From owner-chemistry@ccl.net Mon Jan 19 09:59:01 2015 From: "N. Sukumar nagams^rpi.edu" To: CCL Subject: CCL:G: gaussian basis set less charged Pseudopotentials Message-Id: <-50921-150118034057-22186-0awbFALzOQLh/ZN/IuMTng-*-server.ccl.net> X-Original-From: "N. Sukumar" Content-Transfer-Encoding: 8bit Content-Type: text/plain; charset=UTF-8; format=flowed Date: Sun, 18 Jan 2015 14:10:48 +0530 MIME-Version: 1.0 Sent to CCL by: "N. Sukumar" [nagams^rpi.edu] Would simple point charges for the metal surface serve the purpose? Sukumar On 2015-01-16 01:23, Vijay Gopal Chilkuri shadyvijay-*-gmail.com wrote: > Sent to CCL by: Vijay Gopal Chilkuri [shadyvijay/a\gmail.com] > On Thu, Jan 15, 2015 at 07:19:32AM +0000, Lars Goerigk > lars.goerigk^-^unimelb.edu.au wrote: >> Hi, >> I am not sure that replacing an entire basis set with a >> pseudopotential is helpful, nor that Gaussian would not simply crash. >> What exactly do you try to calculate if I may ask? > > I'm trying to do embedded cluster calculations with G09. So basically > there is a complex > deposited on a metal surface. The complex and the adjacent ions, > treated > with B3LYP, are embedded (AIMP) in a metal. > Such calculations are routinely done, (with all electron > Pseudopotentials) but > with other computational chemistry packages (MOLCAS, NWCHEM). > > What I'm looking for, is to know if it is possible to do embedded > cluster > calculations with gaussian G09 (because it is parallel and fast) using > all > electron (charged) pseudopotentials. > >> >> The method mentioned by Sebastian is designed for London-disperison >> interactions, and it still requires a basis set, of course. >> >> Between, a closer investigation of this approach is presented in >> J. Chem. Theory Comput. 2014, 10, 968. >> http://pubs.acs.org/doi/abs/10.1021/ct500026v >> >> Cheers, >> Lars >> >> --- >> Dr. Lars Goerigk >> ARC DECRA Fellow >> School of Chemistry >> The University of Melbourne >> VIC 3010 >> Australia >> >> Research profile: >> http://www.chemistry.unimelb.edu.au/dr-lars-goerigk >> List of my publications: >> http://www.researcherid.com/rid/D-3717-2009 >> >> On 15 Jan 2015, at 3:24 pm, Sebastian Kozuch >> seb.kozuch^-^gmail.com >> > wrote: >> >> >> Sent to CCL by: Sebastian Kozuch >> [seb.kozuch##gmail.com] >> Maybe this work can help you. >> >> A (Nearly) Universally Applicable Method for Modeling Noncovalent >> Interactions Using B3LYP >> Edmanuel Torres and Gino A. DiLabio >> J. Phys. Chem. Lett., 2012, 3 (13), pp 1738–1744 >> >> http://pubs.acs.org/doi/abs/10.1021/jz300554y >> >> >> >> On 14/1/2015 8:52 PM, vijay CHILKURI vijay.gopal.c!A!gmail.com wrote: >> I would like to know if one could use Pseudopotentials (in gaussian >> G09) for >> metals/anions which are not only for core electrons. >> >> In other words, i want to know if it is possible to use >> Pseudopotentials (in >> G09) for the whole atom without any basis sets and a charge (+ for >> metal - for >> anion). >> >> >> -- >> xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx >> ..........Sebastian Kozuch........... >> xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx >> ......University of North Texas...... >> ..........Denton, Texas, USA......... >> ........ seb.kozuch[]gmail.com ....... >> http://yfaat.ch.huji.ac.il/kozuch.htm >> xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxhttp://www.ccl.net/cgi-bin/ccl/send_ccl_messagehttp://www.ccl.net/chemistry/sub_unsub.shtmlhttp://www.ccl.net/spammers.txt--_000_E0EEC4F34ABF49BCB3E9C2459630023Eunimelbeduau_ >> Content-Type: text/html; charset="Windows-1252" >> Content-ID: >> Content-Transfer-Encoding: quoted-printable >> >> >> >> >> >> >> Hi, >>
I am not sure that replacing an entire basis set with a >> pseudopotential is helpful, nor that Gaussian would not simply >> crash.
>>
What exactly do you try to calculate if I may ask?
>>

>>
>>
The method mentioned by Sebastian is designed for >> London-disperison interactions, and it still requires a basis set, of >> course.
>>

>>
>>
Between, a closer investigation of this approach is presented >> in
>> >>

>>
>>
Cheers,
>>
Lars
>>

>>
>>
>>
>> ---
>>
>> Dr. Lars Goerigk
>>
>> ARC DECRA Fellow
>>
>> School of Chemistry
>>
>> The University of Melbourne
>>
>> VIC 3010
>>
>> Australia
>>
>>
>>
>>
>> Research profile: 
>> >>
>> List of my publications:
>> >>
>>
>>
>>
>>
On 15 Jan 2015, at 3:24 pm, Sebastian Kozuch seb.kozuch^-^> href="http://gmail.com">gmail.com <> href="mailto:owner-chemistry~!~ccl.net">owner-chemistry~!~ccl.net> >> wrote:
>>
>>

>> Sent to CCL by: Sebastian Kozuch [seb.kozuch##> href="http://gmail.com">gmail.com]
>> Maybe this work can help you.
>>
>> A (Nearly) Universally Applicable Method for Modeling Noncovalent >> Interactions Using B3LYP
>> Edmanuel Torres and Gino A. DiLabio
>> J. Phys. Chem. Lett., 2012, 3 (13), pp 1738–1744
>>
>> > href="http://pubs.acs.org/doi/abs/10.1021/jz300554y">http://pubs.acs.org/doi/abs/10.1021/jz300554y
>>
>>
>>
>> On 14/1/2015 8:52 PM, vijay CHILKURI vijay.gopal.c!A!gmail.com >> wrote:
>>
I would like to know if one could use >> Pseudopotentials (in gaussian G09) for
>> metals/anions which are not only for core electrons.
>>
>> In other words, i want to know if it is possible to use >> Pseudopotentials (in
>> G09) for the whole atom without any basis sets and a charge (+ for >> metal - for
>> anion).
>>
>>
>>
>> --
>> xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx
>> ..........Sebastian Kozuch...........
>> xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx
>> ......University of North Texas......
>> ..........Denton, Texas, USA.........
>> ........ seb.kozuch[]gmail.com .......
>> http://yfaat.ch.huji.ac.il/kozuch.htm
>> xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx
>>
>>
>> >> >>     http://www.ccl.net/cgi-bin/ccl/send_ccl_message
>> >>     http://www.ccl.net/cgi-bin/ccl/send_ccl_message
>> >> >> >> >> >>     http://www.ccl.net/spammers.txt
>> >>
>>
>>
>>
>>
>>
>> >> To recover the email address of the author of the message, please > change-- N. SUKUMAR Professor & Head, Department of Chemistry Director, Center for Informatics Shiv Nadar University, India From owner-chemistry@ccl.net Mon Jan 19 17:15:01 2015 From: "Tanay Debnath tanay.iitk^^gmail.com" To: CCL Subject: CCL: ACID software Message-Id: <-50922-150119070026-28902-vs60m50fEAG6g1LtKO0s8A:server.ccl.net> X-Original-From: "Tanay Debnath" Date: Mon, 19 Jan 2015 07:00:25 -0500 Sent to CCL by: "Tanay Debnath" [tanay.iitk^^gmail.com] i would like to do a anisotropy of the current-induced density (ACID) plot for a organic molecule. Could you suggest me to use a convenient free program? From owner-chemistry@ccl.net Mon Jan 19 17:50:01 2015 From: "conor douglas parks coparks2012!=!gmail.com" To: CCL Subject: CCL: Help with CCDC file interpretation Message-Id: <-50923-150119170433-9277-Wlrvp6RtRJ4Oo3vt5/2PKA===server.ccl.net> X-Original-From: "conor douglas parks" Date: Mon, 19 Jan 2015 17:04:32 -0500 Sent to CCL by: "conor douglas parks" [coparks2012[-]gmail.com] Hello, I am a bit puzzled by the files I am looking at from the CCDC. In the case of Tetrolic acid (tetrol) for which I am interested, I know there are two molecules in the asymmetric unit. However, the file output only contains coordinates for one of the molecules. I am not an expert by any means on space groups. I was under the impression that I would need the coordinates of both molecules in the unit cell, and then the symmetry operations of the unit cell could replicate those coordinates in space. What am I missing here? How do I obtain the coordinates of the second molecule? I have attached the .cif file for one of the polymorphs. data_TETROL01 _audit_creation_date 1973-02-27 _database_code_NBS 527264 _chemical_formula_moiety 'C4 H4 O2' _chemical_name_systematic 'Tetrolic acid' _journal_coden_Cambridge 188 _journal_year 1972 _journal_page_first 1763 _journal_name_full 'J.Chem.Soc.,Perkin Trans.2' loop_ _publ_author_name V.Benghiat L.Leiserowitz _chemical_absolute_configuration unk _diffrn_ambient_temperature 295 _exptl_crystal_density_meas 1.287 _exptl_crystal_density_diffrn 1.283 #These two values have been output from a single CSD field. _refine_ls_R_factor_gt 0.04 _refine_ls_wR_factor_gt 0.04 _diffrn_radiation_probe x-ray _symmetry_cell_setting monoclinic _symmetry_space_group_name_H-M 'P 21' _symmetry_Int_Tables_number 4 loop_ _symmetry_equiv_pos_site_id _symmetry_equiv_pos_as_xyz 1 x,y,z 2 -x,1/2+y,-z _cell_length_a 7.887(1) _cell_length_b 7.121(1) _cell_length_c 3.937(1) _cell_angle_alpha 90 _cell_angle_beta 100.18(1) _cell_angle_gamma 90 _cell_volume 217.634 _cell_formula_units_Z 2 loop_ _atom_site_label _atom_site_type_symbol _atom_site_fract_x _atom_site_fract_y _atom_site_fract_z C1 C -0.11578 0.28421 0.13615 C2 C -0.22316 0.14045 0.24486 C3 C -0.30457 0.01597 0.33056 C4 C -0.40438 -0.13882 0.43455 H1 H -0.10700 0.54000 0.09300 H2 H -0.47800 -0.07800 0.63900 H3 H -0.44500 -0.21900 0.26900 H4 H -0.34300 -0.22400 0.61700 O1 O -0.17758 0.45385 0.15657 O2 O 0.01637 0.25317 0.03280 #END From owner-chemistry@ccl.net Mon Jan 19 20:29:01 2015 From: "Alavi, Saman Saman.Alavi^-^nrc-cnrc.gc.ca" To: CCL Subject: CCL: Help with CCDC file interpretation Message-Id: <-50924-150119202735-17047-omMNU/7CpX3k1U6maIpVcQ~!~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, 19 Jan 2015 17:28:14 -0800 MIME-Version: 1.0 Sent to CCL by: "Alavi, Saman" [Saman.Alavi(!)nrc-cnrc.gc.ca] Hi Conor, The symmetry operations of the monoclinic P21 space group generate the so-called Wyckoff positions of the unit cell. In this case, the Wyckoff positions generated by the 2-fold screw axis are: 1 x,y,z 2 -x,1/2+y,-z That is, any point represented by fractional coordinates in the unit cell (x,y,z) is replicated by the symmetry operations to generate a second point (-x,1/2+y,-z). To get this second point to fit in the unit cell, you can add or subtract multiples of 1 to each of the fractional coordinates. So you can take the coordinates of the atoms in the first molecule, which represents the asymmetric unit (given in the CIF file), and generate the coordinates of the second molecule. You can generate the coordinates of the second molecule by hand or use one of the many software programs available, for example the free "Mercury" software available from the CCDC. Mercury will produce the coordinates of all atoms in the unit cell as Cartesian coordinates if you save the output in the "debug" mode. Hopefully this helps! Saman ________________________________________ > From: owner-chemistry+saman.alavi==nrc.ca]![ccl.net [owner-chemistry+saman.alavi==nrc.ca]![ccl.net] On Behalf Of conor douglas parks coparks2012!=!gmail.com [owner-chemistry]![ccl.net] Sent: January 19, 2015 5:04 PM To: Alavi, Saman Subject: CCL: Help with CCDC file interpretation Sent to CCL by: "conor douglas parks" [coparks2012[-]gmail.com] Hello, I am a bit puzzled by the files I am looking at from the CCDC. In the case of Tetrolic acid (tetrol) for which I am interested, I know there are two molecules in the asymmetric unit. However, the file output only contains coordinates for one of the molecules. I am not an expert by any means on space groups. I was under the impression that I would need the coordinates of both molecules in the unit cell, and then the symmetry operations of the unit cell could replicate those coordinates in space. What am I missing here? How do I obtain the coordinates of the second molecule? I have attached the .cif file for one of the polymorphs. data_TETROL01 _audit_creation_date 1973-02-27 _database_code_NBS 527264 _chemical_formula_moiety 'C4 H4 O2' _chemical_name_systematic 'Tetrolic acid' _journal_coden_Cambridge 188 _journal_year 1972 _journal_page_first 1763 _journal_name_full 'J.Chem.Soc.,Perkin Trans.2' loop_ _publ_author_name V.Benghiat L.Leiserowitz _chemical_absolute_configuration unk _diffrn_ambient_temperature 295 _exptl_crystal_density_meas 1.287 _exptl_crystal_density_diffrn 1.283 #These two values have been output from a single CSD field. _refine_ls_R_factor_gt 0.04 _refine_ls_wR_factor_gt 0.04 _diffrn_radiation_probe x-ray _symmetry_cell_setting monoclinic _symmetry_space_group_name_H-M 'P 21' _symmetry_Int_Tables_number 4 loop_ _symmetry_equiv_pos_site_id _symmetry_equiv_pos_as_xyz 1 x,y,z 2 -x,1/2+y,-z _cell_length_a 7.887(1) _cell_length_b 7.121(1) _cell_length_c 3.937(1) _cell_angle_alpha 90 _cell_angle_beta 100.18(1) _cell_angle_gamma 90 _cell_volume 217.634 _cell_formula_units_Z 2 loop_ _atom_site_label _atom_site_type_symbol _atom_site_fract_x _atom_site_fract_y _atom_site_fract_z C1 C -0.11578 0.28421 0.13615 C2 C -0.22316 0.14045 0.24486 C3 C -0.30457 0.01597 0.33056 C4 C -0.40438 -0.13882 0.43455 H1 H -0.10700 0.54000 0.09300 H2 H -0.47800 -0.07800 0.63900 H3 H -0.44500 -0.21900 0.26900 H4 H -0.34300 -0.22400 0.61700 O1 O -0.17758 0.45385 0.15657 O2 O 0.01637 0.25317 0.03280 #ENDhttp://www.ccl.net/cgi-bin/ccl/send_ccl_messagehttp://www.ccl.net/chemistry/sub_unsub.shtmlhttp://www.ccl.net/spammers.txt