From owner-chemistry@ccl.net Fri Apr 27 03:50:00 2012 From: "M Shabbir shabbir193rb ~ gmail.com" To: CCL Subject: CCL: Crystal structures & space groups Message-Id: <-46802-120427034515-10065-Sb7aPnax/jRoiP7aTAhYgg**server.ccl.net> X-Original-From: "M Shabbir" Date: Fri, 27 Apr 2012 03:45:14 -0400 Sent to CCL by: "M Shabbir" [shabbir193rb#%#gmail.com] Dear CCL Colleagues, I am doing some electro-optical structure-property calculations. Although often the calculations are insightful but these will be much more interesting if these are reported with some crystallographic information ( Centrosymmetric or NonCentrosymmetric etc.) of designed derivative molecules. I usually have two situations: i) Sometime I have parent molecules crystal information but not derivatives ii) sometimes nor parent molecules neither derivatives crystal structure information. As now a day, there are several programs that can predict the crystal structures. As there are about more than 200 space groups and of course, to check all one by one is not possible. Is there any way to get some not all ( Centro-symmetric or Non-Centrosymmetric ) crystallographic information about newly designed molecules? How about if two or more molecules be treated with QM/MM and then check their tendency for a space group in unit cell? Or any free source program where we can get crystallographic information by inputting optimized molecular coordinates. Thanks ahead! Dr.Shabbir From owner-chemistry@ccl.net Fri Apr 27 07:48:01 2012 From: "Phil Hasnip phil.hasnip]~[york.ac.uk" To: CCL Subject: CCL: Raman Phonon Calculations Message-Id: <-46803-120427074445-12346-P0GL1OO8xxROfCAbCpILZA^_^server.ccl.net> X-Original-From: Phil Hasnip Content-Type: multipart/alternative; boundary=f46d04478533e1d44d04bea7a0c1 Date: Fri, 27 Apr 2012 12:44:34 +0100 MIME-Version: 1.0 Sent to CCL by: Phil Hasnip [phil.hasnip,+,york.ac.uk] --f46d04478533e1d44d04bea7a0c1 Content-Type: text/plain; charset=ISO-8859-1 May I recommend CASTEP? It can compute Raman-active modes (and intensities) for periodic systems, and is fairly easy to use for a DFT program. See: http://www.castep.org for details, or feel free to email me directly. All the best, Phil Hasnip CASTEP developer, so possibly a bit biased.... ;) On 27 April 2012 02:15, Matthew Reish mreish---chemistry.otago.ac.nz < owner-chemistry|ccl.net> wrote: > > Sent to CCL by: "Matthew Reish" [mreish#,#chemistry.otago.ac.nz] > General question but any help would be appreciated. I find myself needing > to calculate Raman active phonon energies and intensities of crystalline > benzoic > acid and not sure how to get started. A google search makes it seem that > using > the VASP program to calculate force constants then export this into a > separate > program to calculate phonon modes is a common method used but seems fairly > complex. Before I begin using the VASP method I want to make sure this is > the > best way for me to proceed. Any advice for a novice to calculating phonons > would be helpful. > > Cheers, > Matthew Reish > > Chemistry Department > University of Otago > Dunedin, New Zealand> > > -- ----------------------------------------------------------------------------- Dr Phil Hasnip Email: phil.hasnip|york.ac.uk Dept of Physics University of York Tel: +44 (0)1904 324624 York YO10 5DD --f46d04478533e1d44d04bea7a0c1 Content-Type: text/html; charset=ISO-8859-1 Content-Transfer-Encoding: quoted-printable
May I recommend CASTEP? It can compute Raman-act= ive modes (and intensities) for periodic systems, and is fairly easy to use= for a DFT program. See:

http://www.castep.org

for details, or feel free to email me directly.

All the best,
Phil Hasnip
CASTEP developer, so possibly a bit biased.... ;)
On 27 April 2012 02:15, Matthew Reish mreish---chemistry.otago.ac.nz <owner-chemistry|c= cl.net> wrote:

Sent to CCL by: "Matthew =A0Reish" [mreish#,#chemistry.otago.ac.nz]
General question but any help would be appreciated. I find myself needing t= o calculate Raman active phonon energies and intensities of crystalline ben= zoic
acid and not sure how to get started. A google search makes it seem that us= ing
the VASP program to calculate force constants then export this into a separ= ate
program to calculate phonon modes is a common method used but seems fairly<= br> complex. Before I begin using the VASP method I want to make sure this is t= he
best way for me to proceed. Any advice for a novice to calculating phonons<= br> would be helpful.

Cheers,
Matthew Reish

Chemistry Department
University of Otago
Dunedin, New Zealand



-=3D This is automatically added to each message by the mailing script =3D-=
E-mail to subscribers: CHEMISTRY|ccl.n= et or use:
=A0 =A0 =A0http://www.ccl.net/cgi-bin/ccl/send_ccl_message

E-mail to administrators: CHEM= ISTRY-REQUEST|ccl.net or use
=A0 =A0 =A0http://www.ccl.net/cgi-bin/ccl/send_ccl_message

Subscribe/Unsubscribe:
=A0 =A0 =A0http://www.ccl.net/chemistry/sub_unsub.shtml

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

Job: http://www.ccl.n= et/jobs
Conferences: http://server.ccl.net/chemistry/announcements/co= nferences/

Search Messages: http://www.ccl.net/chemistry/searchccl/index.shtml
=A0 =A0 =A0h= ttp://www.ccl.net/spammers.txt

RTFI: http://www.ccl.net/chemistry/aboutccl/instructions/





--
-----------------------= ------------------------------------------------------
Dr Phil Hasnip = =A0 =A0 =A0 =A0 =A0 =A0Email: phil.hasnip|york.ac.uk
Dept of Physics
University of York =A0 =A0 =A0 =A0Tel: =A0+44 (0)1904 32= 4624
York YO10 5DD

--f46d04478533e1d44d04bea7a0c1-- From owner-chemistry@ccl.net Fri Apr 27 09:30:01 2012 From: "Rafal Korlacki rkorlacki2 ~~ unl.edu" To: CCL Subject: CCL: Raman Phonon Calculations Message-Id: <-46804-120427092711-2854-0V6HxAoqYkc5lVQ12Cluyw^_^server.ccl.net> X-Original-From: Rafal Korlacki Content-Language: en-US Content-Transfer-Encoding: 8bit Content-Type: text/plain; charset="us-ascii" Date: Fri, 27 Apr 2012 13:26:58 +0000 MIME-Version: 1.0 Sent to CCL by: Rafal Korlacki [rkorlacki2^_^unl.edu] I recommend you to try Quantum Espresso (http://www.quantum-espresso.org/). I use it to calculate Raman spectra of crystals (it is rather straightforward), but I do not know how its functionality compares to VASP or CASTEP. Regards, Rafal Korlacki -----Original Message----- > From: owner-chemistry+korlacki==unlserve.unl.edu-x-ccl.net [mailto:owner-chemistry+korlacki==unlserve.unl.edu-x-ccl.net] On Behalf Of Matthew Reish mreish---chemistry.otago.ac.nz Sent: Thursday, April 26, 2012 8:16 PM To: Korlacki, Rafal Subject: CCL: Raman Phonon Calculations Sent to CCL by: "Matthew Reish" [mreish#,#chemistry.otago.ac.nz] General question but any help would be appreciated. I find myself needing to calculate Raman active phonon energies and intensities of crystalline benzoic acid and not sure how to get started. A google search makes it seem that using the VASP program to calculate force constants then export this into a separate program to calculate phonon modes is a common method used but seems fairly complex. Before I begin using the VASP method I want to make sure this is the best way for me to proceed. Any advice for a novice to calculating phonons would be helpful. Cheers, Matthew Reish Chemistry Department University of Otago Dunedin, New Zealandhttp://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 Fri Apr 27 10:04:01 2012 From: "Daniele Dondi kaliumster:gmail.com" To: CCL Subject: CCL:G: Example Gaussian 09 Input File for UV/Vis spectrum calculation Message-Id: <-46805-120427052855-19565-d98M/p0pquyq0WUkaSNeeA-$-server.ccl.net> X-Original-From: Daniele Dondi Content-Type: multipart/alternative; boundary=f46d0446318243f56604bea5bbb9 Date: Fri, 27 Apr 2012 11:28:47 +0200 MIME-Version: 1.0 Sent to CCL by: Daniele Dondi [kaliumster%gmail.com] --f46d0446318243f56604bea5bbb9 Content-Type: text/plain; charset=ISO-8859-1 You can try with TDDFT technique. Imagine to have a minimum optimized with B3LYP/6-31G(d). So, put that geometry in a single point calculation like this: # td=(singlets,nstates=12) b3lyp/6-31g(d) scrf=(solvent=water) Title Card Required 0 1 *geometry here* in scrf use your preferred method and solvent. Note that nstates=12 since Gaussian calculate all transitions including those forbidden having f=0. So usually nstates should be greater with respect to expected transitions. You can use gausssum to plot the UV but I suggest you also to open ouput with a text editor and look inside the output. DD 2012/4/26 Christoher Kim ckim===deltacollege.edu > > Sent to CCL by: "Christoher Kim" [ckim- -deltacollege.edu] > Hi All, > > I have been doing some reading and web searching for an example Gaussian 09 > input file that would allow me to calculate the UV/Vis spectrum for aqueous > solutions of transition metal complexes. I would love a system that would > give > me similar results for both experimental and calculated. > > Any help or suggestions would be greatly appreciated. > > I am quite new to all of this, so please me kind. > > Thanks, > -Chris> > > --f46d0446318243f56604bea5bbb9 Content-Type: text/html; charset=ISO-8859-1 Content-Transfer-Encoding: quoted-printable
You can try with TDDFT technique. Imagine to hav= e a minimum optimized with B3LYP/6-31G(d). So, put that geometry in a singl= e point calculation like this:

# td=3D(singlets,nstates=3D12) b3lyp/= 6-31g(d) scrf=3D(solvent=3Dwater)

Title Card Required

0 1
geometry here

in scrf u= se your preferred method and solvent.
Note that nstates=3D12 since Gauss= ian calculate all transitions including those forbidden having f=3D0. So us= ually nstates should be greater with respect to expected transitions. You c= an use gausssum to plot the UV but I suggest you also to open ouput with a = text editor and look inside the output.

DD

2012/4/26 Christoher Kim ckim=3D= =3D=3Ddeltacollege.edu <owne= r-chemistry-,-ccl.net>

Sent to CCL by: "Christoher =A0Kim" [ckim- -deltacollege.edu]
Hi All,

I have been doing some reading and web searching for an example Gaussian 09=
input file that would allow me to calculate the UV/Vis spectrum for aqueous=
solutions of transition metal complexes. =A0I would love a system that woul= d give
me similar results for both experimental and calculated.

Any help or suggestions would be greatly appreciated.

I am quite new to all of this, so please me kind.

Thanks,
-Chris



-=3D This is automatically added to each message by the mailing script =3D-=
E-mail to subscribers: CHEMISTRY-,-ccl.n= et or use:
=A0 =A0 =A0http://www.ccl.net/cgi-bin/ccl/send_ccl_message

E-mail to administrators: CHEM= ISTRY-REQUEST-,-ccl.net or use
=A0 =A0 =A0http://www.ccl.net/cgi-bin/ccl/send_ccl_message

Subscribe/Unsubscribe:
=A0 =A0 =A0http://www.ccl.net/chemistry/sub_unsub.shtml

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

Job: http://www.ccl.n= et/jobs
Conferences: http://server.ccl.net/chemistry/announcements/co= nferences/

Search Messages: http://www.ccl.net/chemistry/searchccl/index.shtml
=A0 =A0 =A0h= ttp://www.ccl.net/spammers.txt

RTFI: http://www.ccl.net/chemistry/aboutccl/instructions/



--f46d0446318243f56604bea5bbb9-- From owner-chemistry@ccl.net Fri Apr 27 10:40:01 2012 From: "quartarolo!^!unical.it" To: CCL Subject: CCL:G: Example Gaussian 09 Input File for UV/Vis spectrum calculation Message-Id: <-46806-120427061055-23927-E89d1liw94YrZPwA/AECLQ[a]server.ccl.net> X-Original-From: quartarolo_+_unical.it Content-Disposition: inline Content-Transfer-Encoding: 7bit Content-Type: text/plain; charset=ISO-8859-1; DelSp="Yes"; format="flowed" Date: Fri, 27 Apr 2012 12:10:43 +0200 MIME-Version: 1.0 Sent to CCL by: quartarolo[#]unical.it Hi Chris, this is an input Gaussian file for simulating the UV/vis spectrum in water of CrF6 molecule: %chk=CrF6 %mem=500MB %nproc=4 # rpbe1pbe/Gen TD=(Nstates=20) scrf=(pcm,solvent=water) Title Card Required 0 1 Cr 0.000000 0.000000 0.000000 F 0.000000 0.000000 1.724653 F 0.000000 1.724653 0.000000 F 1.724653 0.000000 0.000000 F 0.000000 0.000000 -1.724653 F -1.724653 0.000000 0.000000 F 0.000000 -1.724653 0.000000 F 0 6-311+G(d) **** Cr 0 LANL2DZ **** Cr 0 LANL2DZ --And this a reference where you can find the theoretical(gas-phase) and experimental data for this and other molecules: Theor Chem Acc (2000) 105: 169-172 Best regards Quartarolo Domenico Quoting "Christoher Kim ckim===deltacollege.edu" : > > Sent to CCL by: "Christoher Kim" [ckim- -deltacollege.edu] > Hi All, > > I have been doing some reading and web searching for an example Gaussian 09 > input file that would allow me to calculate the UV/Vis spectrum for aqueous > solutions of transition metal complexes. I would love a system that > would give > me similar results for both experimental and calculated. > > Any help or suggestions would be greatly appreciated. > > I am quite new to all of this, so please me kind. > > Thanks, > -Chris> > > ---------------------------------------------------------------- This message was sent using IMP, the Internet Messaging Program. **** Riservatezza / Confidentiality **** In ottemperanza al D.Lgs. n. 196 del 30/6/2003 in materia di protezione dei dati personali, le informazioni contenute in questo messaggio sono strettamente riservate ed esclusivamente indirizzate al destinatario indicato (oppure alla persona responsabile di rimetterlo al destinatario). Vogliate tener presente che qualsiasi uso, riproduzione o divulgazione di questo messaggio e' vietato. Nel caso in cui aveste ricevuto questo messaggio per errore, vogliate cortesemente avvertire il mittente e distruggere il presente messaggio. From owner-chemistry@ccl.net Fri Apr 27 11:21:00 2012 From: "Billy McCann bwm0005/./tigermail.auburn.edu" To: CCL Subject: CCL:G: Help please - CPCM with UAKS radii in Gaussian03 Message-Id: <-46807-120427110529-24203-qYPvde3Cql8hH/nWrZi9Rg(~)server.ccl.net> X-Original-From: Billy McCann Content-Language: en-US Content-Transfer-Encoding: 8bit Content-Type: text/plain; charset="us-ascii" Date: Fri, 27 Apr 2012 15:05:13 +0000 MIME-Version: 1.0 Sent to CCL by: Billy McCann [bwm0005##tigermail.auburn.edu] Hi Jason. The UAKS cavity does not include spheres on the hydrogen atom by default. This is reflected in its acronym, with the UA meaning that it utilizes the "United Atom Topological Model", in which hydrogen aren't explicitly included. From [1], "UAKS: Uses the United Atom Topological Model applied on radii optimized for the PBE1PBE/6-31G(d) level of theory." (I believe that United Atom approach is chemically justified such that hydrogens are typically within the VDW radii of the atom to which it's bonded.) However, this *is* a reference for Gaussian09 and not 03. That being said, one may add a sphere to a particular hydrogen if one wishes to. Again from [1], "SphereOnH=N : When using a United Atom Topological model, places an individual sphere on the hydrogen at the Nth position in the atoms list." See the "SPECIFYING THE MOLECULAR CAVITY" of [1]. If one wishes to add this sphere on H, one would include the 'read' keyword as a parameter to the scrf keyword, as one does to specify the non-default radii in the building of the cavity. The SphereOnH=N parameter would then be appended to the bottom of the input file. Regarding the appropriate citation, I don't have that handy. If you were to come across it, I'd more than welcome you to share that with CCL and me. [1] = http://www.gaussian.com/g_tech/g_ur/k_scrf.htm Hope that helps, All the best, Billy Wayne +++++++++++++++++++ Billy Wayne McCann Ph.D. Candidate Orlando Acevedo Research Auburn University, Alabama Office # = 334-844-6948 +++++++++++++++++++ -----Original Message----- > From: owner-chemistry+bwm0005==auburn.edu**ccl.net [mailto:owner-chemistry+bwm0005==auburn.edu**ccl.net] On Behalf Of Jason G. Gillmore gillmore : hope.edu Sent: Thursday, April 26, 2012 2:52 PM To: Billy McCann Subject: CCL:G: Help please - CPCM with UAKS radii in Gaussian03 Sent to CCL by: "Jason G. Gillmore" [gillmore++hope.edu] Short questions: 1) In Gaussian03, when I do a molecular energy calculation with CPCM using radii=UAKS, does this include explicit spheres for hydrogen in creating the cavity (like UFF) or not (like UA0)? 2) Is there an appropriate reference to that fact I can cite in a paper? Jason Gillmore, gillmore||hope.edu Longer explanation behind question: We developped and published a method for predicting organic reduction potentials (JPCA 2008, 112, 5684)using single point calculations in G03 at B3LYP/6-31G(d) or /6-311+G(d,p) levels of theory with CPCM (in acetonitrile), with the then default UA0 radii. Later on, when we attempted to use this method on molecules that can have intramolecular hydrogen bonds, these jobs often failed to converge. On the basis of advice on the list (e.g., http://www.ccl.net/chemistry/resources/messages/2005/11/17.005-dir/) my student started using radii=UAKS for these jobs and they worked! We've since then greatly updated and expanded our correlations and tested several different variables, among them redoing all our correlations with both UAKS and UA0 radii, and are writing this up in another paper for submission to JPCA or possibly JOC. I'd like to be able to say something cogent about the difference between UAKS and UA0 and more behind out motivation of trying UAKS (besides the fact that in hindsight it worked.) The aforementioned post by Luis Simn Rubio leads the student to believe, that UAKS (like UFF) includes explicit hydrogens. The G03 users manual explcitly specifies that radii= UFF, Pauling, and Bondi, all do include explicit hydrogens, while not mentioning hydrogens for UA0, UAHF, or UAKS. This would imply to me that none of the United Atom Topological Model radii methods include explicity hydrogens. The G09 users manual, where UFF is now the default radii for SCRF PCM/CPCM calcs, explicitly notes that UA0 does not and UFF does include explicity hydrogens, but says nothing about explicit hydrogens for UAHF or UAKS (though again noting that BONDI and PAULING do include them.) Less clear. Can someone help clear this up for us, and ideally point us to a reference we can cite in our paper one way or the other? Gratefully, Jason G. Gillmore Associate Professor of Chemistry Hope College, Holland, MI USA gillmore||hope.eduhttp://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 Fri Apr 27 11:56:00 2012 From: "Sajeewa Pemasinghe sajeewasp- -gmail.com" To: CCL Subject: CCL: Creating concatenated coordinate file in Locally Enhanced Sampling (LES) using AMBER 11 Message-Id: <-46808-120427110534-24302-5w+s0xifrfNnE3Dm1cPUYw.:.server.ccl.net> X-Original-From: Sajeewa Pemasinghe Content-Type: multipart/alternative; boundary=20cf303bf8860cdd7d04beaa6f8a Date: Fri, 27 Apr 2012 11:05:23 -0400 MIME-Version: 1.0 Sent to CCL by: Sajeewa Pemasinghe [sajeewasp- -gmail.com] --20cf303bf8860cdd7d04beaa6f8a Content-Type: text/plain; charset=ISO-8859-1 Hello everyone, I am trying to compare free energy changes along two intramolecular tunnels in a protein, as an ammonia molecule passes through the tunnel from one site to another site. I want to place copies of the ammonia molecule at various points along the tunnel. Instead of running many simulations with the ammonia molecule at different points along the tunnel I am trying to use LES to place 6 copies of the ammonia molecule simultaneously at 6 positions along the tunnel. So the initial positions of the copies will be different. In the chapter on LES in the Amber11 user manual it says I have to concatenate different coordinates into a single file. So if I have an initial .inpcrd file with one ammonia molecule could anyone give me the specifics of creating the concatenated file? Thank you Sajeewa Dewage --20cf303bf8860cdd7d04beaa6f8a Content-Type: text/html; charset=ISO-8859-1 Content-Transfer-Encoding: quoted-printable Hello everyone,

I am trying to compare =A0free energy=20 changes along two intramolecular tunnels in a protein, as an ammonia=20 molecule passes through the tunnel from one site to another site. I want to place copies of the ammonia molecule at various points along the=20 tunnel. Instead of running many simulations with the ammonia molecule at different points along the tunnel I am trying to use LES to place 6=20 copies of the ammonia molecule simultaneously at 6 positions along the=20 tunnel. So the initial positions of the copies will be different. In the chapter on LES in the Amber11 user manual it says I have to concatenate different coordinates into a single file. So if I have an initial=20 .inpcrd file with one ammonia molecule could anyone give me the=20 specifics of creating the concatenated file?

Thank you

Sajeewa Dewage
--20cf303bf8860cdd7d04beaa6f8a-- From owner-chemistry@ccl.net Fri Apr 27 16:57:00 2012 From: "Nikolaos Bouropoulos nbouro+/-upatras.gr" To: CCL Subject: CCL: ADVANCED CHEMISTRY LETTERS -CALL FOR PAPERS Message-Id: <-46809-120427110811-29279-pMHmXRHff+oHukgMQZDV3A{:}server.ccl.net> X-Original-From: "Nikolaos Bouropoulos" Date: Fri, 27 Apr 2012 11:08:07 -0400 Sent to CCL by: "Nikolaos Bouropoulos" [nbouro()upatras.gr] The upcoming journal Advanced Chemistry Letters invites authors to submit articles. Manuscripts must be prepared according to Journals guidelines, available at http://www.aspbs.com/acl/ Submit your manuscripts directly to Dr. N. Bouropoulos via editoracl*upatras.gr All papers submitted to this issue will be subject to a peer review process to ensure high quality articles. Submitted papers should not have been previously published nor be currently under consideration for publication elsewhere. -- Nikolaos Bouropoulos Assistant Professor Department of Materials Science University of Patras, GR-26504 Rio Patras, Greece Phone: (+030) 2610 997874, e-mail: nbouro*upatras.gr Editor-in-Chief: Advanced Chemistry Letters. http://www.aspbs.com/acl/ e-mail: editoracl*upatras.gr