From owner-chemistry@ccl.net Mon Jun 8 08:59:01 2015 From: "Surinder Kaur simmi.msc7{}gmail.com" To: CCL Subject: CCL: Comparison of Raman Spectra of two different water cages Message-Id: <-51426-150608085409-7431-LDunhSfTTEZ+CigbSnRioQ]*[server.ccl.net> X-Original-From: "Surinder Kaur" Date: Mon, 8 Jun 2015 08:54:07 -0400 Sent to CCL by: "Surinder Kaur" [simmi.msc7,,gmail.com] Hello friends I am working on water cages and trying to analyze the different vibrational modes with the help of Raman spectroscopy using quantum chemical calculations. I have the following questions regarding the analysis: 1.Is it possible to compare the Raman spectra of two different cage structures without the availability of experimental data i.e. we do not have any information about characteristic peak? 2.Can we correlate the red shift (lower wave number) or blue shift (higher wave number) of vibrational modes of one cage, relative to second cage with stabilization energy? Thanks in advance. With regards Surinder From owner-chemistry@ccl.net Mon Jun 8 10:04:00 2015 From: "ashika torikora ashika.torikora],[gmail.com" To: CCL Subject: CCL: Determine statistical distribution of chemical species based on energi Message-Id: <-51427-150608094416-25560-+pisV4fndezOlX5MJbayfg#%#server.ccl.net> X-Original-From: "ashika torikora" Date: Mon, 8 Jun 2015 09:44:15 -0400 Sent to CCL by: "ashika torikora" [ashika.torikora*gmail.com] Hello everyone. Suppose you have several different states of a given molecule ( different geometries or different chemical states for example). Can you determine theoretical statistical distributions of these states based on energies calculated by DFT or ab initio calculations? Which types of energies would you need? Single point energies or free energies determined through vibration calculations? How would you do it? Thanks, From owner-chemistry@ccl.net Mon Jun 8 11:50:01 2015 From: "Robert Molt r.molt.chemical.physics###gmail.com" To: CCL Subject: CCL: Determine statistical distribution of chemical species based on energi Message-Id: <-51428-150608114900-14999-vSKLrbY1dKzaxDnqS0+bNQ_._server.ccl.net> X-Original-From: Robert Molt Content-Transfer-Encoding: 7bit Content-Type: text/plain; charset=windows-1252; format=flowed Date: Mon, 08 Jun 2015 11:48:54 -0400 MIME-Version: 1.0 Sent to CCL by: Robert Molt [r.molt.chemical.physics^^^gmail.com] You would need to use statistical mechanics. Depending on what ensemble you feel corresponds to your situation, you would use the "constant" resultant from that ensemble (Gibbs, Helmholtz, etc.). You can get the energies using any electronic structure software, but make sure you understand the stat mech first. On 6/8/15 9:44 AM, ashika torikora ashika.torikora],[gmail.com wrote: > Sent to CCL by: "ashika torikora" [ashika.torikora*gmail.com] > Hello everyone. > > Suppose you have several different states of a given molecule ( different geometries or different chemical states for example). Can you determine theoretical statistical distributions of these states based on energies calculated by DFT or ab initio calculations? > Which types of energies would you need? Single point energies or free energies determined through vibration calculations? > How would you do it? > > Thanks,> > -- Dr. Robert Molt Jr. r.molt.chemical.physics._._.gmail.com Nigel Richards Research Group Department of Chemistry & Chemical Biology Indiana University-Purdue University Indianapolis LD 326 402 N. Blackford St. Indianapolis, IN 46202 From owner-chemistry@ccl.net Mon Jun 8 12:25:01 2015 From: "Robert Molt r.molt.chemical.physics() gmail.com" To: CCL Subject: CCL: Comparison of Raman Spectra of two different water cages Message-Id: <-51429-150608115143-15800-8ygtl/6z+5p/6aHM3afVfA,server.ccl.net> X-Original-From: Robert Molt Content-Transfer-Encoding: 7bit Content-Type: text/plain; charset=windows-1252; format=flowed Date: Mon, 08 Jun 2015 11:51:36 -0400 MIME-Version: 1.0 Sent to CCL by: Robert Molt [r.molt.chemical.physics]*[gmail.com] In principle, your task is straightforward. 1.) Find the relevant structures (maybe you need raw minima, if there is no special conformational floppiness), optimize. 2.) Calculate the Raman spectra (can be done with most electronic structure software codes). It's not different than what you would do with IR spectra, and this is done in many tutorials you can look up online. On 6/8/15 8:54 AM, Surinder Kaur simmi.msc7{}gmail.com wrote: > Sent to CCL by: "Surinder Kaur" [simmi.msc7,,gmail.com] > Hello friends > I am working on water cages and trying to analyze the different vibrational > modes with the help of Raman spectroscopy using quantum chemical > calculations. I have the following questions regarding the analysis: > 1.Is it possible to compare the Raman spectra of two different cage > structures without the availability of experimental data i.e. we do not > have any information about characteristic peak? > 2.Can we correlate the red shift (lower wave number) or blue shift (higher > wave number) of vibrational modes of one cage, relative to second cage with > stabilization energy? > > > Thanks in advance. > > With regards > Surinder> > -- Dr. Robert Molt Jr. r.molt.chemical.physics:gmail.com Nigel Richards Research Group Department of Chemistry & Chemical Biology Indiana University-Purdue University Indianapolis LD 326 402 N. Blackford St. Indianapolis, IN 46202 From owner-chemistry@ccl.net Mon Jun 8 12:59:01 2015 From: "Xing Yin xiy726,+,gmail.com" To: CCL Subject: CCL: visualize q-chem plots by matlab? Message-Id: <-51430-150608121056-23402-xpAcpMC5XycubwQc4AChTg^^^server.ccl.net> X-Original-From: Xing Yin Content-Transfer-Encoding: 7bit Content-Type: text/plain; charset=utf-8; format=flowed Date: Mon, 08 Jun 2015 12:10:42 -0400 MIME-Version: 1.0 Sent to CCL by: Xing Yin [xiy726\a/gmail.com] Dear all, Is there way to visualize the volumetric data in the "plot.*" files directly instead of generating cube files? There seems to be some problem during the internal transformation and I want to check original plots... Maybe someone have a script that can transform these "plot.*" files to a format matlab can plot? Thanks! -- Best wishes, Xing From owner-chemistry@ccl.net Mon Jun 8 13:34:01 2015 From: "Alavi, Saman Saman.Alavi..nrc-cnrc.gc.ca" To: CCL Subject: CCL: Determine statistical distribution of chemical species based on energi Message-Id: <-51431-150608122821-5806-YJjz8cI0Fg0VAt1OESUXZQ*o*server.ccl.net> X-Original-From: "Alavi, Saman" Content-Language: en-CA Content-Transfer-Encoding: 8bit Content-Type: text/plain; charset="us-ascii" Date: Mon, 8 Jun 2015 09:28:09 -0700 MIME-Version: 1.0 Sent to CCL by: "Alavi, Saman" [Saman.Alavi+*+nrc-cnrc.gc.ca] Hello Ashika, You can use the statistical mechanical expression for the equilibrium constant to get the probability distribution of different structures in an equilibrium mixture. At temperature T, if structure A has energy EA and structure B has a higher energy EB, then the equilibrium constant for the two species is: K = q(int,B; T)/q(int,A; T) = [q(rot,B;T)q(vib,B;T)]/[q(rot,A;T)q(vib,A;T)] * exp[-(EB - EA)/RT] The q(int) are the partition functions associated with the internal degrees of freedom. These can be written in terms of the rotational, vibrational, and electronic degrees of freedom. Since the two structures have the same mass, their translational partition functions cancel from this relation. All of the quantities necessary for this calculation can be obtained from DFT or ab initio calculations on the optimal structures followed by a normal mode vibration determination. Note that most DFT codes use the harmonic assumption in the vibrational partition function for the normal modes of vibration and are calculated at 298 K. You can change the temperature of the calculation with a setting in the input files. Saman ________________________________________ > From: owner-chemistry+saman.alavi==nrc.ca[#]ccl.net [owner-chemistry+saman.alavi==nrc.ca[#]ccl.net] On Behalf Of ashika torikora ashika.torikora],[gmail.com [owner-chemistry[#]ccl.net] Sent: June 8, 2015 9:44 AM To: Alavi, Saman Subject: CCL: Determine statistical distribution of chemical species based on energi Sent to CCL by: "ashika torikora" [ashika.torikora*gmail.com] Hello everyone. Suppose you have several different states of a given molecule ( different geometries or different chemical states for example). Can you determine theoretical statistical distributions of these states based on energies calculated by DFT or ab initio calculations? Which types of energies would you need? Single point energies or free energies determined through vibration calculations? How would you do it? Thanks,http://www.ccl.net/cgi-bin/ccl/send_ccl_messagehttp://www.ccl.net/chemistry/sub_unsub.shtmlhttp://www.ccl.net/spammers.txt