From owner-chemistry@ccl.net Thu Apr 12 01:32:00 2012 From: "Alexander Bagaturyants bagaturyants-.-gmail.com" To: CCL Subject: CCL: energy for proton Message-Id: <-46672-120412013058-29844-NBZxECVtJgh6eQ7h2GwBpQ]*[server.ccl.net> X-Original-From: "Alexander Bagaturyants" Content-Language: en-us Content-Transfer-Encoding: 7bit Content-Type: text/plain; charset="utf-8" Date: Thu, 12 Apr 2012 09:30:50 +0400 MIME-Version: 1.0 Sent to CCL by: "Alexander Bagaturyants" [bagaturyants_-_gmail.com] Dear Arturo, Proton has no internal degrees of freedom; therefore, its energy is zero, if we neglect its kinetic energy. Naturally, the kinetic energy (of a free proton) can take on any value, so that we may speak about so-called dissociation threshold. A piece of advice: when you consider chemistry, you should not sometimes forget about physics. Best regards Alexander > -----Original Message----- > From: owner-chemistry+sasha==photonics.ru===ccl.net [mailto:owner- > chemistry+sasha==photonics.ru===ccl.net] On Behalf Of Arturo Espinosa > artuesp|*|um.es > Sent: 11 April, 2012 21:12 > To: Alexander Bagaturyants > Subject: CCL: energy for proton > > > Sent to CCL by: Arturo Espinosa [artuesp(_)um.es] Dear CCL users: > > I am trying to compute ZPE-corrected dissociation energies for some > particular bonds, in order to correlate these values with other > properties computed at the same level (starting from, let's say, B3LYP- > D/def2-TZVP). My problem (perhaps a bit stupid) comes when dealing with > heterolytic dissociations of a A-H bond to give A- (anion) and H+ (a > proton). Moreover I am intending to compare this dissociation with the > other possible heterolytic dissociation and even with the homolytic > one. Calculation of the A-H and A- species is straighforward (no matter > what level of calculation), but the problem is what value (in atomic > units) should I assign to the H+ species. No QC calculation is possible > as there are no electrons. I recognize that I am a bit lost. > Suggestions are wellcome. > Thank you in advance and best regards, > Arturo> To recover the email address of the author of the message, please > change the strange characters on the top line to the === sign. You can > also> From owner-chemistry@ccl.net Thu Apr 12 02:38:01 2012 From: "Alexander Bagaturyants bagaturyants^_^gmail.com" To: CCL Subject: CCL: energy for proton Message-Id: <-46673-120412023715-22425-qg7wiMGDx65Y0TFj817OWw^server.ccl.net> X-Original-From: "Alexander Bagaturyants" Content-Language: en-us Content-Transfer-Encoding: 8bit Content-Type: text/plain; charset="utf-8" Date: Thu, 12 Apr 2012 10:37:07 +0400 MIME-Version: 1.0 Sent to CCL by: "Alexander Bagaturyants" [bagaturyants{=}gmail.com] Dear Arturo, Proton has no internal degrees of freedom; therefore, its energy is zero, if we neglect its kinetic energy. Naturally, the kinetic energy (of a free proton) can take on any value, so that we may speak about so-called dissociation threshold. A piece of advice: when you consider chemistry, you should not sometimes forget about physics. Best regards Alexander PS: Sorry for the repeat posting, but I am not sure that the message came to CCL. > -----Original Message----- > From: owner-chemistry+sasha==photonics.ru^^^ccl.net [mailto:owner- > chemistry+sasha==photonics.ru^^^ccl.net] On Behalf Of Arturo Espinosa > artuesp|*|um.es > Sent: 11 April, 2012 21:12 > To: Alexander Bagaturyants > Subject: CCL: energy for proton > > > Sent to CCL by: Arturo Espinosa [artuesp(_)um.es] Dear CCL users: > > I am trying to compute ZPE-corrected dissociation energies for some > particular bonds, in order to correlate these values with other > properties computed at the same level (starting from, let's say, B3LYP- > D/def2-TZVP). My problem (perhaps a bit stupid) comes when dealing with > heterolytic dissociations of a A-H bond to give A- (anion) and H+ (a > proton). Moreover I am intending to compare this dissociation with the > other possible heterolytic dissociation and even with the homolytic > one. Calculation of the A-H and A- species is straighforward (no matter > what level of calculation), but the problem is what value (in atomic > units) should I assign to the H+ species. No QC calculation is possible > as there are no electrons. I recognize that I am a bit lost. > Suggestions are wellcome. > Thank you in advance and best regards, > Arturo> To recover the email address of the author of the message, please > change the strange characters on the top line to the ^^^ sign. You can > also> From owner-chemistry@ccl.net Thu Apr 12 03:19:00 2012 From: "Tymofii Nikolaienko tim_mail*_*ukr.net" To: CCL Subject: CCL:G: energy for proton Message-Id: <-46674-120412031714-22677-rCtRnQMVaPkJxIugnlCAZQ|-|server.ccl.net> X-Original-From: Tymofii Nikolaienko Content-Transfer-Encoding: 7bit Content-Type: text/plain; charset=UTF-8; format=flowed Date: Thu, 12 Apr 2012 10:17:02 +0300 MIME-Version: 1.0 Sent to CCL by: Tymofii Nikolaienko [tim_mail{=}ukr.net] Yes, ZPE is zero. However, if considering temperatures higher than 0 K, we can NOT neglect the kinetic energy of the proton, since its thermal avarage is 3 * kT / 2 ! It is easy to demonstrate if you run the following for example with H atom: # opt freq b3lyp/aug-cc-pVQZ int=ultrafine H atom 0 2 H 0.0 0.0 0.0 And than you read in the output file: ... - Thermochemistry - ------------------- Temperature 298.150 Kelvin. Pressure 1.00000 Atm. ... Zero-point correction= 0.000000 (Hartree/Particle) Thermal correction to Energy= 0.001416 Thermal correction to Enthalpy= 0.002360 Thermal correction to Gibbs Free Energy= -0.010654 These thermal corrections would be just that same for the proton since when calculating thermochemistry Gaussian assumes ground electron state only (so no electronic degrees of freedom contribute to thermal corrections; see http://www.gaussian.com/g_whitepap/thermo.htm ). Note that "0.001416" (the "Thermal correction to Energy") equals 3/2*k*T for T = 298.15 K, while "0.002360" (" Thermal correction to Enthalpy") equals 3/2*k*T + k*T since the enthalpy is H = U + P*v while P*v = k*T for ideal gas - the model for calculating thermochemistry Gaussian assumes (where v is the gas volume per particle). To obtain Gibbs free energy use the -T*s term where s is the entropy of ideal gas per particle at given temperature. Yours sincerely Tymofii Nikolaienko 12.04.2012 8:30, Alexander Bagaturyants bagaturyants-.-gmail.com wrote: > Sent to CCL by: "Alexander Bagaturyants" [bagaturyants_-_gmail.com] > Dear Arturo, > Proton has no internal degrees of freedom; > therefore, its energy is zero, if we neglect its kinetic energy. > Naturally, the kinetic energy (of a free proton) can take on any value, > so that we may speak about so-called dissociation threshold. > A piece of advice: when you consider chemistry, > you should not sometimes forget about physics. > Best regards > Alexander > >> -----Original Message----- >> From: owner-chemistry+sasha==photonics.ru|,|ccl.net [mailto:owner- >> chemistry+sasha==photonics.ru|,|ccl.net] On Behalf Of Arturo Espinosa >> artuesp|*|um.es >> Sent: 11 April, 2012 21:12 >> To: Alexander Bagaturyants >> Subject: CCL: energy for proton >> >> >> Sent to CCL by: Arturo Espinosa [artuesp(_)um.es] Dear CCL users: >> >> I am trying to compute ZPE-corrected dissociation energies for some >> particular bonds, in order to correlate these values with other >> properties computed at the same level (starting from, let's say, B3LYP- >> D/def2-TZVP). My problem (perhaps a bit stupid) comes when dealing with >> heterolytic dissociations of a A-H bond to give A- (anion) and H+ (a >> proton). Moreover I am intending to compare this dissociation with the >> other possible heterolytic dissociation and even with the homolytic >> one. Calculation of the A-H and A- species is straighforward (no matter >> what level of calculation), but the problem is what value (in atomic >> units) should I assign to the H+ species. No QC calculation is possible >> as there are no electrons. I recognize that I am a bit lost. >> Suggestions are wellcome. >> Thank you in advance and best regards, >> Arturo> To recover the email address of the author of the message, please >> change the strange characters on the top line to the |,| sign. You can >> also> > > > > From owner-chemistry@ccl.net Thu Apr 12 05:54:01 2012 From: "Peeter Burk peeter.burk^ut.ee" To: CCL Subject: CCL:G: energy for proton Message-Id: <-46675-120412041356-8063-5vS6KWq4jxHSy5grIG7/Bg,server.ccl.net> X-Original-From: Peeter Burk Content-Transfer-Encoding: 7bit Content-Type: text/plain; charset=UTF-8; format=flowed Date: Thu, 12 Apr 2012 11:13:44 +0300 MIME-Version: 1.0 Sent to CCL by: Peeter Burk [peeter.burk * ut.ee] Why not perform the calculation on prorton? With Gaussian 09 (if I remember correctly, then with g03 you had to use Freq=NoRaman to get the same results) you will get: ------------------- - Thermochemistry - ------------------- Temperature 298.150 Kelvin. Pressure 1.00000 Atm. Atom 1 has atomic number 1 and mass 1.00783 Molecular mass: 1.00783 amu. Zero-point vibrational energy 0.0 (Joules/Mol) 0.00000 (Kcal/Mol) Vibrational temperatures: (Kelvin) Zero-point correction= 0.000000 (Hartree/Particle) Thermal correction to Energy= 0.001416 Thermal correction to Enthalpy= 0.002360 Thermal correction to Gibbs Free Energy= -0.010000 Sum of electronic and zero-point Energies= 0.000000 Sum of electronic and thermal Energies= 0.001416 Sum of electronic and thermal Enthalpies= 0.002360 Sum of electronic and thermal Free Energies= -0.010000 Peeter Burk University of Tartu On 04/12/2012 10:17 AM, Tymofii Nikolaienko tim_mail*_*ukr.net wrote: > > Sent to CCL by: Tymofii Nikolaienko [tim_mail{=}ukr.net] > Yes, ZPE is zero. > However, if considering temperatures higher than 0 K, we can NOT neglect > the kinetic energy of the proton, > since its thermal avarage is 3 * kT / 2 ! > > It is easy to demonstrate if you run the following for example with H atom: > > # opt freq b3lyp/aug-cc-pVQZ int=ultrafine > > H atom > > 0 2 > H 0.0 0.0 0.0 > > And than you read in the output file: > ... > - Thermochemistry - > ------------------- > Temperature 298.150 Kelvin. Pressure 1.00000 Atm. > ... > Zero-point correction= 0.000000 (Hartree/Particle) > Thermal correction to Energy= 0.001416 > Thermal correction to Enthalpy= 0.002360 > Thermal correction to Gibbs Free Energy= -0.010654 > > These thermal corrections would be just that same for the proton since > when calculating thermochemistry Gaussian assumes ground electron state > only > (so no electronic degrees of freedom contribute to thermal corrections; > see http://www.gaussian.com/g_whitepap/thermo.htm ). > Note that "0.001416" (the "Thermal correction to Energy") equals 3/2*k*T > for T = 298.15 K, while "0.002360" (" Thermal correction to Enthalpy") > equals > 3/2*k*T + k*T since the enthalpy is H = U + P*v while P*v = k*T for > ideal gas - the model for calculating thermochemistry Gaussian assumes > (where v is the gas volume per particle). To obtain Gibbs free energy > use the -T*s term where s is the entropy of ideal gas per particle at > given temperature. > > Yours sincerely > Tymofii Nikolaienko > > > 12.04.2012 8:30, Alexander Bagaturyants bagaturyants-.-gmail.com wrote: >> Sent to CCL by: "Alexander Bagaturyants" [bagaturyants_-_gmail.com] >> Dear Arturo, >> Proton has no internal degrees of freedom; >> therefore, its energy is zero, if we neglect its kinetic energy. >> Naturally, the kinetic energy (of a free proton) can take on any value, >> so that we may speak about so-called dissociation threshold. >> A piece of advice: when you consider chemistry, >> you should not sometimes forget about physics. >> Best regards >> Alexander >> >>> -----Original Message----- >>> From: owner-chemistry+sasha==photonics.ru|,|ccl.net [mailto:owner- >>> chemistry+sasha==photonics.ru|,|ccl.net] On Behalf Of Arturo Espinosa >>> artuesp|*|um.es >>> Sent: 11 April, 2012 21:12 >>> To: Alexander Bagaturyants >>> Subject: CCL: energy for proton >>> >>> >>> Sent to CCL by: Arturo Espinosa [artuesp(_)um.es] Dear CCL users: >>> >>> I am trying to compute ZPE-corrected dissociation energies for some >>> particular bonds, in order to correlate these values with other >>> properties computed at the same level (starting from, let's say, B3LYP- >>> D/def2-TZVP). My problem (perhaps a bit stupid) comes when dealing with >>> heterolytic dissociations of a A-H bond to give A- (anion) and H+ (a >>> proton). Moreover I am intending to compare this dissociation with the >>> other possible heterolytic dissociation and even with the homolytic >>> one. Calculation of the A-H and A- species is straighforward (no matter >>> what level of calculation), but the problem is what value (in atomic >>> units) should I assign to the H+ species. No QC calculation is possible >>> as there are no electrons. I recognize that I am a bit lost. >>> Suggestions are wellcome. >>> Thank you in advance and best regards, >>> Arturo> To recover the email address of the author of the message, >>> please >>> change the strange characters on the top line to the |,| sign. You can >>> alsohttp://www.ccl.net/chemistry/sub_unsub.shtmlConferences: > http://server.ccl.net/chemistry/announcements/conferences/> From owner-chemistry@ccl.net Thu Apr 12 07:30:00 2012 From: "N. Sukumar nagams(a)rpi.edu" To: CCL Subject: CCL:G: energy for proton Message-Id: <-46676-120412072722-10935-nJwagJB1cFSjtRF49FTlVA.:.server.ccl.net> X-Original-From: "N. Sukumar" Content-Disposition: inline Content-Transfer-Encoding: binary Content-Type: text/plain Date: Thu, 12 Apr 2012 7:27:01 -0400 MIME-Version: 1.0 Sent to CCL by: "N. Sukumar" [nagams~~rpi.edu] "Why not perform the calculation on proton?" This is an interesting philosophical/pedagogical question. My answer would be: because for many students (and others), the output from a computer is the end of the problem, not the beginning of the question! If the computation is used as an aid to understand the chemistry, well and good. But many people these days will not believe a numerical answer unless it is produced by a calculator or a computer. And they may see no need to question those numbers/output any further. N. Sukumar Rensselaer Exploratory Center for Cheminformatics Research Professor of Chemistry Shiv Nadar University -------------------------- "When you get exactly the opposite result to what you predict, you know it is right, because there is no bias." -- David Nutt, Imperial College, London. ==============Original message text=============== On Thu, 12 Apr 2012 4:13:44 EDT "Peeter Burk peeter.burk^ut.ee" wrote: Sent to CCL by: Peeter Burk [peeter.burk * ut.ee] Why not perform the calculation on prorton? With Gaussian 09 (if I remember correctly, then with g03 you had to use Freq=NoRaman to get the same results) you will get: ------------------- - Thermochemistry - ------------------- Temperature 298.150 Kelvin. Pressure 1.00000 Atm. Atom 1 has atomic number 1 and mass 1.00783 Molecular mass: 1.00783 amu. Zero-point vibrational energy 0.0 (Joules/Mol) 0.00000 (Kcal/Mol) Vibrational temperatures: (Kelvin) Zero-point correction= 0.000000 (Hartree/Particle) Thermal correction to Energy= 0.001416 Thermal correction to Enthalpy= 0.002360 Thermal correction to Gibbs Free Energy= -0.010000 Sum of electronic and zero-point Energies= 0.000000 Sum of electronic and thermal Energies= 0.001416 Sum of electronic and thermal Enthalpies= 0.002360 Sum of electronic and thermal Free Energies= -0.010000 Peeter Burk University of Tartu On 04/12/2012 10:17 AM, Tymofii Nikolaienko tim_mail*_*ukr.net wrote: > > Sent to CCL by: Tymofii Nikolaienko [tim_mail{=}ukr.net] > Yes, ZPE is zero. > However, if considering temperatures higher than 0 K, we can NOT neglect > the kinetic energy of the proton, > since its thermal avarage is 3 * kT / 2 ! > > It is easy to demonstrate if you run the following for example with H atom: > > # opt freq b3lyp/aug-cc-pVQZ int=ultrafine > > H atom > > 0 2 > H 0.0 0.0 0.0 > > And than you read in the output file: > ... > - Thermochemistry - > ------------------- > Temperature 298.150 Kelvin. Pressure 1.00000 Atm. > ... > Zero-point correction= 0.000000 (Hartree/Particle) > Thermal correction to Energy= 0.001416 > Thermal correction to Enthalpy= 0.002360 > Thermal correction to Gibbs Free Energy= -0.010654 > > These thermal corrections would be just that same for the proton since > when calculating thermochemistry Gaussian assumes ground electron state > only > (so no electronic degrees of freedom contribute to thermal corrections; > see http://www.gaussian.com/g_whitepap/thermo.htm ).> Note that "0.001416" (the "Thermal correction to Energy") equals 3/2*k*T > for T = 298.15 K, while "0.002360" (" Thermal correction to Enthalpy") > equals > 3/2*k*T + k*T since the enthalpy is H = U + P*v while P*v = k*T for > ideal gas - the model for calculating thermochemistry Gaussian assumes > (where v is the gas volume per particle). To obtain Gibbs free energy > use the -T*s term where s is the entropy of ideal gas per particle at > given temperature. > > Yours sincerely > Tymofii Nikolaienko > > > 12.04.2012 8:30, Alexander Bagaturyants bagaturyants-.-gmail.com wrote: >> Sent to CCL by: "Alexander Bagaturyants" [bagaturyants_-_gmail.com] >> Dear Arturo, >> Proton has no internal degrees of freedom; >> therefore, its energy is zero, if we neglect its kinetic energy. >> Naturally, the kinetic energy (of a free proton) can take on any value, >> so that we may speak about so-called dissociation threshold. >> A piece of advice: when you consider chemistry, >> you should not sometimes forget about physics. >> Best regards >> Alexander >> >>> -----Original Message----- >>> From: owner-chemistry+sasha==photonics.ru|,|ccl.net [mailto:owner- >>> chemistry+sasha==photonics.ru|,|ccl.net] On Behalf Of Arturo Espinosa >>> artuesp|*|um.es >>> Sent: 11 April, 2012 21:12 >>> To: Alexander Bagaturyants >>> Subject: CCL: energy for proton >>> >>> >>> Sent to CCL by: Arturo Espinosa [artuesp(_)um.es] Dear CCL users: >>> >>> I am trying to compute ZPE-corrected dissociation energies for some >>> particular bonds, in order to correlate these values with other >>> properties computed at the same level (starting from, let's say, B3LYP- >>> D/def2-TZVP). My problem (perhaps a bit stupid) comes when dealing with >>> heterolytic dissociations of a A-H bond to give A- (anion) and H+ (a >>> proton). Moreover I am intending to compare this dissociation with the >>> other possible heterolytic dissociation and even with the homolytic >>> one. Calculation of the A-H and A- species is straighforward (no matter >>> what level of calculation), but the problem is what value (in atomic >>> units) should I assign to the H+ species. No QC calculation is possible >>> as there are no electrons. I recognize that I am a bit lost. >>> Suggestions are wellcome. >>> Thank you in advance and best regards, >>> Arturo> To recover the email address of the author of the message, >>> please >>> change the strange characters on the top line to the |,| sign. You can >>> alsohttp://www.ccl.net/chemistry/sub_unsub.shtmlConferences:> http://server.ccl.net/chemistry/announcements/conferences/http://www.ccl.net/cgi-bin/ccl/send_ccl_messagehttp://www.ccl.net/chemistry/sub_unsub.shtmlhttp://www.ccl.net/spammers.txt===========End of original message text=========== From owner-chemistry@ccl.net Thu Apr 12 08:11:01 2012 From: "Tina Ritschel t.ritschel-*-cmbi.ru.nl" To: CCL Subject: CCL: International Chemical Discovery and Design Course, June 18th-22nd Message-Id: <-46677-120412035941-27153-kkED8Vpic2zePE35rY/hUw{:}server.ccl.net> X-Original-From: "Tina Ritschel" Date: Thu, 12 Apr 2012 03:59:37 -0400 Sent to CCL by: "Tina Ritschel" [t.ritschel()cmbi.ru.nl] International Chemical Discovery and Design Course June 18th-22nd, the Computational Drug Discovery (CDD) Group of the Radboud University Nijmegen organizes a course about Chemical Design and Discovery, in cooperation with NBIC and the Netherlands eScience Center. This course covers the recent advances in discovery informatics, with a focus on the application of e-science to real life problems. Different scientific concepts and programs will be introduced and discussed, which are part of the modern drug, food supplement and ingredient discovery pipeline from target discovery & validation to lead discovery & optimization. The morning sessions will introduce key concepts related to the use of computers for chemical discovery in the pharmaceutical industry and other life science pursuits and will be of general interest to anybody in these or other chemistry fields. For the first time we were able to invite keynote speakers from the Netherlands and abroad. As experts in their field of research they will summarize the core message of the course in their presentations. The following speakers have accepted their invitation to give a keynote lecture: Dr. John Overington, Computational Chemical Biology, EMBL-EBI, Hinxton, UK Prof. Dr. Hugo Kubinyi, Former Head of Drug Design & Combinatorial Chemistry and Molecular Modelling, BASF AG, Ludwigshafen, Germany Dr. Ir. Fred van de Velde, NIZO food research BV, The Netherlands Prof. Dr. Peter Murray-Rust, Unilever Centre for Molecular Science Informatics, University of Cambridge, UK In the afternoon the hand-ons are targeted at fourth-year university students, PhD students and postdocs, that are interested in the field of computational target and drug discovery. A basic background in bioinformatics or computational chemistry is a prerequisite for attendance. Read more on the course website: http://www.cmbi.ru.nl/ICDD2012 See the course flyer: http://www2.cmbi.ru.nl/site_media/CDD_course2012_flyer2_A4.pdf Contact person: Dr. Tina Ritschel t.ritschel*|*cmbi.ru.nl From owner-chemistry@ccl.net Thu Apr 12 09:21:00 2012 From: "Jean Jules FIFEN julesfifen . gmail.com" To: CCL Subject: CCL:G: energy for proton Message-Id: <-46678-120412091859-25643-m8K/YQXcsG1TlLeMyntT7A ~ server.ccl.net> X-Original-From: Jean Jules FIFEN Content-Type: multipart/alternative; boundary=20cf305b122070389c04bd7b32e7 Date: Thu, 12 Apr 2012 14:18:51 +0100 MIME-Version: 1.0 Sent to CCL by: Jean Jules FIFEN [julesfifen(_)gmail.com] --20cf305b122070389c04bd7b32e7 Content-Type: text/plain; charset=ISO-8859-1 For proton, ZPE is obviously zero, since there is no vibration! There is also no electron and no rotation involved in the possible motion of the proton. Thus, the energy of proton is translational, and E=1.5*RT=0.001416 Hartree, DH=2.5*RT=0.002360 Hartree=6.197 kJ/mol, DG=DH-TDS=-0.01 Hartree. To convert energy into enthalpy, we add PV, which is RT for an ideal gas. The entropy can be calculated using the Sackur Tetrode equation. Note that it is also translational. You can also find this gaussian output helpful: ------------------- - *Thermochemistry -of the proton* ------------------- Temperature 298.150 Kelvin. Pressure 1.00000 Atm. Atom 1 has atomic number 1 and mass 1.00783 Molecular mass: 1.00783 amu. Zero-point vibrational energy 0.0 (Joules/Mol) 0.00000 (Kcal/Mol) Vibrational temperatures: (Kelvin) Zero-point correction= 0.000000 (Hartree/Particle) Thermal correction to Energy= 0.001416 Thermal correction to Enthalpy= 0.002360 Thermal correction to Gibbs Free Energy= -0.010000 Sum of electronic and zero-point Energies= 0.000000 Sum of electronic and thermal Energies= 0.001416 Sum of electronic and thermal Enthalpies= 0.002360 Sum of electronic and thermal Free Energies= -0.010000 E (Thermal) CV S KCal/Mol Cal/Mol-Kelvin Cal/Mol-Kelvin Total 0.889 2.981 26.014 Electronic 0.000 0.000 0.000 Translational 0.889 2.981 26.014 Rotational 0.000 0.000 0.000 Vibrational 0.000 0.000 0.000 Q Log10(Q) Ln(Q) Total Bot 0.397679D+05 4.599533 10.590816 Total V=0 0.397679D+05 4.599533 10.590816 Vib (Bot) 0.100000D+01 0.000000 0.000000 Vib (V=0) 0.100000D+01 0.000000 0.000000 Electronic 0.100000D+01 0.000000 0.000000 Translational 0.397679D+05 4.599533 10.590816 Rotational 0.100000D+01 0.000000 0.00000 Hope this would help. Best regards, On 12 April 2012 08:17, Tymofii Nikolaienko tim_mail*_*ukr.net < owner-chemistry : ccl.net> wrote: > > Sent to CCL by: Tymofii Nikolaienko [tim_mail{=}ukr.net] > Yes, ZPE is zero. > However, if considering temperatures higher than 0 K, we can NOT neglect > the kinetic energy of the proton, > since its thermal avarage is 3 * kT / 2 ! > > It is easy to demonstrate if you run the following for example with H atom: > > # opt freq b3lyp/aug-cc-pVQZ int=ultrafine > > H atom > > 0 2 > H 0.0 0.0 0.0 > > And than you read in the output file: > ... > - Thermochemistry - > ------------------- > Temperature 298.150 Kelvin. Pressure 1.00000 Atm. > ... > Zero-point correction= 0.000000 > (Hartree/Particle) > Thermal correction to Energy= 0.001416 > Thermal correction to Enthalpy= 0.002360 > Thermal correction to Gibbs Free Energy= -0.010654 > > These thermal corrections would be just that same for the proton since > when calculating thermochemistry Gaussian assumes ground electron state only > (so no electronic degrees of freedom contribute to thermal corrections; > see http://www.gaussian.com/g_**whitepap/thermo.htm). > Note that "0.001416" (the "Thermal correction to Energy") equals 3/2*k*T > for T = 298.15 K, while "0.002360" (" Thermal correction to Enthalpy") > equals > 3/2*k*T + k*T since the enthalpy is H = U + P*v while P*v = k*T for ideal > gas - the model for calculating thermochemistry Gaussian assumes > (where v is the gas volume per particle). To obtain Gibbs free energy use > the -T*s term where s is the entropy of ideal gas per particle at given > temperature. > > Yours sincerely > Tymofii Nikolaienko > > > 12.04.2012 8:30, Alexander Bagaturyants bagaturyants-.-gmail.com wrote: > >> Sent to CCL by: "Alexander Bagaturyants" [bagaturyants_-_gmail.com] >> Dear Arturo, >> Proton has no internal degrees of freedom; >> therefore, its energy is zero, if we neglect its kinetic energy. >> Naturally, the kinetic energy (of a free proton) can take on any value, >> so that we may speak about so-called dissociation threshold. >> A piece of advice: when you consider chemistry, >> you should not sometimes forget about physics. >> Best regards >> Alexander >> >> -----Original Message----- >>> From: owner-chemistry+sasha==photoni**cs.ru |,| >>> ccl.net [mailto:owner- >>> chemistry+sasha==photonics.ru|**,|ccl.net] On Behalf Of Arturo Espinosa >>> artuesp|*|um.es >>> Sent: 11 April, 2012 21:12 >>> To: Alexander Bagaturyants >>> Subject: CCL: energy for proton >>> >>> >>> Sent to CCL by: Arturo Espinosa [artuesp(_)um.es] Dear CCL users: >>> >>> I am trying to compute ZPE-corrected dissociation energies for some >>> particular bonds, in order to correlate these values with other >>> properties computed at the same level (starting from, let's say, B3LYP- >>> D/def2-TZVP). My problem (perhaps a bit stupid) comes when dealing with >>> heterolytic dissociations of a A-H bond to give A- (anion) and H+ (a >>> proton). Moreover I am intending to compare this dissociation with the >>> other possible heterolytic dissociation and even with the homolytic >>> one. Calculation of the A-H and A- species is straighforward (no matter >>> what level of calculation), but the problem is what value (in atomic >>> units) should I assign to the H+ species. No QC calculation is possible >>> as there are no electrons. I recognize that I am a bit lost. >>> Suggestions are wellcome. >>> Thank you in advance and best regards, >>> Arturo> To recover the email address of the author of the message, >>> please >>> change the strange characters on the top line to the |,| sign. You can >>> also> http://www.ccl.net/cgi-bin/**ccl/send_ccl_message http://www.ccl.net/cgi-bin/**ccl/send_ccl_message chemistry/announcements/**conferences/ > > Search Messages: http://www.ccl.net/chemistry/**searchccl/index.shtml http://www.ccl.net/spammers.**txt > > RTFI: http://www.ccl.net/chemistry/**aboutccl/instructions/ > > > -- Jules. --20cf305b122070389c04bd7b32e7 Content-Type: text/html; charset=ISO-8859-1 Content-Transfer-Encoding: quoted-printable
For proton, ZPE is obviously zero, since there is no vibra= tion! There is also no electron and no rotation involved in the possible mo= tion of the proton. Thus, the energy of proton is translational, and E=3D1.= 5*RT=3D0.001416 Hartree, DH=3D2.5*RT=3D0.002360 Hartree=3D6.197 kJ/mol, DG= =3DDH-TDS=3D-0.01 Hartree. To convert energy into enthalpy, we add PV, whic= h is RT for an ideal gas. The entropy can be calculated using the Sackur Te= trode equation. Note that it is also translational.

You can also find this gaussian output helpful:

=A0-------------= ------
=A0- Thermochemistry -of the proton
=A0-------------------
=A0Temperature=A0=A0 298.150 Kelvin.=A0 Pressure=A0=A0 1.00000 Atm.
=A0Atom=A0 1 has atomic number=A0 1 and mass=A0=A0 1.00783
=A0Molecular mass:=A0=A0=A0=A0 1.00783 amu.
=A0Zero-point vibrational energy=A0=A0=A0=A0=A0=A0=A0=A0=A0 0.0 (Joules= /Mol)
=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0= =A0=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0 0.00000 (Kcal/Mol)
=A0Vibrational temperatures:=A0
=A0=A0=A0=A0=A0=A0=A0=A0=A0 (Kelvin)
=A0
=A0Zero-point correction=3D=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0= =A0=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0 0.000000 (Hartree/Particle)
=A0Thermal correction to Energy=3D=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0= =A0=A0=A0=A0=A0=A0=A0 0.001416
=A0Thermal correction to Enthalpy=3D=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0= =A0=A0=A0=A0=A0=A0 0.002360
=A0Thermal correction to Gibbs Free Energy=3D=A0=A0=A0=A0=A0=A0=A0 -0.0= 10000
=A0Sum of electronic and zero-point Energies=3D=A0=A0=A0=A0=A0=A0=A0=A0= =A0=A0=A0=A0=A0 0.000000
=A0Sum of electronic and thermal Energies=3D=A0=A0=A0=A0=A0=A0=A0=A0=A0= =A0=A0=A0=A0=A0=A0=A0 0.001416
=A0Sum of electronic and thermal Enthalpies=3D=A0=A0=A0=A0=A0=A0=A0=A0= =A0=A0=A0=A0=A0=A0 0.002360
=A0Sum of electronic and thermal Free Energies=3D=A0=A0=A0=A0=A0=A0=A0= =A0=A0=A0 -0.010000
=A0
=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0 E (Thermal= )=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0 CV=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0= =A0=A0=A0=A0 S
=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0 KCal/Mo= l=A0=A0=A0=A0=A0=A0=A0 Cal/Mol-Kelvin=A0=A0=A0 Cal/Mol-Kelvin
=A0Total=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0 0.889= =A0=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0 2.981=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0= =A0=A0 26.014
=A0Electronic=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0 0.000=A0=A0=A0= =A0=A0=A0=A0=A0=A0=A0=A0=A0=A0 0.000=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0= 0.000
=A0Translational=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0 0.889=A0=A0=A0=A0=A0= =A0=A0=A0=A0=A0=A0=A0=A0 2.981=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0 26.014
=A0Rotational=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0 0.000=A0=A0=A0= =A0=A0=A0=A0=A0=A0=A0=A0=A0=A0 0.000=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0= 0.000
=A0Vibrational=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0 0.000=A0=A0=A0=A0= =A0=A0=A0=A0=A0=A0=A0=A0=A0 0.000=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0 0.= 000
=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0 Q=A0= =A0=A0=A0=A0=A0=A0=A0=A0=A0=A0 Log10(Q)=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0= Ln(Q)
=A0Total Bot=A0=A0=A0=A0=A0=A0 0.397679D+05=A0=A0=A0=A0=A0=A0=A0=A0=A0 = 4.599533=A0=A0=A0=A0=A0=A0=A0=A0 10.590816
=A0Total V=3D0=A0=A0=A0=A0=A0=A0 0.397679D+05=A0=A0=A0=A0=A0=A0=A0=A0= =A0 4.599533=A0=A0=A0=A0=A0=A0=A0=A0 10.590816
=A0Vib (Bot)=A0=A0=A0=A0=A0=A0 0.100000D+01=A0=A0=A0=A0=A0=A0=A0=A0=A0 = 0.000000=A0=A0=A0=A0=A0=A0=A0=A0=A0 0.000000
=A0Vib (V=3D0)=A0=A0=A0=A0=A0=A0 0.100000D+01=A0=A0=A0=A0=A0=A0=A0=A0= =A0 0.000000=A0=A0=A0=A0=A0=A0=A0=A0=A0 0.000000
=A0Electronic=A0=A0=A0=A0=A0 0.100000D+01=A0=A0=A0=A0=A0=A0=A0=A0=A0 0.= 000000=A0=A0=A0=A0=A0=A0=A0=A0=A0 0.000000
=A0Translational=A0=A0 0.397679D+05=A0=A0=A0=A0=A0=A0=A0=A0=A0 4.599533= =A0=A0=A0=A0=A0=A0=A0=A0 10.590816
=A0Rotational=A0=A0=A0=A0=A0 0.100000D+01=A0=A0=A0=A0=A0=A0=A0=A0=A0 0.= 000000=A0=A0=A0=A0=A0=A0=A0=A0=A0 0.00000
Hope this would help.
Best = regards,

On 12 April 2012 08:17, Tymofii = Nikolaienko tim_mail*_*ukr.net <owner-chemistry : ccl.net= > wrote:

Sent to CCL by: Tymofii Nikolaienko [tim_mail{=3D}ukr.net]
Yes, ZPE is zero.
However, if considering temperatures higher than 0 K, we can NOT neglect th= e kinetic energy of the proton,
since its thermal avarage is 3 * kT / 2 !

It is easy to demonstrate if you run the following for example with H atom:=

# opt freq b3lyp/aug-cc-pVQZ int=3Dultrafine

H atom

0 2
H 0.0 0.0 0.0

And than you read in the output file:
...
=A0- Thermochemistry -
=A0-------------------
=A0Temperature =A0 298.150 Kelvin. =A0Pressure =A0 1.00000 Atm.
...
=A0Zero-point correction=3D =A0 =A0 =A0 =A0 =A0 =A0 =A0 =A0 =A0 =A0 =A0 =A0= =A0 0.000000 (Hartree/Particle)
=A0Thermal correction to Energy=3D =A0 =A0 =A0 =A0 =A0 =A0 =A0 =A0 =A0 =A00= .001416
=A0Thermal correction to Enthalpy=3D =A0 =A0 =A0 =A0 =A0 =A0 =A0 =A0 =A00.0= 02360
=A0Thermal correction to Gibbs Free Energy=3D =A0 =A0 =A0 =A0-0.010654

These thermal corrections would be just that same for the proton since when= calculating thermochemistry Gaussian assumes ground electron state only (so no electronic degrees of freedom contribute to thermal corrections; see= http://www.gaussian.com/g_whitepap/thermo.htm ).
Note that "0.001416" (the "Thermal correction to Energy"= ;) equals 3/2*k*T for T =3D 298.15 K, while "0.002360" (" Th= ermal correction to Enthalpy") equals
3/2*k*T + k*T since the enthalpy is H =3D U + P*v while P*v =3D k*T for ide= al gas - the model for calculating thermochemistry Gaussian assumes
(where v is the gas volume per particle). To obtain Gibbs free energy use t= he -T*s term where s is the entropy of ideal gas per particle at given temp= erature.

Yours sincerely
Tymofii Nikolaienko


12.04.2012 8:30, Alexander Bagaturyants bagaturyants-.-gmail.com wrote:
Sent to CCL by: "Alexander Bagaturyants" [bagaturyants_-_gmail.com]
Dear Arturo,
Proton has no internal degrees of freedom;
therefore, its energy is zero, if we neglect its kinetic energy.
Naturally, the kinetic energy (of a free proton) can take on any value,
so that we may speak about so-called dissociation threshold.
A piece of advice: when you consider chemistry,
you should not sometimes forget about physics.
Best regards
Alexander

-----Original Message-----
> From: owner-chemistry+sasha=3D=3Dphotonics.ru|,|ccl.net [mailto:owner-<= /a>
chemistry+sasha=3D=3Dphot= onics.ru|,|ccl.net<= /a>] On Behalf Of Arturo Espinosa
artuesp|*|um.es
Sent: 11 April, 2012 21:12
To: Alexander Bagaturyants
Subject: CCL: energy for proton


Sent to CCL by: Arturo Espinosa [artuesp(_)um.es] Dear CCL users:

I am trying to compute ZPE-corrected dissociation energies for some
particular bonds, in order to correlate these values with other
properties computed at the same level (starting from, let's say, B3LYP-=
D/def2-TZVP). My problem (perhaps a bit stupid) comes when dealing with
heterolytic dissociations of a A-H bond to give A- (anion) and H+ (a
proton). Moreover I am intending to compare this dissociation with the
other possible heterolytic dissociation and even with the homolytic
one. Calculation of the A-H and A- species is straighforward (no matter
what level of calculation), but the problem is what value (in atomic
units) should I assign to the H+ species. No QC calculation is possible
as there are no electrons. I recognize that I am a bit lost.
Suggestions are wellcome.
Thank you in advance and best regards,
Arturo> =A0To recover the email address of the author of the message, pl= ease
change the strange characters on the top line to the |,| sign. You can
also>







-=3D This is automatically added to each message by the mailing script =3D-=
E-mail to subscribers: CHEMISTRY : ccl.net or use:
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--
Jules.
=
--20cf305b122070389c04bd7b32e7-- From owner-chemistry@ccl.net Thu Apr 12 11:20:00 2012 From: "Anglea A. a.anglea90|*|yahoo.com" To: CCL Subject: CCL: Hydrophobic interaction - precise answer Message-Id: <-46679-120412111920-15435-4FHG/9XGMlaK78hTzvnunw~!~server.ccl.net> X-Original-From: "Anglea A." Content-Transfer-Encoding: 8bit Content-Type: text/plain; charset=iso-8859-1 Date: Thu, 12 Apr 2012 08:19:13 -0700 (PDT) MIME-Version: 1.0 Sent to CCL by: "Anglea A." [a.anglea90]![yahoo.com] Dear All (including C. Swain) I am writing to thank you all for your reply which was more than helpful for me. After your reply, I read and followed your answers to catch more behind the scene.  I am now on an good solid point to move forward. Cheers ----- Original Message ----- > From: "Alexander Bagaturyants bagaturyants#,#gmail.com" To: "Anglea, A " Cc: Sent: Saturday, April 7, 2012 6:13 AM Subject: CCL: Hydrophobic interaction - precise answer Sent to CCL by: "Alexander Bagaturyants" [bagaturyants|*|gmail.com] Dear professors and students! Of course, this is a useful discussion. Generally, I completely agree with John Gunn and Mihaly Mezei. What is strange, is that the student did not even carefully searched the Google. Even the first page of the search results gives you correct, physically reasonable, and complete explanations of this term. See, for example, http://www.iams.sinica.edu.tw/lab/jlli/thesis_andy/node7.html, http://en.wikipedia.org/wiki/Hydrophobic_effect, and, finally, the IUPAC definition http://goldbook.iupac.org/H02907.html. These are the first lines that you find by the request. Many good references are given in the WIKI article, and a comprehensive modern review is given by David Chandler, Interfaces and the driving force of hydrophobic assembly, Nature, vol.  437, pp. 640-647. Of course, from a physical point of view, the concept of forces, potentials, and interactions is not restricted to a pure mechanical sense, but can be considered thermodynamically. We live in a thermodynamical World, and almost all (and, might be, all) phenomena that we observe are thermodynamical phenomena. Hydrophobic interactions are a good reminder of that. Best regards Alexander Alexander A. Bagaturyants Photochemistry Center Russian Academy of Sciences ul. Novatorov 7a, b. 1 Moscow 119421 Russia Phone:  +7(495)9362588 (office)         +7(916)5317022 (mobile) Fax:    +7(495)9361255 e-mail: sasha!^!photonics.ru         bagaturyants!^!gmail.com > -----Original Message----- > From: owner-chemistry+sasha==photonics.ru!^!ccl.net [mailto:owner- > chemistry+sasha==photonics.ru!^!ccl.net] On Behalf Of Mezei, Mihaly > mihaly.mezei###mssm.edu > Sent: 07 April, 2012 01:45 > To: Alexander Bagaturyants > Subject: CCL: Hydrophobic interaction - precise answer > > > Sent to CCL by: "Mezei, Mihaly" [mihaly.mezei,+,mssm.edu] I was about > to make this point as well. Especially since potential of men force > between two methanes obtained from explicit water simulations show > definite minima as well. > > Mihaly Mezei > > Department of Structural and Chemical Biology, Mount Sinai School of > Medicine > Voice:  (212) 659-5475   Fax: (212) 849-2456 > WWW (MSSM home): > http://www.mountsinai.org/Find%20A%20Faculty/profile.do?id=000007250000 > 1497192632 > WWW (Lab home - software, publications): http://inka.mssm.edu/~mezei > WWW (Department): http://atlas.physbio.mssm.edu > ____________________________________ > > From: owner-chemistry+mihaly.mezei==mssm.edu^^^ccl.net > > [owner-chemistry+mihaly.mezei==mssm.edu^^^ccl.net] on behalf of John > > Gunn jgunn]*[mailaps.org [owner-chemistry^^^ccl.net] > Sent: Friday, April 06, 2012 9:28 AM > To: Mezei, Mihaly > Subject: CCL: Hydrophobic interaction - precise answer > > Actually, people often use this to refer to an effective attraction > between non-polar solutes due to the water entropy.  You can define a > potential of mean force like this: > > phi(r_1,r_2) = -kTln[ (1/Z(R))int(dR) exp(-beta*E(r_1,r_2,R)) ] - > U(r_1,r_2) > > where r_i is the position of solute i and R is the configuration of all > water molecules and E is the energy of the entire system, in other > words a pair correlation function for the solute.  Note that phi=0 if > E=U(r_1,r_2)+U(R). > Of course this implies an implicit-solvent model, but it can be used as > an empirical correction for MM forcefields, often based on surface area > for the reasons you described. > > -John.> To recover the email address of the author of the message, please > change the strange characters on the top line to the !^! sign. You can > alsohttp://www.ccl.net/cgi-bin/ccl/send_ccl_messagehttp://www.ccl.net/chemistry/sub_unsub.shtmlhttp://www.ccl.net/spammers.txt                        From owner-chemistry@ccl.net Thu Apr 12 13:18:01 2012 From: "Vera Cathrine vera.cathrine]-[yahoo.com" To: CCL Subject: CCL: G09: TDDFT adiabatic excitation energy Message-Id: <-46680-120412131705-20580-0i/D9sHykrMPC/C8Q4x9BQ[#]server.ccl.net> X-Original-From: "Vera Cathrine" Date: Thu, 12 Apr 2012 13:17:02 -0400 Sent to CCL by: "Vera Cathrine" [vera.cathrine+/-yahoo.com] Hello Everyone, I want to calculate the adiabatic energy difference between first excited state and the ground state for my system. I would like to use DFT/BLYP method and TDDFT/BLYP method respectively for optimization of my geometries for these states. However, I am not sure how to calculate the gap between these state from out file. What are the keywords which I have to look for in the out files? I would thank you for your help in advance. Best regards, Vera From owner-chemistry@ccl.net Thu Apr 12 13:53:01 2012 From: "Jose A. Gamez jgamez .. mpi-muelheim.mpg.de" To: CCL Subject: CCL:G: Visualize NLMOs from Gaussian output/checkpoint file Message-Id: <-46681-120412132118-24107-xMFnDSYB5PWkSHn8UzDnNw#%#server.ccl.net> X-Original-From: "Jose A. Gamez" Content-Transfer-Encoding: 8bit Content-Type: Text/Plain; charset="iso-8859-1" Date: Thu, 12 Apr 2012 19:20:55 +0200 MIME-Version: 1.0 Sent to CCL by: "Jose A. Gamez" [jgamez%x%mpi-muelheim.mpg.de] Hi, Pierre, Unfortunately the NBO visualisation is not implemented in Molekel 5. About the accuracy of Molekel, I was not aware of it, so I cannot answer. Anyway, thank you for the comment, I'll be cautious in the future. Cheers, Jose On Saturday 07 April 2012 10:30:02 you wrote: > Sent to CCL by: VITORGE Pierre 094605 [Pierre.VITORGE : cea.fr] > Is it also possible to visualize these orbitals with the last version of > Molekel? > > Does Molekel 4.3 give correct results? I had some surprises when comparing > orbitals plotted with Molekel 4.3 and -from gaussian cube file- with VMD. > > -- > Pierre Vitorge > Directeur de recherche CEA > > Laboratoire Analyse et Modelisation pour la Biologie et l Environnement, > LAMBE, UMR 8587, CEA, Univ Evry, CNRS, Bd. Francois Mitterrand, Bat. > Maupertuis, s 02 > F-91025 Evry, France > tel.01.69.47.01.40 (+33.1.69.47.01.40) > pierre.vitorge..univ-evry.fr > http://www.lambe.univ-evry.fr/pvitorge > http://www.vitorge.name -- Dr. Jose A. Gamez Max-Planck-Institut für Kohlenforschung Kaiser-Wilhelm-Platz 1 45470 Mülheim an der Ruhr/Germany Tel.: +49 208 306 2171 From owner-chemistry@ccl.net Thu Apr 12 14:27:01 2012 From: "Alexander Bagaturyants sasha#photonics.ru" To: CCL Subject: CCL:G: energy for proton Message-Id: <-46682-120412131754-21816-nAxgjRwRFgqwAVWT8rYd0Q_+_server.ccl.net> X-Original-From: "Alexander Bagaturyants" Content-Language: en-us Content-Transfer-Encoding: 7bit Content-Type: text/plain; charset="windows-1251" Date: Thu, 12 Apr 2012 21:17:46 +0400 MIME-Version: 1.0 Sent to CCL by: "Alexander Bagaturyants" [sasha .. photonics.ru] A good comment by Prof. Sukumar! However, it seems that it was not too straightforward, because some misleading comments still appear and appear. The matter of fact is that neither enthalpy, nor entropy, nor temperature of a free proton makes physical sense. One cannot construct a (thermodynamic) ensemble of free protons. A reaction in which a proton is detached from a molecule can proceed only under nonequilibrium conditions, it is a dynamic rather than thermodynamic process. That is, it senseless to calculate formally any thermodynamic function of a free (individual) proton. Hope this will make things a little bit more clear. Best regards Alexander > -----Original Message----- > From: owner-chemistry+sasha==photonics.ru|,|ccl.net [mailto:owner- > chemistry+sasha==photonics.ru|,|ccl.net] On Behalf Of N. Sukumar > nagams(a)rpi.edu > Sent: 12 April, 2012 15:27 > To: Alexander Bagaturyants > Subject: CCL:G: energy for proton > > > Sent to CCL by: "N. Sukumar" [nagams~~rpi.edu] "Why not perform the > calculation on proton?" > > This is an interesting philosophical/pedagogical question. My answer > would be: because for many students (and others), the output from a > computer is the end of the problem, not the beginning of the question! > If the computation is used as an aid to understand the chemistry, well > and good. But many people these days will not believe a numerical > answer unless it is produced by a calculator or a computer. And they > may see no need to question those numbers/output any further. > > N. Sukumar > Rensselaer Exploratory Center for Cheminformatics Research Professor of > Chemistry Shiv Nadar University > -------------------------- > "When you get exactly the opposite result to what you predict, you know > it is right, because there is no bias." -- David Nutt, Imperial > College, London. > > ==============Original message text=============== On Thu, 12 Apr 2012 > 4:13:44 EDT "Peeter Burk peeter.burk^ut.ee" wrote: > > > Sent to CCL by: Peeter Burk [peeter.burk * ut.ee] Why not perform the > calculation on prorton? With Gaussian 09 (if I remember correctly, then > with g03 you had to use Freq=NoRaman to get the same results) you will > get: > > ------------------- > - Thermochemistry - > ------------------- > Temperature 298.150 Kelvin. Pressure 1.00000 Atm. > Atom 1 has atomic number 1 and mass 1.00783 > Molecular mass: 1.00783 amu. > Zero-point vibrational energy 0.0 (Joules/Mol) > 0.00000 (Kcal/Mol) > Vibrational temperatures: > (Kelvin) > > Zero-point correction= 0.000000 > (Hartree/Particle) > Thermal correction to Energy= 0.001416 > Thermal correction to Enthalpy= 0.002360 > Thermal correction to Gibbs Free Energy= -0.010000 > Sum of electronic and zero-point Energies= 0.000000 > Sum of electronic and thermal Energies= 0.001416 > Sum of electronic and thermal Enthalpies= 0.002360 > Sum of electronic and thermal Free Energies= -0.010000 > > > Peeter Burk > University of Tartu > > On 04/12/2012 10:17 AM, Tymofii Nikolaienko tim_mail*_*ukr.net wrote: > > > > Sent to CCL by: Tymofii Nikolaienko [tim_mail{=}ukr.net] Yes, ZPE is > > zero. > > However, if considering temperatures higher than 0 K, we can NOT > > neglect the kinetic energy of the proton, since its thermal avarage > is > > 3 * kT / 2 ! > > > > It is easy to demonstrate if you run the following for example with H > atom: > > > > # opt freq b3lyp/aug-cc-pVQZ int=ultrafine > > > > H atom > > > > 0 2 > > H 0.0 0.0 0.0 > > > > And than you read in the output file: > > ... > > - Thermochemistry - > > ------------------- > > Temperature 298.150 Kelvin. Pressure 1.00000 Atm. > > ... > > Zero-point correction= 0.000000 (Hartree/Particle) Thermal correction > > to Energy= 0.001416 Thermal correction to Enthalpy= 0.002360 Thermal > > correction to Gibbs Free Energy= -0.010654 > > > > These thermal corrections would be just that same for the proton > since > > when calculating thermochemistry Gaussian assumes ground electron > > state only (so no electronic degrees of freedom contribute to thermal > > corrections; see http://www.gaussian.com/g_whitepap/thermo.htm ).> > > Note that "0.001416" (the "Thermal correction to Energy") equals > > 3/2*k*T for T = 298.15 K, while "0.002360" (" Thermal correction to > > Enthalpy") equals 3/2*k*T + k*T since the enthalpy is H = U + P*v > > while P*v = k*T for ideal gas - the model for calculating > > thermochemistry Gaussian assumes (where v is the gas volume per > > particle). To obtain Gibbs free energy use the -T*s term where s is > > the entropy of ideal gas per particle at given temperature. > > > > Yours sincerely > > Tymofii Nikolaienko > > > > > > 12.04.2012 8:30, Alexander Bagaturyants bagaturyants-.-gmail.com > wrote: > >> Sent to CCL by: "Alexander Bagaturyants" [bagaturyants_-_gmail.com] > >> Dear Arturo, Proton has no internal degrees of freedom; therefore, > >> its energy is zero, if we neglect its kinetic energy. > >> Naturally, the kinetic energy (of a free proton) can take on any > >> value, so that we may speak about so-called dissociation threshold. > >> A piece of advice: when you consider chemistry, you should not > >> sometimes forget about physics. > >> Best regards > >> Alexander > >> > >>> -----Original Message----- > >>> From: owner-chemistry+sasha==photonics.ru|,|ccl.net [mailto:owner- > >>> chemistry+sasha==photonics.ru|,|ccl.net] On Behalf Of Arturo > >>> chemistry+Espinosa > >>> artuesp|*|um.es > >>> Sent: 11 April, 2012 21:12 > >>> To: Alexander Bagaturyants > >>> Subject: CCL: energy for proton > >>> > >>> > >>> Sent to CCL by: Arturo Espinosa [artuesp(_)um.es] Dear CCL users: > >>> > >>> I am trying to compute ZPE-corrected dissociation energies for some > >>> particular bonds, in order to correlate these values with other > >>> properties computed at the same level (starting from, let's say, > >>> B3LYP- D/def2-TZVP). My problem (perhaps a bit stupid) comes when > >>> dealing with heterolytic dissociations of a A-H bond to give A- > >>> (anion) and H+ (a proton). Moreover I am intending to compare this > >>> dissociation with the other possible heterolytic dissociation and > >>> even with the homolytic one. Calculation of the A-H and A- species > >>> is straighforward (no matter what level of calculation), but the > >>> problem is what value (in atomic > >>> units) should I assign to the H+ species. No QC calculation is > >>> possible as there are no electrons. I recognize that I am a bit > lost. > >>> Suggestions are wellcome. > >>> Thank you in advance and best regards, > >>> Arturo> To recover the email address of the author of the message, > >>> please > >>> change the strange characters on the top line to the |,| sign. You > >>> can alsohttp://www.ccl.net/chemistry/sub_unsub.shtmlConferences:> > >>> > http://server.ccl.net/chemistry/announcements/conferences/http://www > >>> .ccl.net/cgi- > bin/ccl/send_ccl_messagehttp://www.ccl.net/chemistry/su > >>> b_unsub.shtmlhttp://www.ccl.net/spammers.txt===========End of > >>> original message text===========> To recover the email address of the author of the message, please > change the strange characters on the top line to the |,| sign. You can > also> From owner-chemistry@ccl.net Thu Apr 12 15:02:01 2012 From: "Soren Eustis soreneustis- -gmail.com" To: CCL Subject: CCL:G: G09: TDDFT adiabatic excitation energy Message-Id: <-46683-120412141318-32345-FL6ms6n2RLY2/aHYctg5Ug_._server.ccl.net> X-Original-From: Soren Eustis Content-type: multipart/alternative; boundary="B_3417106364_10332773" Date: Thu, 12 Apr 2012 20:12:35 +0200 Mime-version: 1.0 Sent to CCL by: Soren Eustis [soreneustis-#-gmail.com] > This message is in MIME format. Since your mail reader does not understand this format, some or all of this message may not be legible. --B_3417106364_10332773 Content-type: text/plain; charset="ISO-8859-1" Content-transfer-encoding: quoted-printable Vera, Hello. I am making the assumption that you are working with the Gaussia= n code. If this is the case you will need will need to search your .log or .out files. Depending on the type of calculation you performed for each state (ex. S0 and S1), you will be looking for the following lines which correspond to the final geometry. If you performed a straight geometry calculation for each state, these outputs would immediately proceed the "optimization completed" statement. For example: For S1 This state for optimization and/or second-order correction. Total Energy, E(TD-HF/TD-KS) =3D -1225.82750771 Copying the excited state density for this state as the 1-particle RhoCI density. S0 Error on total polarization charges =3D 0.01689 SCF Done: E(UCAM-B3LYP) =3D -1225.88017379 A.U. after 13 cycles Best, Soren Soren N. Eustis, Ph.D. ETH =AD Z=FCrich Environmental Chemistry Group Inst. for Biogeochem. and Pollutant Dynamics Universit=E4tstrasse 16 CHN F33 8092 Z=FCrich SWITZERLAND +41 44 632 93 48 (office) +41 44 632 14 38 (fax) soren|,|env.ethz.ch > From: "Vera Cathrine vera.cathrine]-[yahoo.com" Reply-To: Ccl Date: Thu, 12 Apr 2012 13:17:02 -0400 To: Soren Eustis Subject: CCL: G09: TDDFT adiabatic excitation energy >=20 > Sent to CCL by: "Vera Cathrine" [vera.cathrine+/-yahoo.com] > Hello Everyone, >=20 > I want to calculate the adiabatic energy difference between first excited > state and the ground state for my system. I would like to use DFT/BLYP m= ethod > and TDDFT/BLYP method respectively for optimization of my geometries for = these > states. However, I am not sure how to calculate the gap between these sta= te > from out file. What are the keywords which I have to look for in the out > files? > I would thank you for your help in advance. > Best regards, > Vera >=20 >=20 >=20 > -=3D This is automatically added to each message by the mailing script =3D->=20>=20>=20>=20>=20>=20>=20>=20>=20 >=20 >=20 --B_3417106364_10332773 Content-type: text/html; charset="ISO-8859-1" Content-transfer-encoding: quoted-printable
Vera,
   Hello.  I am making the assumption that you ar= e working with the Gaussian code.  If this is the case you will need wi= ll need to search your .log or .out files.  Depending on the type of ca= lculation you performed for each state (ex. S0 and S1), you will be looking = for the following lines which correspond to the final geometry.  If you= performed a straight geometry calculation for each state, these outputs wou= ld immediately proceed the "optimization completed" statement.  For exa= mple:

For S1

This s= tate for optimization and/or second-order correction.
 Total = Energy, E(TD-HF/TD-KS) =3D  -1225.82750771    
 = Copying the excited state density for this state as the 1-particle RhoCI den= sity.

S0

Erro= r on total polarization charges =3D  0.01689
 SCF Done: &n= bsp;E(UCAM-B3LYP) =3D  -1225.88017379     A.U. after   13 = cycles

Best,

Soren



Soren N. Eustis, Ph.D.
ETH – Z=FCrich
Environmental Chemistry Group
Inst. for Biogeochem. and = Pollutant Dynamics
<= span style=3D"font-size:11pt"> Universit=E4tstrasse 16
CHN F33
8092 Z=FCrich
= SWITZERLAND

+41 44 632 93 48 (office)
+41 44 632 14 38 (fax)

soren|,|env.ethz.ch=
From: = "Vera Cathrine vera.cathrine]-[yahoo.com" <owner-chemistry|,|ccl.net>
Reply-To: Ccl <chemis= try|,|ccl.net>
Date: Thu, 12 = Apr 2012 13:17:02 -0400
To: Soren = Eustis <soreneustis|,|gmail.com&= gt;
Subject: CCL: G09: TDDFT adiab= atic excitation energy


Sent to CCL by: "Vera &= nbsp;Cathrine" [vera.cathrine+/-yahoo.com]
Hello Everyone,

I want to calculate the adiabatic energy difference betwee= n first excited state and the ground state for  my system. I would= like to use DFT/BLYP method and TDDFT/BLYP method respectively for optimiza= tion of my geometries for these states. However, I am not sure how to calcul= ate the gap between these state from out file. What are the keywords which I= have to look for in the out files?
I would thank you for your hel= p in advance.
Best regards,
Vera



-=3D This is automatically added to each messa= ge by the mailing script =3D-
To recover the email address of the au= thor of the message, please change
the strange characters on the t= op line to the |,| sign. You can also
look up the X-Original-From: l= ine in the mail header.

E-mail to subscribers: CHEMISTRY|,|ccl.net or use:
<= br>
E-mail to administrators: CHEMISTRY-REQUEST|,|ccl.net or use

Sub= scribe/Unsubscribe:

Before posting, check wait time = at: http://www.ccl.net

=
--B_3417106364_10332773-- From owner-chemistry@ccl.net Thu Apr 12 15:38:01 2012 From: "Edward Holland hollandej/a\Cardiff.ac.uk" To: CCL Subject: CCL:G: energy for proton Message-Id: <-46684-120412151142-29538-Q5SjJ7Nj5VwV7lG80kgEOA!=!server.ccl.net> X-Original-From: Edward Holland Content-Type: multipart/signed; boundary="Apple-Mail=_E4E80916-CA1A-4C53-8DAB-2ABD4C101464"; protocol="application/pgp-signature"; micalg=pgp-sha1 Date: Thu, 12 Apr 2012 20:11:20 +0100 Mime-Version: 1.0 (Apple Message framework v1257) Sent to CCL by: Edward Holland [hollandej^^Cardiff.ac.uk] --Apple-Mail=_E4E80916-CA1A-4C53-8DAB-2ABD4C101464 Content-Transfer-Encoding: quoted-printable Content-Type: text/plain; charset=windows-1251 If one is considering a reaction in which a proton is lost it may well = be more appropriate to consider what it is being lost to.=20 i.e=20 R-H + H2O -> R- + H3O+ The enthalpy of reaction for this process seems much more likely to = yield useful results in this type of situation=20 Yours Ed Holland Cardiff University=20 =20 On 12 Apr 2012, at 18:17, Alexander Bagaturyants sasha#photonics.ru = wrote: >=20 > Sent to CCL by: "Alexander Bagaturyants" [sasha .. photonics.ru] > A good comment by Prof. Sukumar! > However, it seems that it was not too straightforward,=20 > because some misleading comments still appear and appear.=20 > The matter of fact is that neither enthalpy, nor entropy, nor = temperature of > a free proton makes physical sense. One cannot construct a = (thermodynamic) > ensemble of free protons. A reaction in which a proton is detached = > from a > molecule can proceed only under nonequilibrium conditions, it is a = dynamic > rather than thermodynamic process.=20 > That is, it senseless to calculate formally any thermodynamic function = of a > free (individual) proton.=20 > Hope this will make things a little bit more clear. > Best regards > Alexander >=20 >> -----Original Message----- >> From: owner-chemistry+sasha=3D=3Dphotonics.ru=3D=3D=3Dccl.net = [mailto:owner- >> chemistry+sasha=3D=3Dphotonics.ru=3D=3D=3Dccl.net] On Behalf Of N. = Sukumar >> nagams(a)rpi.edu >> Sent: 12 April, 2012 15:27 >> To: Alexander Bagaturyants >> Subject: CCL:G: energy for proton >>=20 >>=20 >> Sent to CCL by: "N. Sukumar" [nagams~~rpi.edu] "Why not perform the >> calculation on proton?" >>=20 >> This is an interesting philosophical/pedagogical question. My answer >> would be: because for many students (and others), the output from a >> computer is the end of the problem, not the beginning of the = question! >> If the computation is used as an aid to understand the chemistry, = well >> and good. But many people these days will not believe a numerical >> answer unless it is produced by a calculator or a computer. And they >> may see no need to question those numbers/output any further. >>=20 >> N. Sukumar >> Rensselaer Exploratory Center for Cheminformatics Research Professor = of >> Chemistry Shiv Nadar University >> -------------------------- >> "When you get exactly the opposite result to what you predict, you = know >> it is right, because there is no bias." -- David Nutt, Imperial >> College, London. >>=20 >> =3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3DOriginal message = text=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D On Thu, 12 Apr 2012 >> 4:13:44 EDT "Peeter Burk peeter.burk^ut.ee" wrote: >>=20 >>=20 >> Sent to CCL by: Peeter Burk [peeter.burk * ut.ee] Why not perform the >> calculation on prorton? With Gaussian 09 (if I remember correctly, = then >> with g03 you had to use Freq=3DNoRaman to get the same results) you = will >> get: >>=20 >> ------------------- >> - Thermochemistry - >> ------------------- >> Temperature 298.150 Kelvin. Pressure 1.00000 Atm. >> Atom 1 has atomic number 1 and mass 1.00783 >> Molecular mass: 1.00783 amu. >> Zero-point vibrational energy 0.0 (Joules/Mol) >> 0.00000 (Kcal/Mol) >> Vibrational temperatures: >> (Kelvin) >>=20 >> Zero-point correction=3D 0.000000 >> (Hartree/Particle) >> Thermal correction to Energy=3D 0.001416 >> Thermal correction to Enthalpy=3D 0.002360 >> Thermal correction to Gibbs Free Energy=3D -0.010000 >> Sum of electronic and zero-point Energies=3D 0.000000 >> Sum of electronic and thermal Energies=3D 0.001416 >> Sum of electronic and thermal Enthalpies=3D 0.002360 >> Sum of electronic and thermal Free Energies=3D -0.010000 >>=20 >>=20 >> Peeter Burk >> University of Tartu >>=20 >> On 04/12/2012 10:17 AM, Tymofii Nikolaienko tim_mail*_*ukr.net wrote: >>>=20 >>> Sent to CCL by: Tymofii Nikolaienko [tim_mail{=3D}ukr.net] Yes, ZPE = is >>> zero. >>> However, if considering temperatures higher than 0 K, we can NOT >>> neglect the kinetic energy of the proton, since its thermal avarage >> is >>> 3 * kT / 2 ! >>>=20 >>> It is easy to demonstrate if you run the following for example with = H >> atom: >>>=20 >>> # opt freq b3lyp/aug-cc-pVQZ int=3Dultrafine >>>=20 >>> H atom >>>=20 >>> 0 2 >>> H 0.0 0.0 0.0 >>>=20 >>> And than you read in the output file: >>> ... >>> - Thermochemistry - >>> ------------------- >>> Temperature 298.150 Kelvin. Pressure 1.00000 Atm. >>> ... >>> Zero-point correction=3D 0.000000 (Hartree/Particle) Thermal = correction >>> to Energy=3D 0.001416 Thermal correction to Enthalpy=3D 0.002360 = Thermal >>> correction to Gibbs Free Energy=3D -0.010654 >>>=20 >>> These thermal corrections would be just that same for the proton >> since >>> when calculating thermochemistry Gaussian assumes ground electron >>> state only (so no electronic degrees of freedom contribute to = thermal >>> corrections; see http://www.gaussian.com/g_whitepap/thermo.htm ).> >>> Note that "0.001416" (the "Thermal correction to Energy") equals >>> 3/2*k*T for T =3D 298.15 K, while "0.002360" (" Thermal correction = to >>> Enthalpy") equals 3/2*k*T + k*T since the enthalpy is H =3D U + P*v >>> while P*v =3D k*T for ideal gas - the model for calculating >>> thermochemistry Gaussian assumes (where v is the gas volume per >>> particle). To obtain Gibbs free energy use the -T*s term where s is >>> the entropy of ideal gas per particle at given temperature. >>>=20 >>> Yours sincerely >>> Tymofii Nikolaienko >>>=20 >>>=20 >>> 12.04.2012 8:30, Alexander Bagaturyants bagaturyants-.-gmail.com >> wrote: >>>> Sent to CCL by: "Alexander Bagaturyants" [bagaturyants_-_gmail.com] >>>> Dear Arturo, Proton has no internal degrees of freedom; therefore, >>>> its energy is zero, if we neglect its kinetic energy. >>>> Naturally, the kinetic energy (of a free proton) can take on any >>>> value, so that we may speak about so-called dissociation threshold. >>>> A piece of advice: when you consider chemistry, you should not >>>> sometimes forget about physics. >>>> Best regards >>>> Alexander >>>>=20 >>>>> -----Original Message----- >>>>> From: owner-chemistry+sasha=3D=3Dphotonics.ru|,|ccl.net = [mailto:owner- >>>>> chemistry+sasha=3D=3Dphotonics.ru|,|ccl.net] On Behalf Of Arturo >>>>> chemistry+Espinosa >>>>> artuesp|*|um.es >>>>> Sent: 11 April, 2012 21:12 >>>>> To: Alexander Bagaturyants >>>>> Subject: CCL: energy for proton >>>>>=20 >>>>>=20 >>>>> Sent to CCL by: Arturo Espinosa [artuesp(_)um.es] Dear CCL users: >>>>>=20 >>>>> I am trying to compute ZPE-corrected dissociation energies for = some >>>>> particular bonds, in order to correlate these values with other >>>>> properties computed at the same level (starting from, let's say, >>>>> B3LYP- D/def2-TZVP). My problem (perhaps a bit stupid) comes when >>>>> dealing with heterolytic dissociations of a A-H bond to give A- >>>>> (anion) and H+ (a proton). Moreover I am intending to compare this >>>>> dissociation with the other possible heterolytic dissociation and >>>>> even with the homolytic one. Calculation of the A-H and A- species >>>>> is straighforward (no matter what level of calculation), but the >>>>> problem is what value (in atomic >>>>> units) should I assign to the H+ species. No QC calculation is >>>>> possible as there are no electrons. I recognize that I am a bit >> lost. >>>>> Suggestions are wellcome. >>>>> Thank you in advance and best regards, >>>>> Arturo> To recover the email address of the author of the message, >>>>> please >>>>> change the strange characters on the top line to the |,| sign. You >>>>> can alsohttp://www.ccl.net/chemistry/sub_unsub.shtmlConferences:> >>>>>=20 >> http://server.ccl.net/chemistry/announcements/conferences/http://www >>>>> .ccl.net/cgi- >> bin/ccl/send_ccl_messagehttp://www.ccl.net/chemistry/su >>>>> b_unsub.shtmlhttp://www.ccl.net/spammers.txt=3D=3D=3D=3D=3D=3D=3D=3D= =3D=3D=3DEnd of >>>>> original message text=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D> To recover = the email address of the author of the message, please >> change the strange characters on the top line to the =3D=3D=3D sign. = You can >> also> >=20 >=20 >=20 > -=3D This is automatically added to each message by the mailing script = =3D- > To recover the email address of the author of the message, please = change>=20>=20>=20 > Subscribe/Unsubscribe:=20>=20>=20 > Job: http://www.ccl.net/jobs=20 > Conferences: = http://server.ccl.net/chemistry/announcements/conferences/ >=20>=20>=20>=20 >=20 --Apple-Mail=_E4E80916-CA1A-4C53-8DAB-2ABD4C101464 Content-Transfer-Encoding: 7bit Content-Disposition: attachment; filename=signature.asc Content-Type: application/pgp-signature; name=signature.asc Content-Description: Message signed with OpenPGP using GPGMail -----BEGIN PGP SIGNATURE----- Version: GnuPG/MacGPG2 v2.0.17 (Darwin) iQEcBAEBAgAGBQJPhyjZAAoJEEJc9s8gBQlyCY0H/2+JAxiJ9N6YxbAk+P0i1XRP t5iJmqB/GVwNzapb6u0trgVfOlZvENW7wPXmf7hx196wAJHVSJ6hDNsEEXNuvt72 k6MkhN3nQxWaViM7XiftLTZNIq0mxuDRkMlP/kz+vz2Xq+nBDPWwDSvfhbb+xyX+ nxIaPJZ6Haa/GkSGCFprWQYL7ii6P1zvIYr1NdW3TdsRI7ARmIrw4Bba0GK7NGQX TY1lQj68vP1OJKSKKyDoT92uJxsy3sPPe5I1umixrUX65F8RHbaO8n6d48EsZawN 47K5uvQNM2RFPBN+jl/ON0IAbnBEJNF2O4E++v6AF2T22HmJO3ZzpMuKAJFwww0= =0EQm -----END PGP SIGNATURE----- --Apple-Mail=_E4E80916-CA1A-4C53-8DAB-2ABD4C101464-- From owner-chemistry@ccl.net Thu Apr 12 16:13:01 2012 From: "David Anthony Mannock dmannock[a]ualberta.ca" To: CCL Subject: CCL: Advice on sterol/steroid QC calculations wanted. Message-Id: <-46685-120412155347-11962-wAHvYlPlU9x2CwGv/gV1hw(_)server.ccl.net> X-Original-From: "David Anthony Mannock" Date: Thu, 12 Apr 2012 15:53:42 -0400 Sent to CCL by: "David Anthony Mannock" [dmannock[#]ualberta.ca] Greetings fellow molecular chemists! We have recently completed a series of experiments on a range of 30+ sterol structures in model lipid bilayers using calorimetric and spectroscopic techniques with considerable help from a student. I have already performed a number of DFT calculations using the opt/freq option in G09 and B3LYP/6.31 or 311++ (d,p). [I hope I got that right!] This has generated a number of conformations for each sterol/steroid structure in the ground state and I am not unhappy with the results. However, I need advice on a number of issues. [I do have the Handbook of computational chemistry (Cook) and Electronic Structure Modeling (Shillady)for back up]. 1) Is this approach sufficient to examine the electronic structures of the various sterol/steroid conformations that are evident? Would similar calculations with AIM be beneficial either in providing more accurate/realistic orbital energies or would a Hirschfeld type of analysis be more appropriate? 2) I have seen various messages here on conformations in excited states and energies. What is a good approach in such calculations in G09? 3) Sterols exhibit definite anomeric electronic effects that interact with nearby orbitals originating from double bonds. There are also possible inter- and intra-molecular CH-pi interactions present in some molecules. What is the best calculation solution? 4) Similarly in some of the steroids, resonance effects exist. I am not clear whether these would be covered in calculations of the excited states. 5) With 8-cores some calculations take a week or more. Upgrading to 12 and now 64-cores helps for those subroutines that can run in parallel in G09, but I am wondering if there is a way to break down this extensive computation into parts to decrease the computation time? I am thinking that I could perform some calculations on my 12-core server and others on the 64-core machine. I am thinking that this will be possible by using a line such as "(guess = read)" to access a checkpoint file. 6) I have an Nvidia M2075 card and I know there are mp software solutions which use CUDA that are free for academic use. Any suggestions would be welcome, as I am not familiar with using that software. Finally, I should add that while I have learned a lot, I know just enough to be dangerous! Guidance from experts would be most helpful in getting this done correctly. Thanks in advance, Dr David Mannock dmannock*o*ualberta.ca From owner-chemistry@ccl.net Thu Apr 12 20:44:00 2012 From: "John McKelvey jmmckel],[gmail.com" To: CCL Subject: CCL: G09: TDDFT adiabatic excitation energy Message-Id: <-46686-120412204037-26482-SDvZVsytDiydtjwew10+SA{=}server.ccl.net> X-Original-From: John McKelvey Content-Transfer-Encoding: 8bit Content-Type: text/plain; charset=ISO-8859-1 Date: Thu, 12 Apr 2012 20:40:28 -0400 MIME-Version: 1.0 Sent to CCL by: John McKelvey [jmmckel],[gmail.com] One might some papers on this by Stefan Grimme by Googling him and looking at his pub list . John McKelvey On Thu, Apr 12, 2012 at 1:17 PM, Vera Cathrine vera.cathrine]-[yahoo.com wrote: > > Sent to CCL by: "Vera  Cathrine" [vera.cathrine+/-yahoo.com] > Hello Everyone, > > I want to calculate the adiabatic energy difference between first excited state and the ground state for  my system. I would like to use DFT/BLYP method and TDDFT/BLYP method respectively for optimization of my geometries for these states. However, I am not sure how to calculate the gap between these state from out file. What are the keywords which I have to look for in the out files? > I would thank you for your help in advance. > Best regards, > Vera>      http://www.ccl.net/cgi-bin/ccl/send_ccl_message>      http://www.ccl.net/cgi-bin/ccl/send_ccl_message>      http://www.ccl.net/chemistry/sub_unsub.shtml>      http://www.ccl.net/spammers.txt> > -- John McKelvey 10819 Middleford Pl Ft Wayne, IN 46818 260-489-2160 jmmckel]_[gmail.com