From chemistry-request@server.ccl.net Sun Jan 20 02:03:04 2002 Received: from web12802.mail.yahoo.com ([216.136.174.37]) by server.ccl.net (8.11.6/8.11.0) with SMTP id g0K733I04040 for ; Sun, 20 Jan 2002 02:03:03 -0500 Message-ID: <20020120054921.76790.qmail@web12802.mail.yahoo.com> Received: from [61.9.73.249] by web12802.mail.yahoo.com via HTTP; Sat, 19 Jan 2002 21:49:21 PST Date: Sat, 19 Jan 2002 21:49:21 -0800 (PST) From: amor san juan Subject: AutoDock Tools run problem To: chemistry@ccl.net MIME-Version: 1.0 Content-Type: text/plain; charset=us-ascii Greetings to all AutoDockers: I encountered a problem in compiling AutoDock Tools. The message i get is: Traceback (innermost last): File "/bin/adt1.5", line 50, in ? import AutoDockTools ImportError: No module named AutoDockTools hit enter to continue Any suggestions to be given is highly appreciated. Amor San Juan University of the Philippines-Diliman Philippines __________________________________________________ Do You Yahoo!? Send FREE video emails in Yahoo! Mail! http://promo.yahoo.com/videomail/ From chemistry-request@server.ccl.net Sat Jan 19 21:12:42 2002 Received: from dns.sce.tsinghua.edu.cn ([166.111.18.14]) by server.ccl.net (8.11.6/8.11.0) with ESMTP id g0K2CeI27210 for ; Sat, 19 Jan 2002 21:12:41 -0500 Message-Id: <200201200212.g0K2CeI27210@server.ccl.net> Received: from denny ([166.111.27.50]) by dns.sce.tsinghua.edu.cn (Netscape Messaging Server 3.01) with SMTP id 621 for ; Sun, 20 Jan 2002 09:51:17 +0800 Date: Sun, 20 Jan 2002 10:15:36 +0800 From: Denny To: "chemistry@ccl.net" Subject: about size-consistent method Organization: Tsinghu University X-mailer: FoxMail 3.0 beta 1 [cn] Mime-Version: 1.0 Content-Type: text/plain; charset="us-ascii" Content-Transfer-Encoding: 7bit Dear all, Can someone comment something on size-consistent method? For example, I calculated potential energy curve for molecule AB with B3LYP,CCSD(T) and QCISD(T) methods and aug-cc-pvtz even aug-cc-pvqz, the interaction including BSSE correction E(AB,equilibrium position)-E(A,equilibrium)-E(B,equiblibrium) is -6.5eV, and E(AB,equilibrium)-E(A,single body)-E(B,single body) is also about -6.5eV. However E(AB,nuclei distance R=1nm)-E(A,R=1nm)-E(B,R=1nm) is not 0eV but 0.8eV. Then the real calculated dissociation energy is 6.5eV or (6.5+0.8)eV? I found CCSD(T) and QCISD(T) is also size-inconsistent though someone say CCSD(T) is size-consistent. Any comments will be welcome!!! Best Regards, Denny Chen **************************** * Denny Chen * * Center for Astrophysics * * Tsinghua University * * Beijing, P.R.China * * 8610-62792126(phone) * * 8610-62792125(fax) * **************************** Email:dilys98@mails.tsinghua.edu.cn From chemistry-request@server.ccl.net Sun Jan 20 11:44:16 2002 Received: from gordon.chem.wayne.edu (tyan@[141.217.26.2]) by server.ccl.net (8.11.6/8.11.0) with ESMTP id g0KGiFI19525 for ; Sun, 20 Jan 2002 11:44:15 -0500 Received: from localhost (tyan@localhost) by gordon.chem.wayne.edu (8.10.2+Sun/8.10.2) with ESMTP id g0KGhvE07502 for ; Sun, 20 Jan 2002 11:43:57 -0500 (EST) Date: Sun, 20 Jan 2002 11:43:57 -0500 (EST) From: Tianying Yan To: chemistry@ccl.net Subject: looking for accurate Au-Au force constant Message-ID: MIME-Version: 1.0 Content-Type: TEXT/PLAIN; charset=US-ASCII Dear all, Does anybody know an accurate force constant which can be used to represent Au{111} surface? or some way to fit the force constant by its phonon dispersion? Any reference or suggestion is welcome. I am doing classical MD simulation, Au{111} is used as substrate which is not supposed to be involved too much into the dynamical process of whole system. Therefore, a simple Au-Au force constant should be great helpful. Regards, Tianying Tianying Yan Department of Chemistry Wayne State University tyan@chem.wayne.edu From chemistry-request@server.ccl.net Sun Jan 20 12:33:52 2002 Received: from relay-1v.club-internet.fr ([194.158.96.112]) by server.ccl.net (8.11.6/8.11.0) with ESMTP id g0KHXqI20818 for ; Sun, 20 Jan 2002 12:33:52 -0500 Received: from sungam (212-195-14-216.rsv.n.club-internet.fr [212.195.14.216]) by relay-1v.club-internet.fr (Postfix) with SMTP id 18F9C16F6 for ; Sun, 20 Jan 2002 18:33:26 +0100 (CET) Message-ID: <001c01c1a1d9$6946b020$d80ec3d4@sungam> From: "Julien MICHEL" To: Subject: Hartree fock energy evaluation modus operandi Date: Sun, 20 Jan 2002 18:36:42 +0100 MIME-Version: 1.0 Content-Type: text/plain; charset="Windows-1252" Content-Transfer-Encoding: 7bit X-Priority: 3 X-MSMail-Priority: Normal X-Mailer: Microsoft Outlook Express 5.00.2919.6600 X-MimeOLE: Produced By Microsoft MimeOLE V5.00.2919.6600 Dear CCLers, I know my request might seem a bit strange, but I'm looking for a document which would summarize ALL the calculations performed to evaluate the energy of a simple molecular system using an Hartree-Fock hamiltonien. Since I'm aware that the computations can become pretty quickly untraceable I'd like to see a documents which used a simple basis set ( i.e STO-3G ) for a very simple molecular system (H2 would be the ideal case). The purpose of this request is to obtain sources to help me perform an energy evaluation "by-hand". This probably sounds strange as my home computer would probably be a zillion times faster than I, but altough I'm aware of the way the self-consistent field theory works, I feel frustrated to not know exactly what my computer is doing when I perform an Hartree Fock calculation. MICHEL Julien Graduate student in chemistry From chemistry-request@server.ccl.net Sun Jan 20 20:09:46 2002 Received: from mail.etang.com ([61.152.250.207]) by server.ccl.net (8.11.6/8.11.0) with ESMTP id g0L19jI32641 for ; Sun, 20 Jan 2002 20:09:45 -0500 Received: from lizhenhua (socks.fudan.edu.cn [202.120.224.18]) by mail.etang.com (Postfix) with ESMTP id 707AC1C87EB53 for ; Mon, 21 Jan 2002 09:11:00 +0800 (CST) From: "Zhenhua Li" To: "CCL" Subject: Summary Is "Vibrational Spectroscopy" generally equals to "IR spectroscopy"? Date: Mon, 21 Jan 2002 09:23:11 +0800 Message-ID: MIME-Version: 1.0 Content-Type: text/plain; charset="gb2312" Content-Transfer-Encoding: 7bit X-Priority: 3 (Normal) X-MSMail-Priority: Normal X-Mailer: Microsoft Outlook IMO, Build 9.0.2416 (9.0.2910.0) Importance: Normal In-Reply-To: X-MimeOLE: Produced By Microsoft MimeOLE V6.00.2600.0000 Thanks for everyone. Here is my summary. In my original question, I made a mistake typing "absorption" to "adsorption". It seems most listers agree that Vibrational Spectroscopy does not equal to IR spectroscopy. It is more general than the later. Original question: Hi, Dear listers, Today several staffs have a discussion about what is the implied or generally accepted meaning of "vibrational spectroscopy". One guy insisted that it is generally accepted that when we talked about vibrational spectroscopy, without specify IR or Raman before it, we must say that it is an "adsorption spectroscopy". But I insisted that any spectroscopy that originated from vibrational adsorption or emission can be called "vibrational spectroscopy". Thus, when we talked about "vibrational spectroscopy", we do not really means it is an IR spectroscopy. This is important since the meaning of this term has appeared in an exam paper. It is important to ensure not to give students wrong concept. Thanks a lot. Li Zhenhua Comments: 1. Kimberley Cousins Vibrational spectroscopy means any method that caused vibrations (stretches bends). Some molecular stretching and bending occurs outside the "normal" mid range IR region, hence could not fully and correctly be called IR spectroscopy. 2. Gary Strahan You are correct, "vibrational spectroscopy" refers to any method of spectroscopy which involves the vibrational modes or energy levels of a molecule. Note that "absorption spectroscopy" does not need to involve vibrations, but can also involve rotational energy levels and the link. Hence, "absorption spectroscopy" it includes many other spectroscopic techniques besides besides UV, IR and Raman. Indeed, Raman and fluorescence are not strictly "absorption" spectroscopies as they also involve scattering and emmission processes, respectively. In other words, the terms "absorption" and "vibrational" describe different things. Some techniques fall into only one of the two categories, while other techniques fall into both categories. So, to be completely correct, one should use terms such as, "vibrational IR absorption," "vibrational Raman spectroscopy," "rotational fluorescence emmission." More general terms might be "vibrational absorption spectroscopy," "rotational absorption spectroscopy," "vibrational Raman scattering," etc. Note that you used the term "adsorption" below, instead of "absorption." These are also quite different things. Adsorption is the phenomenon of one molecule sticking to the surface of something else, usually a chromatographic column. 3. Steve Cabaniss In my opinion, the term 'vibrational spectroscopy' refers to both IR absorption and to Raman scattering. This is how we use the term in our analytical spectroscopy classes. Graybeal (Molecular Spectroscopy 1988) discusses Raman in his chapter on vibration, and McHale (Molecular Spectroscopy 1999) discusses Raman in her chapters on vibrational spectroscopy. This appears to be a generally accepted useage. 4. David Shobe My own opinion only: In practice "vibrational spectroscopy" is generally synonymous with "IR spectroscopy." However, there is a reason for having the 2 terms, since they are not *precisely* synonymous, and different concepts are involved in the 2 terms even if in practice the spectra being discussed are the same. "Vibrational" spectroscopy refers to the method in which the substance gains energy as a result of absorption: the energy goes largely into nuclear motions which involve changing of bond lengths & angles. "IR" (= "infrared") spectroscopy refers to the frequencies of electromagnetic energy being absorbed. As for "absorption" spectroscopy (I expect "adsorption" is a mistake, since I still get those words mixed up on occasion myself :-), this is an entirely separate issue. Absorption spectroscopy means that material is gaining energy at the expense of the electromagnetic field; emission spectroscopy means that the material is emitting energy as electromagnetic radiation. 5. Steve Williams As one whose graduate training was in one of more unusual vibrational spectroscopies, I would suggest that a vibrational spectroscopy is one of any methods that probes differences between vibrational energy levels. This would include IR (the usual absorbance method as well as emission) as well as a whole host of inelastic scattering methods: Raman spectroscopy for which the selection rules are well understood; Inelastic Neutron Scattering Inelastic Electron Tunneling Spectroscopy (IETS) Low energy Electron Energy Loss Spectroscopy (LEELS) There are probably more such techniques now. I think that the selection rules for the later scattering methods are not as well understood as IR and Raman. In addition to the direct vibrational methods, there is often a significant amount of information about ground and excited vibrational levels in the electronic spectrum of a molecule as well. 6. Stefan Grimme In my opinion, vibrational spectroscopy invloves transitions between (ro)vibrational wave functions (i.e. depending mainly on nuclear degrees of freedom) and is independent how these transitions are induced and how the selection rules look like (think e.g. of vibrational CD) 7. Roy Jensen In my opinion, INFRARED SPECTROSCOPY is any method that probes the vibrational levels in a single electronic state of a molecule. Similar definitions can be applied to ROTATIONAL and ELECTRONIC spectroscopy. In all cases, all lower energy transitions are coupled to the given transtion. They may not be resolved, but they account for features. For example, the rotational transitions associated with a given infrared transition generate the PQR bands common in conventional infrared spectroscopy. 8. Ida N. L. Ma Vibrational spectroscopy describes the physical origin of the absorption/emission of the energy transition. IR is just at the correct wavelength for this to happen. From chemistry-request@server.ccl.net Sun Jan 20 20:39:44 2002 Received: from sirius.chem.vt.edu (IDENT:root@[128.173.181.42]) by server.ccl.net (8.11.6/8.11.0) with ESMTP id g0L1diI01403 for ; Sun, 20 Jan 2002 20:39:44 -0500 Received: from localhost (crawdad@localhost) by sirius.chem.vt.edu (8.11.0/8.11.0) with ESMTP id g0L1dQw20040; Sun, 20 Jan 2002 20:39:26 -0500 X-Authentication-Warning: sirius.chem.vt.edu: crawdad owned process doing -bs Date: Sun, 20 Jan 2002 20:39:26 -0500 (EST) From: "T. Daniel Crawford" X-Sender: To: Denny cc: Subject: Re: CCL:about size-consistent method In-Reply-To: <200201200212.g0K2CeI27210@server.ccl.net> Message-ID: MIME-Version: 1.0 Content-Type: TEXT/PLAIN; charset=US-ASCII On Sun, 20 Jan 2002, Denny wrote: > Dear all, > > Can someone comment something on size-consistent method? For example, I calculated potential energy curve for molecule AB > with B3LYP,CCSD(T) and QCISD(T) methods and aug-cc-pvtz even aug-cc-pvqz, the interaction including BSSE correction > E(AB,equilibrium position)-E(A,equilibrium)-E(B,equiblibrium) is -6.5eV, and E(AB,equilibrium)-E(A,single body)-E(B,single > body) is also about -6.5eV. However E(AB,nuclei distance R=1nm)-E(A,R=1nm)-E(B,R=1nm) is not 0eV but 0.8eV. Then the real > calculated dissociation energy is 6.5eV or (6.5+0.8)eV? I found CCSD(T) and QCISD(T) is also size-inconsistent though > someone say CCSD(T) is size-consistent. > > Any comments will be welcome!!! > > Best Regards, > Denny Chen > I'm not certain how to interpret all the calculations you describe above, but the basic definition of size-consistency involves non-interacting fragments. If you take two water molecules, for example, and place them an infinite distance apart, the energy you compute using a size-consistent method will be twice that for a single isolated water molecule. For this example, both QCISD(T) and CCSD(T) are size-consistent. One complication in the concept of size-consistency arises for closed-shell electronic states dissociating into open-shell fragments. If the non-interacting dimer involves an overall singlet state, for example, and the fragments are high-spin, then the single-determinant RHF method will not be size-consistent because two determinants are required for the dimer while only one is required for each high-spin fragment. I hope this helps. -TDC -- 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