From owner-chemistry@ccl.net Wed Jan 3 05:36:00 2018 From: "Subrahmanyam Sappati subrahmanyamsappati^^gmail.com" To: CCL Subject: CCL:G: Pseudo hydrogens in Gaussian software Message-Id: <-53130-180103053459-5905-4EM9QGQhDz/0cFr3r52v3g-.-server.ccl.net> X-Original-From: Subrahmanyam Sappati Content-Type: multipart/alternative; boundary="001a1134fc7ee8a85f0561dcc36b" Date: Wed, 3 Jan 2018 16:04:50 +0530 MIME-Version: 1.0 Sent to CCL by: Subrahmanyam Sappati [subrahmanyamsappati..gmail.com] --001a1134fc7ee8a85f0561dcc36b Content-Type: text/plain; charset="UTF-8" Dear All, I want to perform (setup) a TDDFT (excited state) calculation for a Dye-ZnO cluster ((ZnO)100 atoms) for probable photocatalytic water splitting material in Gaussian software. I want to passivate the surface atoms (non-bonded) of ZnO clusters with pseudo-hydrogens (H_0.5 for Oxygen atoms and H_1.5 for Zinc atoms) [http://aip.scitation.org/doi/ full/10.1063/1.3463412]. These pseudo-hydrogens are used for following reasons: 1) to maintain the coordination and charge balance, and 2) if we do not passivate surface atoms of the ZnO cluster ( with pseudo-hydrogens), then surface states will appear in the bandgap region, as a result, excited state spectra will be affected. This procedure of pseudo hydrogens passivation to ZnO clusters are there in pseudo potential plane wave (PW) based codes such as Quantum ESPRESSO, VASP, etc. I do not know how to use the concept of pseudo hydrogen in Gaussian. So, could anyone please suggest me in this perspective. Thanking you Regards Subrahmanyam Sappati P. S: I tried following experiments on my system in order to get ground state density. However, I am not successful. Sample input %chk=input_symmetry_part_rlx-met_full-mod-3.chk %mem=100gb %NprocLinda=4 %NProcShared=112 #sp lc-wpbe/genecp scrf=(iefpcm,solvent=methanol) scf=qc Title required 0 1 H 16.34775783 -12.78224038 23.29179261 O 17.12744738 -13.02765240 23.81003616 C 18.37100140 -12.84366773 23.20731384 H 18.52148916 -13.49716035 22.33079332 H 18.54521437 -11.79966542 22.89330698 H 19.14462230 -13.09864447 23.94133771 C 14.19266462 -12.80057214 17.00804173 : : : Zn 20.65823605 -9.74105110 8.01538316 Zn 19.05591176 -12.37657290 8.91114171 Zn 19.02906647 -9.75506323 10.80341194 Zn 20.70493658 -12.37982252 11.69383654 Zn 19.04738481 -12.22843858 14.22186066 O 19.09533441 -13.01265752 5.20439252 H 19.09273728 -12.66799083 4.22797214 O 20.60747317 -10.37802661 6.17026858 O 20.64351849 -13.02710294 7.92923230 O 19.04979286 -10.38723823 8.92416372 O 19.05782491 -13.00616094 10.79453101 O 20.58265437 -10.45157896 11.76019606 O 20.62372231 -13.07175153 13.55992987 O 18.87583924 -10.44422028 14.58150344 Zn 19.08071980 -14.97264712 5.11589802 Zn 20.69981051 -14.98501963 7.91562312 Zn 19.06495645 -14.98854078 10.73949079 Zn 20.68877977 -15.03732694 13.58855069 O 20.65796403 -15.65205996 6.07267572 O 19.09277413 -15.62760543 8.85706473 O 20.69790577 -15.64926758 11.67261208 O 19.09278113 -15.78206939 14.29467180 H 19.09590531 -10.27236480 3.62858296 H1 15.86936926 -10.21966051 3.59875399 ! pseudo hydrogen H2 12.64270518 -10.21930411 3.51718957 ! pseudo hydrogen : : contd. of molecular specification Zn 0 LANL2DZ **** C H O N 0 6-311G++(d,p) **** Zn 0 LANL2DZ *H1 0.56-311G++(d,p)***** * H2 -0.56-311G++(d,p)***** -- Subrahmanyam.Sappati C/o Dr. Prasenjit Ghosh IISER PUNE Pin code : 411 008 Phone : +91 94 03 59 35 18 --001a1134fc7ee8a85f0561dcc36b Content-Type: text/html; charset="UTF-8" Content-Transfer-Encoding: base64 PGRpdiBkaXI9Imx0ciI+PGRpdiBjbGFzcz0iZ21haWxfZGVmYXVsdCIgc3R5bGU9ImZvbnQtZmFt aWx5OnRpbWVzIG5ldyByb21hbixzZXJpZiI+PGRpdiBjbGFzcz0iZ21haWxfZGVmYXVsdCIgc3R5 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DQo= --001a1134fc7ee8a85f0561dcc36b-- From owner-chemistry@ccl.net Wed Jan 3 11:07:01 2018 From: "Andreas Klamt klamt*_*cosmologic.de" To: CCL Subject: CCL: electrostatics in force-fields Re: CCL: Reference for structural details not amenable to forcefield analysis? Message-Id: <-53131-180103014515-8461-mJcdC3KSw49tShCEVrQHNQ^_^server.ccl.net> X-Original-From: Andreas Klamt Content-Language: de-DE Content-Transfer-Encoding: 7bit Content-Type: text/plain; charset=utf-8 Date: Wed, 3 Jan 2018 07:45:02 +0100 MIME-Version: 1.0 Sent to CCL by: Andreas Klamt [klamt\a/cosmologic.de] The discussion confirms my opinion and reveals the fundamental problems of the electrostatics in forcefields. Mohamed Safi suggested extra point charges, specially fitted for certain atom types in order to remove the lack of halogen bonding (or let us call it the apparent "halogen repulsion") in forcefields. Ullrich Siehl suggest a scheme for specially fitting parameters for a polarizable extension of forcefields, which might be good for some effects, but which will not remove the wrong directionality and sign of the chloride-oxygen interaction in halogen bonds, i.e. it has little to do withthe case I talked about. Indeed, the paper by Ullrich even seems to present a kind of self-fulfilling prophecy: First some new adjustable parameters are introduced, and then it is shown that after optimization these parameters really the agreement between the QM point charges (which are an ill-defined concept by themselves) and the resulting forcefield charges are inbetter agreement than before. What I am missing is any predictive application, demonstrating how the prediction of properties not subject to the fitting improve. It is interesting to observe, that the carbon-chlorine distance, which was not subject to the optimization, but which should be very important for the interaction energy, even got worse by the CEq method compared to original OPLS (where it already was significantly too long compared to the QM result). Furthermore, it would be interesting to know, how much the calculation time increases by the polarization in the force-field. Again: For every individual flaw of forcefields there will be a way how to overcome it by special parameter fitting, and maybe there is already a paper where someone proofs that this can be done, but the concept of describing the complicated electrostatics of molecules by fixed atom centered point charges is so poor, that one would need a polarizable, multi-center decription to overcome it in general. But that would require so many parameters to be fitted to the special systems, and it would increase the calculation time of simulations strongly. Best regards Andreas Am 02.01.2018 um 20:12 schrieb Hans-Ullrich SIEHL ullrich.siehl..uni-ulm.de: > > Sent to CCL by: Hans-Ullrich SIEHL [ullrich.siehl|uni-ulm.de] > > To get rid of the limitation of fixed charges im MM calculations, the > consistent charge equilibration method (CQEq) has been introduced. > > We have applied this concept to a special group of ionic liquids. > "An application of the consistent charge equilibration (CQEq) method > to guanidinium ionic liquid systems > Chemical Physics Letters, Volume 457, Issue 1, p. 263-266. > DOI:10.1016/j.cplett.2008.03.087 > > best regards Ulli From owner-chemistry@ccl.net Wed Jan 3 13:31:00 2018 From: "Mohamed E. A. Safy m.safy#%#compchem.net" To: CCL Subject: CCL: electrostatics in force-fields Re: CCL: Reference for structural details not amenable to forcefield analysis? Message-Id: <-53132-180103132834-4396-+o3jgKjt6z+qr/ojXvx6VQ!A!server.ccl.net> X-Original-From: "Mohamed E. A. Safy" Date: Wed, 3 Jan 2018 13:28:31 -0500 Sent to CCL by: "Mohamed E. A. Safy" [m.safy|-|compchem.net] Thanks, Dr. Andreas Klamt for your clarification. it was so interesting to read your response