From ADAMO@CHEMNA.DICHI.UNINA.IT Thu May 12 09:53:53 1994 Received: from CHEMNA.DICHI.UNINA.IT for ADAMO@CHEMNA.DICHI.UNINA.IT by www.ccl.net (8.6.4/930601.1506) id JAA24668; Thu, 12 May 1994 09:40:55 -0400 From: Received: from CHEMNA.DICHI.UNINA.IT by CHEMNA.DICHI.UNINA.IT (PMDF V4.2-11 #3559) id <01HC8XYCB2780001GK@CHEMNA.DICHI.UNINA.IT>; Thu, 12 May 1994 10:13:36 CET Date: Thu, 12 May 1994 10:13:35 +0100 (CET) Subject: Schaefer, Horna and Ahlrich's basis sets To: chemistry@ccl.net Message-id: <01HC8XYCBBUE0001GK@CHEMNA.DICHI.UNINA.IT> X-VMS-To: IN%"chemistry@ccl.net" X-VMS-Cc: ADAMO MIME-version: 1.0 Content-type: TEXT/PLAIN; CHARSET=US-ASCII Content-transfer-encoding: 7BIT Dear CCl friends, I am looking for the basis sets of Scaefer, Horn and Ahlrichs, published in J. Chem. Phys. 97 (1992) 2571. The authors reported in this article an internet address from which pick up the basis sets. I was not able to connect with him. Do you know if this internet address is still good or if there is another site from which pick up the basis sets? Thank Ciao Carlo From MTALIB@FRCU.EUN.EG Thu May 12 10:56:28 1994 Received: from FRCU.EUN.EG for MTALIB@FRCU.EUN.EG by www.ccl.net (8.6.4/930601.1506) id KAA28072; Thu, 12 May 1994 10:38:19 -0400 From: Received: from FRCU.EUN.EG by FRCU.EUN.EG (PMDF V4.2-11 #3805) id <01HC9CGJZI2O0045LS@FRCU.EUN.EG>; Thu, 12 May 1994 17:37:30 O Date: Thu, 12 May 1994 17:37:30 +0000 (O) Subject: Help for a new user ...... To: CHEMISTRY@ccl.net Message-id: <01HC9CGK0KNM0045LS@FRCU.EUN.EG> X-VMS-To: IN%"CHEMISTRY@ccl.net" MIME-version: 1.0 Content-type: TEXT/PLAIN; CHARSET=US-ASCII Content-transfer-encoding: 7BIT Hello everybody .. I am a new user of ab initio method , I have tried gamess and G92 . When i use double zeta basis sets i get the " POPULATION OF EACH ATOMIC ORBITAL" with the basis sets functions and not the atomic orbital. I was told to add the popullation of the inner and the outer functions assuming that each two functions represent one atomic orbital . When i ran a job containing only one Ca atom , i found that the first molecular orbital ( 1s atomic orbital in this case ) , contains significant contributions >from all the s functions in the basis set , and the same with the 2s etc .. So , what does it mean to get the population of a basis set function if this function contributes to more than one atomic orbital , and how can one get the population of the atomic orbitals ...... Please reply directly to me as i am not a memeber of this group . M.T. Ali From tripos!krypton!mike@uunet.UU.NET Thu May 12 11:06:44 1994 Received: from relay3.UU.NET for tripos!krypton!mike@uunet.UU.NET by www.ccl.net (8.6.4/930601.1506) id KAA28494; Thu, 12 May 1994 10:46:23 -0400 Received: from uucp5.uu.net by relay3.UU.NET with SMTP (5.61/UUNET-internet-primary) id AA17805; Thu, 12 May 94 10:46:17 -0400 Received: from tripos.UUCP by uucp5.uu.net with UUCP/RMAIL ; Thu, 12 May 1994 10:46:16 -0400 Received: from krypton.tripos by tripos (4.1/SMI-4.0) id AA07374; Thu, 12 May 94 09:31:22 CDT Received: by krypton.tripos (920330.SGI/5.6) id AA04817; Thu, 12 May 94 09:31:22 -0500 Date: Thu, 12 May 94 09:31:22 -0500 From: tripos!krypton!mike@uunet.UU.NET (Mike Sullivan Krypton) Message-Id: <9405121431.AA04817@krypton.tripos> To: uunet!ccl.net!chemistry@uunet.UU.NET Subject: Conf. Searching on the PC A new Windows-based program for conformational searching is now available >from Tripos called PowerSearch. Sharing the same molecular mechanics force field as ALCHEMY and SYBYL, PowerSearch allows PC users to explore molecular conformations and related energies in search for a global minimum. Both Monte Carlo and Systematic Search operations may be performed using PowerSearch's Windows menus and dialog boxes. Used along with Tripos' ALCHEMY and ChemPrint, PowerSearch links advanced analysis with 3D molecular visualization and 2D presentation. PowerSearch is priced at $395 ($275 for academics). System requirements: 386 processor (or higher), Windows 3.0 or higher, and at least 2 megabytes of RAM. For complete literature send/fax/e-mail your postal address to Tripos, 1699 S. Hanley, St. Louis, MO 63144. Phone: (800) 323-2960 FAX: (314) 647-9241 or e-mail mike@tripos.com. From ccl@probe.ac1.uni-duesseldorf.de Thu May 12 11:16:31 1994 Received: from probe.ac1.uni-duesseldorf.de for ccl@probe.ac1.uni-duesseldorf.de by www.ccl.net (8.6.4/930601.1506) id KAA28803; Thu, 12 May 1994 10:51:54 -0400 Received: by probe.ac1.uni-duesseldorf.de (5.61/1.34) id AA07149; Thu, 12 May 94 16:50:41 +0200 From: ccl@probe.ac1.uni-duesseldorf.de (Computational Chemistry List) Message-Id: <9405121450.AA07149@probe.ac1.uni-duesseldorf.de> Subject: thermal energy (summary) To: chemistry@ccl.net (Theochem-Liste) Date: Thu, 12 May 1994 15:50:40 +0100 (MET) Cc: dronia@clio.ac1.uni-duesseldorf.de, boetzel@convex.ac1.uni-duesseldorf.de X-Mailer: ELM [version 2.4 PL2] Content-Type: text Content-Length: 11645 Hi netters! A long time ago (as I was remembered recently), I asked a question about "thermal energy". I received interesting replies and now I will post them. After that I will describe what opinion I am of now, comparing your suggestions. Thanks for your help! ********************************************* My original question was: Dear Netters! I have a question about the thermal energy, concerning rotational barriers. How can you calculate this energy in dependence of the absolute temperature? Some people told me it must be E = 3/2 * RT for a non-linear molecule, but this doesn't fit to experimental data (Ethane has a rotational barrier of approx. 3 kcal/mol and 3/2 * RT would be only 0.89 kcal/mol for T=298K). Any suggestions? Kay. ********************************************* And now the replies. Thanks for all of them! ********************************************* From: Michael A. Lee I assume that you will be getting responses that explain that the classical result for 1/2 kT per degree of freedom is modified at low temperature due to quantum discrete states. Low temperature is defined as when the energy difference between states is not much smaller than the thermal energy (kT). Mike ********************************************* From: GKING@arserrc.gov [ my question - deleted ] Hello Kay, It sounds like you may be confusing the rotational barrier height with the rotational thermal energy. The rotational energy barrier is determined by a molecule's potential energy function, and is independent of temperature. The rotational thermal energy is the average kinetic energy one would expect to find in any given rotational degree of freedom, based on statistical probabilities. Hope this helps. Let me know if you still have a question about this. Regards, Greg ================================================================= Gregory King Internet: gking@arserrc.gov Eastern Reg. Res. Ctr., ARS, USDA Voice: (1) 215 233 6675 600 East Mermaid Lane Fax: (1) 215 233 6559 Philadelphia, PA 19118-2551 ================================================================= ********************************************* From: soperpd@nylon.es.dupont.com (Paul Soper) Kay, A distinction must be made between rotation of the molecule as whole and internal rotation about a bond. The first does indeed contribute 3RT/2 to the energy of a non-linear molecule. The energy of around 3 kcal/mole refers to internal rotation. Internal rotation about a bond usually must be treated quantum mechanically. The energy levels can be calculated using perturbation theory (see W.H. Flygare, "Molecular Structure and Dynamics," chapter 4). You then need to calculate the partition function to get thermodynamic properties (see D.A. McQuarrie, "Statistical Mechanics," chapter 8). You should be able to find a treatment of internal rotation in any statistical mechanics text. - Paul Soper Paul Soper soperpd@esvax.dnet.dupont.com DuPont FAX (302)-695-1717 Tel (302)-695-1757 All the usual disclaimers apply ********************************************* From: "Janet Del Bene" Kay, The 3/2 RT refers to the energy of the three degrees of rotational freedom of a nonlinear molecule. The rotational barrier (in ethane, for example) is an INTERNAL rotation about a specific bond. In order to calculation the internal rotational energy barrier you need to optimize the structure of the molecule to get its energy, and then optimized the transition structure for rotation. In ethane, for example, you would fully optimize the staggered conformation, and then fully optimize the eclipsed conformation. The energy difference would be the rotational energy barrier. Janet E. Del Bene ********************************************* From: gene@jersey.cray.com (Eugene Fleischmann) [ my question - deleted ] If I understand your question correctly, what you want is the population split between two rotational states separated by a barrier of Er, where E2 > E1. This is the population ratio: P(E2)/P(E1) = e**(-Er/RT) = .006 for Er=3 kcal/mole and RT=.593 (i.e.T=298) [P(E1)/P(E2)=.994 ] therefore, the fraction of the population in state 2 with respect to the whole is: P(E2)=.006*P(E1)=.006*(1-P(E2)), P(E2)=.006/1.006=.006 or .6% [P(E1)=99.4%] P(E2)/P(E1)=.221 at T=1000K, therefore, P(E2)=.181 or 18.1% [P(E1)=81.9%] +++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ Eugene D. Fleischmann, Ph.D. Computational Chemist Cray Research, Inc. (609) 252-1250 121 Commons Way gene@calv2.cray.com Princeton, NJ 08540 +++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ ********************************************* From: GOVENDEM [my questions - deleted] Dear Kay, If my memory serves me correct, I think the above equation is only for ideal systems of gases and not real gases, hence explaining the descrepancies in your results. Hope this helps MaganMagan Govender Dept of Chemistry University of Natal Durban South Africa ********************************************* From: ev@dim.jussieu.fr (Earl EVLETH p 74208) On rotational corrections to either enthalpy or entropy read Benson's book on Thermochemical Kinetics. Otherwise one goes back to Pitzer in the 1950s (his Quantum Chemistry text is pretty good also for a number of similar subjects that are not treated in modern texts) Evleth(Paris) ********************************************* From: jolly@IRIS.medc.umn.edu (James "Jolly" Rodgers) Dear Kay, [ my question - deleted ] I take it you are referring to the barrier of rotation about the central bond in ethane. I prefer to refer to this as a "torsional barrier" to distinguish it from a barrier for molecular rotation. Anyway, I believe the correct formula for the ensemble average for available thermal energy is actually 3/2 * nRT where n is the number of atoms. For ethane, it is thus 8 * 0.89 = 7.1 kcal/mole. This is the average total energy that is available to the molecule and includes contributions due to stretching and bending as well as molecular translation and rotation. Thus, the energy is divided over a number of degrees of freedom, with a range of atomic speeds given by the Boltzmann distribution. At any particular instant, some degrees of freedom will have very little kinetic energy while others may have considerable kinetic energy. What you are perhaps more interested in is the rate at which structures of a particular energy are observed (such as the transition state in a conformational interconversion). This is: Rate = dN/dt = A * exp (- delta E/ RT) Or the integrated form: delta N = A * delta t * exp (- delta E/ RT) where A is a preexponential factor which is dependent on entropic factors; t is time; and delta E is the difference in energy between the structure of interest and that of a stable state, often presumed to be the global minimum. The preexponential factor is basically the probability of obtaining a particular structure, given sufficient kinetic energy is available. It can have contributions due to a number of factors (for example orientational factors) and I believe that the preexponential factor is usually derived experimentally, although it can in principle be derived by theoretical means, such as through a molecular dynamics simulation. Anyway, the essence of the above equation is that the number of times that a particular structure is observed decreases exponentially as the energy of the structure increases, increases in an exponential manner with regard to absolute temperature, and also increases linearly as one observes for longer periods of time. I don't know offhand what the preexponential factor is for torsional interconversion in ethane, I can say though that on the time scale of molecular dynamics simulations (i.e. picoseconds) it is common to observe fluctuations in conformational energy of 3 to 5 kcal/mole, so for ethane on an experimental time scale (i.e. usually milliseconds or longer), one would expect to see rapid conformational interconversions. Hope this helps! Sincerely, James "Jolly" Rodgers Dept. Of Medicinal Chemistry University Of Minnesota ********************************************* From: "Carlos F. S. Castro" [my question deleted] Dear Mr. K. Kreidler, Concerning the calculations of rotational barriers, maybe i can have the answer. Using ab initio molecular calculation you can estimate them throught a vibracinal frequency job. In the Gaussian program, which i use, one of the out- puts is the thermal energies (hartree/particle). Doing it in the two forms, the lower one and the highest one in energy and getting the difference should give you the answer desired: for Ethane, the forms should be staggerd and eclipsed, i guess. If i'm right, please call back, because i would like to know for sure. Thanks, Carlos F. S. Castro Comp. Chem. Lab. University of Brasilia, Brazil. ********************************************* From: "Joao O.M.A. Lins" Dear Dr. Kreidler, I would like to receive the summary of this question. Thanks in advance, Joao/// ********************************************* From: davide@stinch0.csmtbo.mi.cnr.it dear Kay did you received any answer to your interesting inquire? [ my question - deleted ] thank you Davide ------------------------------------------------------------------- Davide M. Proserpio - Istituto di Chimica Strutturistica Inorganica Universita' di Milano, Via Venezian, 21 - 20133 Milano, Italy phone +39-2-70635120 fax 70635288 - davide@stinch0.csmtbo.mi.cnr.it ------------------------------------------------------------------- From: "RUBEN E. VENEGAS" Hi Kay, I saw your posting regarding thermal energy a while ago. I was thinking I was going to see some replies, but nothing so far. Have you got any replies , if so could you share them with me ?? I really appreciate it. my e-mail is venegas_r@casper.fisons.com Thank you very much. Ruben Venegas ********************************************* And now I will a summary of what I think is right, after I have compared all the results. There is a difference between 1. the rotation of the whole molecule and 2. the rotational barrier along one specific bond. First depends on the degrees of freedom of the molecule, which is actually 1.5 nRT in the case of a non-linear molecule (with n being the number of atoms). So this energy depends on the temperature. The rotational barrier height along one bond is described by the potential function of the molecule, and this function is temperature independent. If you have a difference in energy between to states, you must use Boltzmann's equation to calculate the distribution of the species on these states. So you cannot attach a sharp energy value to a chosen temperature, but always have a distribution of energy. What I wanted to describe, was the second case. Now, after your advice and a bit of thought it's seems all so simple. Again, thanks for your help and my apologies for letting you wait for so long! Bye bye. Kay Kreidler. From shenkin@still3.chem.columbia.edu Thu May 12 11:53:45 1994 Received: from still3.chem.columbia.edu for shenkin@still3.chem.columbia.edu by www.ccl.net (8.6.4/930601.1506) id LAA29691; Thu, 12 May 1994 11:39:38 -0400 Received: by still3.chem.columbia.edu (931110.SGI/930416.SGI.AUTO) for chemistry@ccl.net id AA11358; Thu, 12 May 94 11:39:21 -0400 From: "Peter Shenkin" Message-Id: <9405121139.ZM11356@still3.chem.columbia.edu> Date: Thu, 12 May 1994 11:39:07 -0400 In-Reply-To: bewilson@emn.com (Wilson_Bruce) "CCL:Energies of conformations" (May 10, 4:58pm) References: <9405102058.AA14027@emngw1.emn.com> X-Mailer: Z-Mail (3.1.0 22feb94 MediaMail) To: bewilson@emn.com (Wilson_Bruce), chemistry@ccl.net Subject: Re: CCL:Energies of conformations Content-Type: text/plain; charset=us-ascii Mime-Version: 1.0 On May 10, 4:58pm, Wilson_Bruce wrote: > Subject: CCL:Energies of conformations > Patrick Bultinck asks: > > I would like to hear different opinions to how to more or less draw a > > line between confomers that may show an ***important*** occupation at a > > temperature T, and which conformers do not show any ***important*** > > occupation! I have thusfar found a number of quite contradictory > > statements, and would like to hear other peoples opinions. > Sure, I'll wade in with a very equivocal answer: "It depends!". > Seriously. If the Boltzman distribution shows a 1% population of > a conformer level, that may be insignificant for some applications, but > it may be highly significant for others. But the simple answer is that > I'll do a Boltzman analysis... Another thing that people sometimes forget: this depends on the density of states as well as the energy difference. For example, suppose in a conformational search one locates a particular conformer which is kT in energy above the minimum found; let's also assume that the search was exhaustive, and the the minimum found really is the global minimum. All one can deduce from the information I've given so far is that the higher energy conformer is present to the extent of about 37% (that is, exp(-1) ) of the lower-energy conformer. If these were the only two conformers present the two percentage occurrences would be 1/1.37 and 0.37/1.37, or 73% and 27%. I have seen people make statements like, "This conformer had energy kT above the global minimum, and is therefore present 27% of the time." Of course, if there are many other conformers, all of them will be populated to some extent, and the figure of 27% will be a gross overestimate; this is particularly true when the region between the global minimum and kT above it is densely populated. Bruce's Bolzmann analysis would take this into account; I mention it because in casual discussion it is sometimes forgotten. Also, a comment on Patrick's term, "*** important ***". When trying to figure out what is important, it is best to think in terms of experiment. If you are looking at proton NMR data, then each proton has the same "extinction coefficient", and a species present at less than 1% in total concentration may not even be visible if there are several other species present. Thus, if you are comparing your computation with NMR data, 1% might be unimportant. But if you are using UV spectroscopy, that species might have an extinction coefficient 1000 times greater than some other species which is present at 100 times its concentration -- so here, that 1% would be highly important. Similarly, if the assay is biological, a low-concentration isomer might be the only one that is active. -P. -- *********** After the revolution, everyone will have a home page. *********** Peter S. Shenkin, Box 768 Havemeyer Hall, Dept. of Chemistry, Columbia Univ., New York, NY 10027; shenkin@still3.chem.columbia.edu; (212) 854-5143 ***************************************************************************** From mercie@mail.med.cornell.edu Thu May 12 13:53:50 1994 Received: from mail.med.cornell.edu for mercie@mail.med.cornell.edu by www.ccl.net (8.6.4/930601.1506) id NAA01355; Thu, 12 May 1994 13:27:37 -0400 Received: (from mercie@localhost) by mail.med.cornell.edu (8.6.8/ech1.65) id NAA05347; Thu, 12 May 1994 13:27:29 -0400 Date: Thu, 12 May 1994 13:27:28 -0400 (EDT) From: Gustavo Mercier Subject: Re: CCL:Energies of conformations To: Peter Shenkin cc: Wilson_Bruce , chemistry@ccl.net In-Reply-To: <9405121139.ZM11356@still3.chem.columbia.edu> Message-ID: MIME-Version: 1.0 Content-Type: TEXT/PLAIN; charset=US-ASCII One final comment ... If you wish to compare with experiments, you must use the appropriate Free Energy in your Boltzman population analysis. It is "common" to compute internal energy and "forget" about the entropy. gus mercier mercie@cumc.cornell.edu