uk [193.62.43.13]) by www.ccl.net (8.8.3/8.8.6/OSC/CCL 1.0) with ESMTP id FAA02954 Fri, 19 Mar 1999 05:12:31 -0500 (EST) Received: from nibsc.ac.uk (dlinmf.nibsc.ac.uk [193.62.42.144]) by comsig.nibsc.ac.uk (980427.SGI.8.8.8/970903.SGI.AUTOCF) via ESMTP id KAA11603; Fri, 19 Mar 1999 10:10:03 GMT Message-ID: <36F2228A.DF401E3E@nibsc.ac.uk> Date: Fri, 19 Mar 1999 10:10:18 +0000 From: Mark Forster Organization: NIBSC X-Mailer: Mozilla 4.05 [en] (Win95; I) MIME-Version: 1.0 To: Govindan Subramanian , chemistry@www.ccl.net Subject: Re: CCL:G:NMR shifts for amino acids References: <199903181835.MAA28980@vi1.medc.umn.edu> Content-Type: text/plain; charset=us-ascii Content-Transfer-Encoding: 7bit Dear Govindan Eric Oldfield has done some very nice work in computing the shielding / chemical shift tensor for 13C, 15N and 19F as a function of amino acid conformation. A review article that discusses applications to proteins can be found in J. Biol. NMR, vol 5, 217-225 (1995). Govindan Subramanian wrote: > Dear CCL'ers > I am looking for literature references that has dealt with the comparison of > computed vs experimental proton, carbon shifts for amino-acids and polypeptides. > Pointers to the choice of basis sets, the effects of solvents and the reliability > of the results are also welcome. > I am currently using the GIAO method implemented in Gaussian9x. > Will summarize if there are sufficient responses. Thanks > -subramanian.g > > -------This is added Automatically by the Software-------- > -- Original Sender Envelope Address: chemistry-request@www.ccl.net > -- Original Sender From: Address: govindan@vwl.medc.umn.edu > CHEMISTRY@www.ccl.net: Everybody | CHEMISTRY-REQUEST@www.ccl.net: Coordinator > MAILSERV@www.ccl.net: HELP CHEMISTRY or HELP SEARCH | Gopher: www.ccl.net 73 > Anon. ftp: www.ccl.net | CHEMISTRY-SEARCH@www.ccl.net -- archive search > Web: http://www.ccl.net/chemistry.html -- Dr Mark J Forster Ph.D. Principal Scientist Informatics Laboratory National Institute for Biological Standards and Control Blanche Lane, South Mimms, Hertfordshire EN6 3QG, United Kingdom. Tel +44 (0)1707 654753 FAX +44 (0)1707 646730 E-mail mforster@nibsc.ac.uk From chemistry-request@www.ccl.net Fri Mar 19 10:58:36 1999 Received: from syr.edu (syr.edu [128.230.1.49]) by www.ccl.net (8.8.3/8.8.6/OSC/CCL 1.0) with ESMTP id KAA04524 Fri, 19 Mar 1999 10:58:32 -0500 (EST) Received: from gamera.syr.edu (dgallis@gamera.syr.edu [128.230.18.14]) by syr.edu (8.8.8/8.8.8) with SMTP id KAA12874 for ; Fri, 19 Mar 1999 10:53:34 -0500 (EST) Date: Fri, 19 Mar 1999 10:58:33 -0500 (EST) From: "Damian G. Allis" X-Sender: dgallis@gamera.syr.edu Reply-To: "Damian G. Allis" To: chemistry@www.ccl.net Subject: ab initio / "Static" vs. Resonant Hyperpolarizability Message-ID: MIME-Version: 1.0 Content-Type: TEXT/PLAIN; charset=US-ASCII Greetings all, I was wondering if anyone has any references to studies of the accuracy of polarizability and hyperpolarizability calculations as a function of basis set used. I would like to know how much worse a 3-21g calculation will be over a 6-31g, or how much worse a 6-31g will be over a 6-311g**, etc. I'm looking for numbers AND reasons, if possible. Also, does anyone know definitively if the beta calculated by a standard MOPAC97 "POLAR" run is the resonant beta, or is it a specific beta for some transition which can be determined with more reading of the output files? Any references on this would be very helpful. I'll summarize everything. thanks in advance, Damian A. ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ Home Address: | Chemistry Address: 349 Buckingham Ave. | 1-014,2-023,2-016e Center for Sci&Tech Syracuse, NY 13210 | Syracuse University email: dgallis@syr.edu | Syracuse, NY 13244 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~#8^(= -)*-+-< everything about me: web.syr.edu/~dgallis/ Cornucopia Music: www.cornucopiamusic.com/ From chemistry-request@www.ccl.net Fri Mar 19 11:11:49 1999 Received: from bioc1.msi.com (bioc1.msi.com [146.202.0.2]) by www.ccl.net (8.8.3/8.8.6/OSC/CCL 1.0) with SMTP id LAA04624 Fri, 19 Mar 1999 11:11:48 -0500 (EST) Received: by bioc1.msi.com (940816.SGI.8.6.9/930416.SGI) for id IAA17261; Fri, 19 Mar 1999 08:10:55 -0800 Received: from mica.msi.com(146.202.6.217) by bioc1.msi.com via smap (V2.0) id xma017252; Fri, 19 Mar 99 08:10:31 -0800 Received: from by mica.biosym.com.msi.com (4.1/SMI-4.1) id AB08977; Fri, 19 Mar 99 08:15:42 PST Message-Id: <3.0.32.19990319080458.006b57fc@146.202.6.217> X-Sender: marvin@146.202.6.217 X-Mailer: Windows Eudora Pro Version 3.0 (32) Date: Fri, 19 Mar 1999 08:10:50 -0800 To: chemistry@www.ccl.net From: Marvin Waldman Subject: RE:CCL potential surface Mime-Version: 1.0 Content-Type: text/plain; charset="us-ascii" On 6-Mar-99, Konrad Hinsen wrote: > > I would like to understand why when working in cartesian coordinates > > and diagonalizing the hessian matrix on a potential surface at a point > > which is not a stationnary point I find only 3 zero eigenvalues (what > > about the rotations). > > Not being at a stationary point means that there is a non-zero energy > gradient. So when you rotate the whole system, the energy gradient > follows the rotation as well. The difference between the rotated and > the original gradient is thus not zero, meaning that this motion does > not correspond to a zero eigenvalue. > ------------------------------------------------------------------------- > Konrad Hinsen | E-Mail: hinsen@cnrs-orleans.fr > Centre de Biophysique Moleculaire (CNRS) | Tel.: +33-2.38.25.55.69 > Rue Charles Sadron | Fax: +33-2.38.63.15.17 > 45071 Orleans Cedex 2 | Deutsch/Esperanto/English/ > France | Nederlands/Francais > ------------------------------------------------------------------------- Sorry for this delayed response to the original question. I tried sending this message last week, but it didn't get delivered due to some e-mail problems. Here is my analysis of what is happening. The hessian matrix represents the mass-normalized energy second derivatives of the molecule with respect to atomic Cartesian coordinates. The eigenvectors formed by the diagonalization of this matrix represent atomic motions (the normal modes) with respect to mass-normalized atomic Cartesian displacements. Therefore, the modes corresponding to rotation are represented as displacements in Cartesian coordinates. Now, for an infinitesimal motion of the atoms, this is OK. However, if one were to take a rotational mode expressed this way and move the atoms a finite amount along these Cartesian displacements, one would find that more than a rotation has taken place and the motions in the Cartesian directions are starting to cause bond stretching, angle bending, etc. This is because pure rotations need to be expressed in curvilinear coordinates and expressing them in Cartesian coordinates is only correct for infinitesimal displacements. Now, at a stationary point on the potential energy surface, it works out that the eigenvalues for rotational modes are zero, but at non-stationary points they are not zero because of this effect. Here is a simple example to illustrate why this happens. Consider a diatomic molecule. Place one atom at the origin and the other atom along the X-axis. Make the atom at the origin have extremely large (virtually infinite) mass while the atom on the X-axis is very light. Then, rotational motion for this system corresponds to the light atom moving (infinitesimally) in the Y-direction. How do the energy derivatives of the system behave for this type of motion. Let r represent the bond length of the molecule. For any placement of the light atom in the X-Y plane, we have: r = sqrt( x*x + y*y) Let E be the energy of the system which is strictly a function of r, the bond length. Then, the derivative of the energy with respect to motion along y (starting out with the light atom on the X-axis) is: dE/dy = (dr/dy) * (dE(r)/dr) = (y/r) * (dE/dr) d^2E/dy^2 = (d^2r/dy^2) * (dE/dr) + (dr/dy)^2 * (d^2E/dr^2) = (d^2r/dy^2) * (dE/dr) (since dr/dy = y/r and y = 0) Now, at equilibrium or a stationary point, we have dE/dr = 0, so this last term also drops out and we get a second derivative d^2E/dy^2 = 0. However, away from equilibrium this term is not zero, and d^2r/dy^2 is not zero, so we get a non-zero value for d^2E/dy^2, which is the second derivative of the energy with respect to rotational motion expressed in Cartesian coordinates. A similar, but more general, form of the argument/analysis applies to the case of polyatomic molecules. The jist of the argument is that rotational motion expressed in Cartesian coordinates causes internal coordinate distortions in second order (d^2r/dy^2) which multiplies the first order energy derivative in internal coordinates (dE/dr). At a stationary point, the energy derivative vanishes, and we get a zero second derivative of the energy with respect to rotation expressed in Cartesian coords (and a zero eigenvalue in the corresponding eigenvector of the hessian matrix). Away from equilibrium, the energy first derivative with respect to internal coords is non-zero, leading to a non-zero value for the energy second derivative with respect to rotational motion, when the rotation is represented in Cartesian coords. Hope this helps clarify the situation. Marv Waldman From chemistry-request@www.ccl.net Fri Mar 19 14:18:31 1999 Received: from kirk.anderson.edu (kirk.anderson.edu [199.8.6.1]) by www.ccl.net (8.8.3/8.8.6/OSC/CCL 1.0) with ESMTP id OAA05889 Fri, 19 Mar 1999 14:18:30 -0500 (EST) Received: from [199.8.2.192] ([199.8.2.192] (may be forged)) by kirk.anderson.edu (8.8.6 (PHNE_14041)/8.8.2) with SMTP id OAA29428 for ; Fri, 19 Mar 1999 14:21:29 -0500 (EST) Date: Fri, 19 Mar 1999 14:21:29 -0500 (EST) Message-Id: <199903191921.OAA29428@kirk.anderson.edu> From: "Mike Falcetta" Reply-To: "Mike Falcetta" To: chemistry@www.ccl.net Subject: CCL: Q re multi ref CCSD(T) or MP4 I was wondering if anyone knows if multi-reference MP4(SDTQ) or CCSD(T) methods were being developed and what the status of such work might be. The particular application I am thinking of regards calculating highly accurate potential energy surfaces for charge transfer excited states of ion-molecule systems (where dispersion contributions can be significant). Thanks in advance for your help Mike Falcetta ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ + Mike Falcetta phone: 765-641-4371 + + Anderson University email: falcetta@kirk.anderson.edu + + Anderson, IN 46012 + ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ From chemistry-request@www.ccl.net Fri Mar 19 16:15:15 1999 Received: from broadway.gc.cuny.edu (broadway.gc.cuny.edu [146.96.128.10]) by www.ccl.net (8.8.3/8.8.6/OSC/CCL 1.0) with SMTP id QAA06676 Fri, 19 Mar 1999 16:15:14 -0500 (EST) Received: by broadway.gc.cuny.edu id AA25392; Fri, 19 Mar 1999 16:15:06 -0500 Date: Fri, 19 Mar 1999 16:15:05 -0500 (EST) From: Artem Masunov X-Sender: amasunov@broadway.gc.cuny.edu To: "Dr. Eric Walters" Cc: CHEMISTRY@www.ccl.net Subject: Re: CCL:Question about literature retrieval... In-Reply-To: Message-Id: Mime-Version: 1.0 Content-Type: TEXT/PLAIN; charset=US-ASCII Eric, I use stneasy.cas.org, it lets you do any search for $2. You can choose the titles you are interested in to get the abstract & reference (for $4 each). All chemical journals are at http://www.chemconnect.com/library/journals_all.html Artem > __ _________ Artem.Masunov@usa.net;tel 212-772-5751;fax212-772-5332 > / \ / _ _ \ text pager: instantmessage@bigfoot.com (max. 120 char.) > / \\ \\ \\ \ Chemistry Department, Hunter College, City U. of NY > / /\ \\ \\ \\ \ 695 Park Avenue, New York, NY 10021 > / ____ \\ \\ \\ \ --------------------------------------------------- > /__/\__/\__\\__\\__\\__\ "Freedom's just another word for > \__\/ \/__//__//__//__/ nothing left to lose." (B. Yeltsin)