From jkl@ccl.net Tue Mar 5 11:04:59 1991 Date: Tue, 05 Mar 91 10:51:32 EST From: jkl@ccl.net Subject: Correction to basis set intro Part 3/3 To: chemistry@ccl.net Status: RO Thanks to Melanie Pepper from OSU(Chemistry) we have first typo. The typo is in Part 3/3 of the Basis Set Intro series: Look for a string 6-311++G(2d1f,2p1d) and change it to 6-311+G(2d1f,2p1d) Sorry and thanks to Melanie for pointing it out. Jan Labanowski jkl@ccl.net, JKL@OHSTPY.BITNET --- From chemistry-request@ccl.net Tue Mar 5 11:30:17 1991 Date: Tue, 5 Mar 91 10:18 CST From: AHOLDER@VAX1.UMKC.EDU Subject: BASIS SETS AND POLARIZATION FUNCTIONS To: CHEMISTRY@ccl.net Status: RO Ahh, polarization. Are they functions or are they orbitals? This is a persistent conceptual dilemma, especially for those new to quantum mechanical methods. There is a relatively recent literature examination of this (Reed, Schleyer, JACS, 112 (1990) 1434) in the con- text of hypervalency. Take a look. Andy Holder U. of Missouri-Kansas City Dept. of Chemistry AHOLDER@UMKCAVX1 (Bitnet) (816)235-2293 --- From jkl@ccl.net Tue Mar 5 12:09:05 1991 Date: Tue, 05 Mar 91 11:55:56 EST From: jkl@ccl.net Subject: Append to Part 3/3 of Basis set Intro. To: chemistry@ccl.net Status: RO Seems like these few lines were chopped from the Part 3/3 of the Basis Intro. Just append them to the Part 3/3 at the end. Jan Labanowski jkl@ccl.net =================== cut here and append to Part 3/3 at the end ========= specific to this potential. As a result of applying the ECP's you drastically reduce number of needed basis functions, since only functions for valence electrons are required. In many cases, it would simply be impossible to perform some calculations on systems involving heavier elements without ECP's (try to calculate number of functions in TZ2P basis set for e.g. U, and you will know why). --- From chemistry-request@ccl.net Tue Mar 5 12:58:34 1991 Date: Tue, 5 Mar 91 12:45:20 EST From: bernhold@qtp.ufl.EDU Subject: Re: BASIS SETS AND POLARIZATION FUNCTIONS To: AHOLDER@VAX1.UMKC.EDU, CHEMISTRY@ccl.net Status: R Certainly many (most?) chemists like to think in terms of orbitals, but this is only a _model_ we have created -- it does not necessarily represent reality. (I'm sure that statement will generate some replies!) And very soon the appropriate definition of an "orbital" comes into question. Consider that to improve the quality of an ab initio calculation, you have two choices: improve the basis or improve the level of calculation. If you improve the basis beyond single zeta, how do you define the orbitals? Say I'm using a triple zeta basis. I get three times more orbitals than the orbital picture tells me how to deal with. Sure, I can consider only the valence orbtials, but there are properties & situations where the core orbtials are important too. And, of course, what if you use floating orbitals or magnetic field dependent orbitals? Improving the level of calculation is the big killer, though. As soon as I change from SCF to a correlated method, I only think of "orbitals" a place to excite electrons to or from. How does a molecule for which correlation effects are significant (there are many examples) fit into the orbital picture? If I tell you that the effect of triple excitations is very important in the description of a molecule, what does that say about the orbitals? IMHO (that's "in my humble opinion") it safest to always think of the basis set in ab inito calculations as mathematical functions which are used to describe the wavefunction. Mapping results into the orbital picture may or may not be appropriate depending on the case. Perhaps when we have enough experience with ab initio calculations we'll be able to develop a model which goes beyond the orbital picture by allowing for the description of correlation effects, etc. -- David Bernholdt bernhold@qtp.ufl.edu Quantum Theory Project bernhold@ufpine.bitnet University of Florida Gainesville, FL 32611 904/392 6365 --- From chemistry-request@ccl.net Tue Mar 5 13:08:51 1991 Date: Tue, 5 Mar 91 12:54 EST From: "YATES, JOHN H." Subject: 3j Fortran routine To: chemistry@ccl.net Status: R Where can I get a Fortran program to compute 3j symbols? Please reply directly to me, I am not subscribed yet (request is in). Thanks, John yates@c.chem.upenn.edu --- From jkl@ccl.net Tue Mar 5 15:25:57 1991 Date: Tue, 05 Mar 91 15:14:37 EST From: jkl@ccl.net Subject: Protein Data Bank site To: chemistry@ccl.net Status: R Protein Data Bank Brookhaven National Laboratory announced their anonymous ftp site in their Januray 91 Newsletter. Do not get excited though. There are no PDB files there. However, they have a file with current newsletter and current list of PDB entries. Here is how to get there (adapted from their file "access_info.txt" from pub directory): ==================================================================== File Server Available: The PDB now has an e-mail file server available for your use. This server will be providing PDB general information, documentation and other specialized material. To receive more information, send a message to FILESERV@PB1.CHM.BNL.GOV and include the following text: send info your_e-mail_address A user named "jones" at machine "demo.div.inst.edu" would send an e-mail message to FILESERV@PB1.CHM.BNL.GOV with the following text included: send info jones@demo.div.inst.edu Anonymous FTP available: The PDB now has an anonymous ftp account available on the system: IRISC2.CHM.BNL.GOV(130.199.129.8). It is possible to transfer files to and >from this system using "anonymous" as the username and your real username as password. PDB general information and documentation will be available for downloading. You can also upload files you may wish to send to the PDB. Anyone experiencing problems or having questions related to the above network services is requested to send an e-mail message to: SKORA@PB1.CHM.BNL.GOV. ======================================================================= Jan Labanowski Ohio Supercomputer Center 1224 Kinnear Rd Columbus, OH 43212-1163 jkl@ccl.net JKL@OHSTPY.BITNET --- From chemistry-request@ccl.net Tue Mar 5 22:18:39 1991 Date: Tue, 05 Mar 91 20:43:52 CST From: Jan Jensen Subject: Concepts vs. Accuracy?? To: chemistry@ccl.net Organization: North Dakota Higher Education Computer Network Status: R In response to David Bernhold's thoughts, a quote from Levine's 'classical' QUANTUM CHEMISTRY: Approximation of the helium ground-state wave function as a product of hydrogenlike 1s orbitals with effective nuclear charge zeta [...] provides a simple physical picture that is in accord with the usual chemical concepts; however, this function does not give a very accurate value for the energy. When we use a function like [...] with a hundred or so terms, we get an extremely accurate wave function and energy, but we lose the simple physical interpretation. This is a general occurrence in quantum chemistry; "the more accurate the calculations become the more the concepts tend to vanish into thin air."[6] [6] R. S. Mulliken, J. Chem. Phys., 43, s2 (1965). Levin, pg. 209 Jan Jensen (NU145752@NDSUVM1.EDU) Dept. of Chemistry North Dakota State University Fargo, ND 58105 ---