From owner-chemistry@ccl.net Sun Dec 14 00:31:01 2008 From: "Mr shabbir shabbir###nenu.edu.cn" To: CCL Subject: CCL:G: First hyperpolarizability by Finite Field Message-Id: <-38296-081214002944-23383-DLlIbQYtBjb3CmQ29WzH5w()server.ccl.net> X-Original-From: "Mr shabbir" Date: Sun, 14 Dec 2008 00:29:39 -0500 Sent to CCL by: "Mr shabbir" [shabbir=nenu.edu.cn] Dear CCL users! I am in dire need of some comments about my problem. I have calculated First Hyperpolarizability (Bo) with Finite Field method. I have put following key words in rout section #P polar=Enonly b3lyp/6-31G* test I got the ten components according to G03 manual, sum up 9 of them on individual axis and took their square and square root to get Beta(Total). I read in many papers like this First hyperpolarizability is calculated using the field value of 0.0010au.,the default convergence criteria in G03 was used". or "First hyperpolarizability is calculated using the field frequency of 0.0010au.,the default convergence criteria in G03 was used Now My questions 1. what about the external electric field value in my case? Is it 0.001au or zero (I mean what is by default in G03)? 2. Is it of same intensity along all three axes? 3. How can I justify this choice of external field for my system? 4. What is the difference b/w freq dependent and field dependent hyperpolarizability from the theoretical point of view? Mr.Shabbir From owner-chemistry@ccl.net Sun Dec 14 11:48:00 2008 From: "VITORGE Pierre 094605 Pierre.VITORGE^^cea.fr" To: CCL Subject: CCL: translational entropy in solution Message-Id: <-38297-081214072837-14991-iVy4L0k3XofCT/NNBFGWSQ|-|server.ccl.net> X-Original-From: "VITORGE Pierre 094605" Content-class: urn:content-classes:message Content-Transfer-Encoding: quoted-printable Content-Type: text/plain; charset="iso-8859-1" Date: Sun, 14 Dec 2008 12:03:54 +0100 MIME-Version: 1.0 Sent to CCL by: "VITORGE Pierre 094605" [Pierre.VITORGE,cea.fr] A dimmer with very long distance between the 2 monomers is meaningless.=20 Deciding you have a dimmer (or any chemical species) means you make an = approximation where you split atomic interactions between (strong) = intramolecular and (weak or even zero for the ideal systems) = intermolecular ones: when the dimmer is formed there is a strong enough = bound between the monomers and they are at short distance.=20 This difference between strong/zero interatomic interactions is at the = basis of the thermodynamic demonstration of the law of mass action and = the corresponding equilibrium "constant" (actually a function of P and = T) K, where delta_G=B0 =3D -RTlnK (G=B0, not G) and so on... Besides this thermodynamic feature, note that solvation often has a huge = contribution to the total energy with eventually both enthalpic and = entropic contributions. --=20 Pierre Vitorge http://www.vitorge.name -----Message d'origine----- De=A0: owner-chemistry+pierre.vitorge=3D=3Dcea.fr_+_ccl.net = [mailto:owner-chemistry+pierre.vitorge=3D=3Dcea.fr_+_ccl.net] De la part = de Andreas Klamt klamt/./cosmologic.de Envoy=E9=A0: vendredi 12 d=E9cembre 2008 08:46 =C0=A0: VITORGE Pierre 094605 Objet=A0: CCL: translational entropy in solution Sent to CCL by: Andreas Klamt [klamt%a%cosmologic.de] > > Let us for a moment assume that A =3D B i.e. consider > =20 >> A +A --> AA >> >> and the interactions and surface of AA are just twice the = interactions=20 >> of A. We may consider the case of 2 cyclohexane molecules getting = bound=20 >> together by a virtual stiff bond which is long enough so that there = are=20 >> no relevant interactions between the 2 parts. In the gasphase this = leads=20 >> to a large loss of free energy due to the loss of the translational = and=20 >> rotational free energy (not just entropy) of one of the particles >> =20 > > Actually if there is a loss in the entropy of the system its free = energy increases: > > dG =3D dH - TdS > dS < 0 , dG increases. > =20 Sorry for being a little unprecise here regardig the sign, but I think=20 it is clear what I am talking about. > Also, there is an increase in the enthalpy of the system(considering = that no kind of interaction is going on between A and A,what is quite = contradictory anyway) after the reaction. The new vibrational modes in = AA are going to have a zero point energy that is bigger than the = rotational and translational energies of the reagents, increasing the = enthalpy of the system, which is another reason for an increase in G and = for this reaction to be non-spontaneous > > =20 >> I believe that the physics is correct here. The solvent definitely=20 >> reduces the motional (kinetic) phase space. The molecules cannot move = >> and rotate as freely as they can in the gasphase, and hence the part = of=20 >> the free energy arising from the integration over momentum and=20 >> rotational momentum must be reduced in solution. Obviously, and here = I=20 >> agree with the other people in the discussion, the solute can take = all=20 >> positions and orientations, as in the gasphase, and hence the free=20 >> energy arsing from these integrals are the same as in the gasphase. >> =20 > =20 > Actually, although the solute can take all positions and orientations, = in solution some of these are going to be very disfavored energetically, = while others are going to be more favored, and that is introduced by the = term U (potential energy) in the integral used to calculate the = molecular partition function. So the molecular partition function is not = going to be the same as in the gas phase. > =20 Indeed, I mentioned this in the next partof my last CCL entry (see=20 below) . My argument is that these contributions are unlikely to cancel. = Indeed, I have no estimate which contribution is stronger. We have no=20 chance to sest that, because my virtual case of a dimerization with a=20 virtual long connection between the two parts will never be realized in=20 nature. Association here alway goes along with interactions and hence=20 with large changes in the interaction integrals. Usually the overall=20 external polarity of the dimer will be strongly reduced in association.=20 Hence we will never be able to proof my arguments in reality. > =20 > =20 >> Obviously, in reality, if we generate real close contact associates = or=20 >> even product molecules, the loss of the external degrees of freedom = will=20 >> be partly compensated by additional internal vibrational modes. But = it=20 >> is unlikely that this exactly matches the loss of external degrees of = >> freedom. Please note, that usually the change in the vibrational free = >> energies upon solvation is parameterized int the surface proportinal=20 >> part of solvation models, i.e. the non-electrostatic parts. >> =20 > =20 > Non-electrostactic contributions in most of the solvent models = also(actually they should, but in most cases don't) account for the = change in all of the other components of free energy. What about = COSMO-RS? I don't have access to your book and I'm going to read a paper = on COSMO-RS soon, but I'm very curious on the physical foundations of = the 2 extra terms (the one proportional to lnV and the one that depends = on the temperature) you've mentioned. Where does these terms come from? = What is parametrized in the model?=20 > =20 There are typically 3 contributions to the non-electrostatic terms: 1) the "cavitation energy" often expressed as a kind of solvent specific = surface tension. This part is not required in COSMO-RS but it=20 automatically aises from the statistical thermodynamics for the slute=20 and solvent surface interactions. The free energy required to break the=20 solvent-solvent contacts in order to enable solute-solvent contacts=20 automatically and termodynamically consistently follows rom that. Hence=20 COSMO-RS does not need such a thing as a solvent surface tension: This=20 automatically follows from the sigma-profile (COSMO charges) of the = solvent. 2) the non-electrostatic interactions: The hydrogen bond interations in=20 COSMO-RS are part of the surface interations taken into account in the=20 statistical thermodynamics, quantified approximately based on the=20 surface polarities (COSMO polarization charge densities) of donor and=20 acceptor. The vdW-interactions are the weekest part of COSMO-RS: They=20 are just taken into account as surface proportial with element specific=20 vdW-surface tensions (one of the 2 element specific parameters of=20 COSMO-RS, the other being the element specific radius). We assume that=20 the the vdW-interactions have a generic temperature dependence (hence a=20 split into enthalpic and entropic contributions). Other solvation models need to parameterize all this into empirical=20 corrections or solvent specific radii scaling, ... > =20 >> This=20 >> allows for the treatment of phase diagrams, vapor pressures, .... the = >> entire fluid phase equilibrium thermodynamics. And in difference to=20 >> dielectric solavtion models COSMO-RS yields entropic and enthalpic=20 >> contributions of the solvation energy (because it does a statistical=20 >> thermodynamics!!!) For example, it correctly describes the solvation = of=20 >> alkanes n water as a mainly entropic effect, in best agreement with = the=20 >> experiment. >> =20 > =20 > Do you mean that COSMO-RS yields each = component(translational/rotational/vibrational/electronic) of entropy = and enthalpy or that it only separates the free energy of solvation in = enthalpy and entropy contributions? No, COSMO-RS does not yield all the contributions separately. What we=20 can separate are the electrostatic, hydrogen bonding and vdWs=20 contribution to the interaction enthalpy. The other components are=20 essentially parameterized into the few adjusted pareters of COSMO-RS.=20 Since there is no fundamental theory of the translations, rotations and=20 vibrations in solution, there is no chance to do this rigorously. And=20 fitting to exp. free energies of solvation does not allow us to split=20 the contributions with respect to the physical origin. But we can quite=20 clearly say that we find a significant (~3 kcal/mol at 298 K)=20 contribution to the free energy of solvation which is directly connected = to the molecule and not indirectly via its interactions and surface. Best regards Andreas --=20 -------------------------------------------------------------------------= - Dr. habil. Andreas Klamt COSMOlogic GmbH&CoKG Burscheider Str. 515 51381 Leverkusen, Germany Tel.: +49-2171-73168-1 Fax: +49-2171-73168-9 e-mail: klamt],[cosmologic.de web: www.cosmologic.de -------------------------------------------------------------------------= - COSMOlogic Your Competent Partner for Computational Chemistry and Fluid Thermodynamics -------------------------------------------------------------------------= - Please note our COSMO-RS Symposium in 2009=20 (For details see: http://www.cosmologic.de/Symposium/symposium.html) -=3D This is automatically added to each message by the mailing script = =3D-http://www.ccl.net/cgi-bin/ccl/send_ccl_messageSubscribe/Unsubscribe:=20Job: http://www.ccl.net/jobs=20Search Messages: http://www.ccl.net/htdig (login: ccl, Password: = search)http://www.ccl.net/spammers.txt From owner-chemistry@ccl.net Sun Dec 14 13:19:01 2008 From: "VITORGE Pierre 094605 Pierre.VITORGE/a\cea.fr" To: CCL Subject: CCL: translational entropy and solvation Message-Id: <-38298-081214072824-14954-WGjVCRvdpdQjs7YULJcHcw[A]server.ccl.net> X-Original-From: "VITORGE Pierre 094605" Content-class: urn:content-classes:message Content-Transfer-Encoding: quoted-printable Content-Type: text/plain; charset="iso-8859-1" Date: Sun, 14 Dec 2008 12:09:33 +0100 MIME-Version: 1.0 Sent to CCL by: "VITORGE Pierre 094605" [Pierre.VITORGE:_:cea.fr] Following your reasoning I believe the partition function of the solute = has the same form as in the gas phase + a constant term for the (mean) = solute-solvent interaction (ant this is also at the basis of the analogy = between partial pressure and osmotic pressure). "the same form" does not = mean equal to, just the same mathematical form because the ideal = solution is an ideal gas + a constant (mean) interaction with the = solvent --=20 Pierre Vitorge http://www.vitorge.name -----Message d'origine----- De=A0: owner-chemistry+pierre.vitorge=3D=3Dcea.fr-x-ccl.net = [mailto:owner-chemistry+pierre.vitorge=3D=3Dcea.fr-x-ccl.net] De la part = de Michael K. Gilson gilsona/umbi.umd.edu Envoy=E9=A0: vendredi 12 d=E9cembre 2008 05:15 =C0=A0: VITORGE Pierre 094605 Objet=A0: CCL: translational entropy and solvation Sent to CCL by: "Michael K. Gilson" [gilson^umbi.umd.edu] Dear Raphael, Actually, the mathematical model I'm talking about is not based on the=20 ideal gas model. Rather, it is based upon the lovely mathematical fact=20 that one can write solution theory in a form that looks like ideal gas=20 theory even though it accounts, at least formally, for all=20 intermolecular interactions. This correspondence, which I believe was=20 proven by McMillan and Mayer in the '40s, is connected with the fact=20 that, just as PV=3DnRT in gas phase, so \Pi V =3DnRT in solution phase,=20 where \Pi is the osmotic pressure and n is the number of solutes. However, this parallel between ideal gas theory and ideal solution=20 theory does not imply that one can properly compute the quantum energy=20 levels of a solution by treating the solute as a particle in a box with=20 the dimensions of the container. Therefore, I agree with you that the=20 quantum mechanical translational partition functions are not the same in = the ideal gas phase and in the solvated phase, and that the quantum=20 mechanical molecular partition functions we are accustomed to cannot be=20 directly applied to a molecule in solution. In fact, I believe the=20 solute has no well-defined translational partition function; its=20 translational motions are strongly coupled with solvent motions, so=20 there aren't any quantum numbers that correspond to purely translational = states of the solute. Nonetheless, going to the classical approximation=20 allows the integral over solute translation to be cleanly separated from = the integrals over other spatial coordinates, so one obtains a well=20 defined translational contribution to the molecular partition function=20 of a solute. I am saying only that there is a definition of translational entropy=20 with these properties, not that this is the only possible definition.=20 Indeed, Siebert and Amzel, in the link you provided, appear to offer a=20 different definition of translational entropy. Since they work in the=20 paradigm of classical stat thermo, my feeling is that that their=20 approach needlessly sacrifices the simplicity and elegance of the=20 definition I have been espousing, but perhaps it has its own merits. Best regards, Mike -=3D This is automatically added to each message by the mailing script = =3D-http://www.ccl.net/cgi-bin/ccl/send_ccl_messageSubscribe/Unsubscribe:=20Job: http://www.ccl.net/jobs=20Search Messages: http://www.ccl.net/htdig (login: ccl, Password: = search)http://www.ccl.net/spammers.txt From owner-chemistry@ccl.net Sun Dec 14 14:55:01 2008 From: "Michael K. Gilson gilson[a]umbi.umd.edu" To: CCL Subject: CCL: translational entropy and solvation Message-Id: <-38299-081214145245-1989-mgfQJZeoUjsSUoyFrqy1hw===server.ccl.net> X-Original-From: "Michael K. Gilson" Content-Transfer-Encoding: 7bit Content-Type: text/plain; charset=ISO-8859-1; format=flowed Date: Sun, 14 Dec 2008 14:51:59 -0500 MIME-Version: 1.0 Sent to CCL by: "Michael K. Gilson" [gilson]*[umbi.umd.edu] Dear Pierre, Yes, that's correct, within the classical approximation. Best regards, Mike VITORGE Pierre 094605 Pierre.VITORGE/acea.fr wrote: > Sent to CCL by: "VITORGE Pierre 094605" [Pierre.VITORGE:_:cea.fr] > Following your reasoning I believe the partition function of the solute has the same form as in the gas phase + a constant term for the (mean) solute-solvent interaction (ant this is also at the basis of the analogy between partial pressure and osmotic pressure). "the same form" does not mean equal to, just the same mathematical form because the ideal solution is an ideal gas + a constant (mean) interaction with the solvent > > -- Michael K. Gilson, M.D., Ph.D. CARB Fellow and Professor Center for Advanced Research in Biotechnology University of Maryland Biotechnology Institute 9600 Gudelsky Drive Rockville, MD 20850 Voice: 240-314-6217 Fax: 240-314-6255 gilsonumbi.umd.edu Lab Page: gilsonlab.umbi.umd.edu BindingDB: www.bindingdb.org