From owner-chemistry@ccl.net Wed Nov 10 00:06:01 2010 From: "Liu Jing jliu*_*cuhk.edu.hk" To: CCL Subject: CCL: help Message-Id: <-43118-101109235111-11490-soxG48zrlzoVVHRZBmfsyw()server.ccl.net> X-Original-From: Liu Jing Content-Type: multipart/alternative; boundary=e0cb4e385676afb5e30494ab9afc Date: Wed, 10 Nov 2010 12:51:02 +0800 MIME-Version: 1.0 Sent to CCL by: Liu Jing [jliu^_^cuhk.edu.hk] --e0cb4e385676afb5e30494ab9afc Content-Type: text/plain; charset=ISO-8859-1 Hi, have u checked the SCF energy, does it vibrate with a small fluctuation or decrease always? If it fluctuates, maybe a small maxstep will work, and if it keeps decreaseing maybe u can increase the maxcycle number or give a little change to your initial structure. Good luck Jane --e0cb4e385676afb5e30494ab9afc Content-Type: text/html; charset=ISO-8859-1 Content-Transfer-Encoding: quoted-printable
Hi, have u checked the SCF energy, does it vibrate with a small fluctu= ation or decrease always?
If it fluctuates, maybe a small maxstep will = work, and if it keeps decreaseing maybe u can increase
the maxcycle numb= er or give a little change to your initial structure.
Good=A0 luck
Jane
--e0cb4e385676afb5e30494ab9afc-- From owner-chemistry@ccl.net Wed Nov 10 00:41:00 2010 From: "jing liu jshaohai#gmail.com" To: CCL Subject: CCL:G: help Message-Id: <-43119-101109231732-26703-OEvQ4LBIfQEyMQCxyQ2k8A{}server.ccl.net> X-Original-From: jing liu Content-Type: multipart/alternative; boundary=e0cb4e3856760e34250494ab22d6 Date: Wed, 10 Nov 2010 12:17:18 +0800 MIME-Version: 1.0 Sent to CCL by: jing liu [jshaohai]^[gmail.com] --e0cb4e3856760e34250494ab22d6 Content-Type: text/plain; charset=ISO-8859-1 Hi, have u checked the SCF energy, does it vibrate with a small fluctuation or decrease always? If it fluctuates, maybe a small maxstep will work, and if it keeps decreaseing maybe u can increase the maxcycle number or give a little change to your initial structure. Good luck Jane 2010/11/8 Jean Jules FIFEN julesfifen[a]gmail.com > To hope very effecient solution, you would have send all geometry > optimization steps results. > Despite of this, regarding the last step of your geometry optimization, the > thing you can do to solve the problem, > > 1. is to restart the computation from the last geometry optimizations > step by adding the key word:* opt(maxcycle=999) scf(maxcycle=999) *instead > of merely type *opt* for geometry optimization. Note that this will > increase the number of iterations for geometry optimization and energy > computation. > 2. If this does not work, analyse carrefully the output file to find > from which step the computation begins to diverge. Then send a new job from > the previous step by adding the key words *Geom=(check,step=n) > guess=read* if the target step is the step number n. Obviously, you > need to have save the checkpoint file from the previous job. > 3. If previous steps are unsuccessfull, try modifying the geometry of > the molecule regarding physical senses. > > > Best regards, > > Jules. > > On 7 November 2010 12:02, Bilel Mansouri bilelmansouri80/ayahoo.fr < > owner-chemistry[A]ccl.net> wrote: > >> >> >> HI >> > I'm doing a (what I thought was simple) test job of tow water molecules >> whith supermolecule methode using B3LYP >> > and the 6-311G basis set. >> I have the error message >> >> Item Value Threshold Converged? >> Maximum Force 0.000882 0.000450 NO >> RMS Force 0.000269 0.000300 YES >> Maximum Displacement 0.056470 0.001800 NO >> RMS Displacement 0.014132 0.001200 NO >> Predicted change in Energy=-1.659919D-03 >> Optimization stopped. >> -- Number of steps exceeded, NStep= 100 >> -- Flag reset to prevent archiving. >> ---------------------------- >> ! Non-Optimized Parameters ! >> ! (Angstroms and Degrees) ! >> -------------------------- >> -------------------------- >> ! Name Definition Value Derivative >> Info. ! >> >> -------------------------------------------------------------------------------- >> ! R1 R(1,3) 3.9996 -DE/DX = >> -0.0023 ! >> ! R2 R(1,5) 1.003 -DE/DX = >> 0.0 ! >> ! R3 R(1,6) 1.003 -DE/DX = >> 0.0 ! >> ! R4 R(1,7) 2.9817 -DE/DX = >> -0.0009 ! >> ! R5 R(1,9) 3.0732 -DE/DX = >> -0.001 ! >> ! R6 R(2,4) 3.9997 -DE/DX = >> -0.0029 ! >> ! R7 R(2,7) 0.9737 -DE/DX = >> 0.0004 ! >> ! R8 R(2,8) 0.9697 -DE/DX = >> 0.0007 ! >> ! R9 R(3,9) 0.9722 -DE/DX = >> -0.0013 ! >> ! R10 R(3,10) 0.9664 -DE/DX = >> -0.0001 ! >> ! R11 R(3,11) 1.7428 -DE/DX = >> 0.0002 ! >> ! R12 R(4,8) 4.4728 -DE/DX = >> -0.0008 ! >> ! R13 R(4,11) 0.981 -DE/DX = >> 0.0003 ! >> ! R14 R(4,12) 0.9659 -DE/DX = >> 0.0 ! >> ! A1 A(3,1,5) 99.0096 -DE/DX = >> 0.0 ! >> ! A2 A(3,1,6) 99.0096 -DE/DX = >> 0.0 ! >> ! A3 A(3,1,7) 68.5648 -DE/DX = >> 0.0 ! >> ! A4 A(5,1,6) 104.9845 -DE/DX = >> -0.0007 ! >> ! A5 A(5,1,7) 60.6293 -DE/DX = >> -0.0003 ! >> ! A6 A(5,1,9) 101.859 -DE/DX = >> 0.0001 ! >> ! A7 A(6,1,7) 60.6293 -DE/DX = >> -0.0003 ! >> ! A8 A(6,1,9) 101.859 -DE/DX = >> 0.0001 ! >> ! A9 A(7,1,9) 73.3866 -DE/DX = >> 0.0 ! >> ! A10 A(4,2,7) 3.2523 -DE/DX = >> 0.001 ! >> ! A11 A(7,2,8) 110.0485 -DE/DX = >> 0.0001 ! >> ! A12 A(1,3,10) 126.5996 -DE/DX = >> 0.0001 ! >> ! A13 A(1,3,11) 96.7028 -DE/DX = >> -0.0001 ! >> ! A14 A(9,3,10) 111.1913 -DE/DX = >> -0.0001 ! >> ! A15 A(9,3,11) 112.1111 -DE/DX = >> 0.0001 ! >> ! A16 A(10,3,11) 136.6976 -DE/DX = >> 0.0 ! >> ! A17 A(2,4,11) 95.2594 -DE/DX = >> -0.0002 ! >> ! A18 A(2,4,12) 154.9369 -DE/DX = >> -0.0001 ! >> ! A19 A(8,4,11) 106.7444 -DE/DX = >> -0.0002 ! >> ! A20 A(8,4,12) 143.4519 -DE/DX = >> -0.0001 ! >> ! A21 A(11,4,12) 109.8037 -DE/DX = >> 0.0003 ! >> ! A22 L(1,7,2,4,-1) 285.8641 -DE/DX = >> -0.0011 ! >> ! A23 L(3,11,4,2,-1) 168.2659 -DE/DX = >> -0.0003 ! >> ! A24 L(1,7,2,4,-2) 180.0 -DE/DX = >> 0.0 ! >> ! A25 L(3,11,4,2,-2) 180.0 -DE/DX = >> 0.0 ! >> ! D1 D(3,1,2,4) 0.0 -DE/DX = >> 0.0 ! >> ! D2 D(3,1,2,8) 180.0 -DE/DX = >> 0.0 ! >> ! D3 D(5,1,2,4) 102.9058 -DE/DX = >> 0.0001 ! >> ! D4 D(5,1,2,8) -77.0942 -DE/DX = >> 0.0001 ! >> ! D5 D(6,1,2,4) -102.9058 -DE/DX = >> -0.0001 ! >> ! D6 D(6,1,2,8) 77.0942 -DE/DX = >> -0.0001 ! >> ! D7 D(9,1,2,4) 0.0 -DE/DX = >> 0.0 ! >> ! D8 D(9,1,2,8) 180.0 -DE/DX = >> 0.0 ! >> ! D9 D(5,1,3,10) 126.5651 -DE/DX = >> 0.0004 ! >> ! D10 D(5,1,3,11) -53.4349 -DE/DX = >> 0.0004 ! >> ! D11 D(6,1,3,10) -126.5651 -DE/DX = >> -0.0004 ! >> ! D12 D(6,1,3,11) 53.4349 -DE/DX = >> -0.0004 ! >> ! D13 D(7,1,3,10) 180.0 -DE/DX = >> 0.0 ! >> ! D14 D(7,1,3,11) 0.0 -DE/DX = >> 0.0 ! >> ! D15 D(7,2,4,11) 180.0 -DE/DX = >> 0.0 ! >> ! D16 D(7,2,4,12) 0.0 -DE/DX = >> 0.0 ! >> ! D17 D(1,3,4,2) 0.0 -DE/DX = >> 0.0 ! >> ! D18 D(1,3,4,8) 0.0 -DE/DX = >> 0.0 ! >> ! D19 D(1,3,4,12) 180.0 -DE/DX = >> 0.0 ! >> ! D20 D(9,3,4,2) 0.0 -DE/DX = >> 0.0 ! >> ! D21 D(9,3,4,8) 0.0 -DE/DX = >> 0.0 ! >> ! D22 D(9,3,4,12) 180.0 -DE/DX = >> 0.0 ! >> ! D23 D(10,3,4,2) 180.0 -DE/DX = >> 0.0 ! >> ! D24 D(10,3,4,8) 180.0 -DE/DX = >> 0.0 ! >> ! D25 D(10,3,4,12) 0.0 -DE/DX = >> 0.0 ! >> >> -------------------------------------------------------------------------------- >> GradGradGradGradGradGradGradGradGradGradGradGradGradGradGradGradGradGrad >> Input orientation: >> --------------------------------------------------------------------- >> Center Atomic Atomic Coordinates (Angstroms) >> Number Number Type X Y Z >> --------------------------------------------------------------------- >> 1 8 0 0.184505 0.000000 0.154984 >> 2 8 0 0.033034 0.000000 2.881640 >> 3 8 0 4.161469 0.000000 0.583652 >> 4 8 0 4.011921 0.000000 3.292071 >> 5 1 0 -0.032703 -0.765799 0.712955 >> 6 1 0 -0.032703 0.765799 0.712955 >> 7 1 0 0.995253 0.000000 3.035531 >> 8 1 0 -0.438867 0.000000 3.727326 >> 9 1 0 3.261177 0.000000 0.215677 >> 10 1 0 4.826475 0.000000 -0.117892 >> 11 1 0 4.189967 0.000000 2.324276 >> 12 1 0 4.842678 0.000000 3.787965 >> --------------------------------------------------------------------- >> Distance matrix (angstroms): >> 1 2 3 4 5 >> 1 O 0.000000 >> 2 O 2.730860 0.000000 >> 3 O 4.000000 4.724906 0.000000 >> 4 O 4.948780 4.000000 2.712545 0.000000 >> 5 H 0.972090 2.300862 4.265472 4.857702 0.000000 >> 6 H 0.972090 2.300862 4.265472 4.857702 1.531598 >> 7 H 2.992467 0.974448 4.004577 3.027557 2.652829 >> 8 H 3.626323 0.968439 5.571875 4.472020 3.136535 >> 9 H 3.077270 4.186678 0.972590 3.166673 3.418096 >> 10 H 4.649983 5.654580 0.966641 3.505901 4.988824 >> 11 H 4.555168 4.194133 1.740858 0.984036 4.584076 >> 12 H 5.907378 4.894293 3.275922 0.967506 5.814764 >> 6 7 8 9 10 >> 6 H 0.000000 >> 7 H 2.652829 0.000000 >> 8 H 3.136535 1.592257 0.000000 >> 9 H 3.418096 3.617456 5.101177 0.000000 >> 10 H 4.988824 4.962090 6.519933 1.600445 0.000000 >> 11 H 4.584076 3.272932 4.836802 2.304093 2.523753 >> 12 H 5.814764 3.920311 5.281894 3.906711 3.905890 >> 11 12 >> 11 H 0.000000 >> 12 H 1.602627 0.000000 >> Stoichiometry H8O4 >> Framework group CS[SG(H6O4),X(H2)] >> Deg. of freedom 20 >> Full point group CS >> Largest Abelian subgroup CS NOp 2 >> Largest concise Abelian subgroup CS NOp 2 >> Standard orientation: >> --------------------------------------------------------------------- >> Center Atomic Atomic Coordinates (Angstroms) >> Number Number Type X Y Z >> --------------------------------------------------------------------- >> 1 8 0 -2.501070 0.069787 0.000000 >> 2 8 0 -0.827351 2.227623 0.000000 >> 3 8 0 0.782472 -2.214584 0.000000 >> 4 8 0 2.445684 -0.071777 0.000000 >> 5 1 0 -2.299150 0.633470 0.765799 >> 6 1 0 -2.299150 0.633470 -0.765799 >> 7 1 0 0.000000 1.712804 0.000000 >> 8 1 0 -0.629035 3.175540 0.000000 >> 9 1 0 -0.138519 -1.901999 0.000000 >> 10 1 0 0.824466 -3.180313 0.000000 >> 11 1 0 1.945446 -0.919177 0.000000 >> 12 1 0 3.398064 -0.242189 0.000000 >> --------------------------------------------------------------------- >> Rotational constants (GHZ): 3.6566956 1.7161673 1.1744164 >> ********************************************************************** >> Population analysis using the SCF density. >> ********************************************************************** >> Electronic spatial extent (au): = 919.2008 >> Charge= 0.0000 electrons >> Dipole moment (field-independent basis, Debye): >> X= 1.8028 Y= -0.6387 Z= 0.0000 Tot= 1.9126 >> Quadrupole moment (field-independent basis, Debye-Ang): >> XX= -30.6350 YY= -7.6894 ZZ= -26.4884 >> XY= -5.0915 XZ= 0.0000 YZ= 0.0000 >> Traceless Quadrupole moment (field-independent basis, Debye-Ang): >> XX= -9.0307 YY= 13.9149 ZZ= -4.8841 >> XY= -5.0915 XZ= 0.0000 YZ= 0.0000 >> Octapole moment (field-independent basis, Debye-Ang**2): >> XXX= 53.7799 YYY= -7.6173 ZZZ= 0.0000 XYY= 5.7536 >> XXY= -2.5321 XXZ= 0.0000 XZZ= -7.1177 YZZ= 1.2264 >> YYZ= 0.0000 XYZ= 0.0000 >> Hexadecapole moment (field-independent basis, Debye-Ang**3): >> XXXX= -509.3830 YYYY= -156.7525 ZZZZ= -23.2511 XXXY= 30.6051 >> XXXZ= 0.0000 YYYX= 48.4794 YYYZ= 0.0000 ZZZX= 0.0000 >> ZZZY= 0.0000 XXYY= -160.2397 XXZZ= -90.8949 YYZZ= -82.4570 >> XXYZ= 0.0000 YYXZ= 0.0000 ZZXY= 26.3538 >> Atom 7 needs variable 8= 0.9744477035 but is 0.9720898606 >> Input z-matrix variables are not compatible with final structure. >> >> FAULTILY FAULTLESS, ICILY REGULAR, SPLENDIDLY NULL... >> MAUDE BY TENNYSON >> Error termination request processed by link 9999. >> Error termination via Lnk1e in C:\G03W\l9999.exe at Thu Nov 04 19:09:35 >> 2010. >> Job cpu time: 0 days 1 hours 13 minutes 15.0 seconds. >> File lengths (MBytes): RWF= 20 Int= 0 D2E= 0 Chk= 11 >> Scr= 1 >> Any insight would be very helpful. >> >> Thanks! >> >> >> > > > -- > Jean Jules FIFEN, > +237 75 21 61 39 > +237 94 67 65 05 > University of Ngaoundere, > PO.BOX 454 Ngaoundere > --e0cb4e3856760e34250494ab22d6 Content-Type: text/html; charset=ISO-8859-1 Content-Transfer-Encoding: base64 SGksIGhhdmUgdSBjaGVja2VkIHRoZSBTQ0YgZW5lcmd5LCBkb2VzIGl0IHZpYnJhdGUgd2l0aCBh IHNtYWxsIGZsdWN0dWF0aW9uIG9yIGRlY3JlYXNlIGFsd2F5cz8gCjxkaXYgY2xhc3M9ImdtYWls 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IGNsZWFyPSJhbGwiPjxicj4tLSA8YnI+SmVhbiBKdWxlcyBGSUZFTiw8YnI+KzIzNyA3NSAyMSA2 MSAzOTxicj4rMjM3IDk0IDY3IDY1IDA1PGJyPlVuaXZlcnNpdHkgb2YgTmdhb3VuZGVyZSw8YnI+ ClBPLkJPWCA0NTQgTmdhb3VuZGVyZTxicj48L2Rpdj48L2Jsb2NrcXVvdGU+PC9kaXY+PGJyPgo= --e0cb4e3856760e34250494ab22d6-- From owner-chemistry@ccl.net Wed Nov 10 01:42:00 2010 From: "Chenghua Zhang zchua126.com~!~126.com" To: CCL Subject: CCL: bond lengths and angles for atoms groups of proteins Message-Id: <-43120-101109235556-12132-fCMs9XPa4Cghd7bqLtWL5g-$-server.ccl.net> X-Original-From: "Chenghua Zhang" Content-Type: multipart/alternative; boundary="----=_Part_161353_2122967691.1289353973317" Date: Wed, 10 Nov 2010 09:52:53 +0800 (CST) MIME-Version: 1.0 Sent to CCL by: "Chenghua Zhang" [zchua126.com[a]126.com] ------=_Part_161353_2122967691.1289353973317 Content-Type: text/plain; charset=gbk Content-Transfer-Encoding: 7bit hi, you can look the top and parameter files of CHARMM or AMBER -- Sincerely Chenghua Zhang College of Chemistry Sichuan University, China. ------=_Part_161353_2122967691.1289353973317 Content-Type: text/html; charset=gbk Content-Transfer-Encoding: 7bit hi, you can look the top and parameter files of CHARMM or AMBER
--
Sincerely
Chenghua Zhang
College of Chemistry
Sichuan University, China.




------=_Part_161353_2122967691.1289353973317-- From owner-chemistry@ccl.net Wed Nov 10 05:24:01 2010 From: "elsayed elmeselhy elsayed.elmes-*-yahoo.com" To: CCL Subject: CCL:G: Antiferromagentism of dinulear transition metal complexes Message-Id: <-43121-101110044116-8306-rTEd6iMaa+auc+9fsk6PFw]=[server.ccl.net> X-Original-From: elsayed elmeselhy Content-Type: multipart/alternative; boundary="0-469450589-1289382066=:71656" Date: Wed, 10 Nov 2010 01:41:06 -0800 (PST) MIME-Version: 1.0 Sent to CCL by: elsayed elmeselhy [elsayed.elmes~!~yahoo.com] --0-469450589-1289382066=:71656 Content-Type: text/plain; charset=iso-8859-1 Content-Transfer-Encoding: quoted-printable Dear All, Thanks for Dr. Nesse for his help and his excellent review which explain th= e concept. On the other hand, for dinuclear cobalt complex, I have optimize= d the closed shell singlet state and the open shell triplet, quintet and se= ptet states, I found that the septet state has the lowest energy. To model = the anti-ferromagnetic singlet state, I have to start with the optimized ge= ometry of septet state, right?. Then divide the complex into three fragment= s (Co1, Co2 and the ligand). The charge and multiplicities will be: 4 1, 2 3, 2 -3, 0 1 respectively.=A0 where=20 4 1 charge and multiplicity of=A0 the whole complex 2 3 charge and multiplicity of=A0 Co2+ with three alpha electron spin =0A2 -3=A0 charge and multiplicity of=A0 Co2+ with three beta=A0 electron s= pin =0A1 0=A0 charge and multiplicity of=A0 the ligand =0A Is this scenario is right or not? Regards, Sayed --- On Sun, 11/7/10, Frank Neese neese%a%thch.uni-bonn.de wrote: > From: Frank Neese neese%a%thch.uni-bonn.de Subject: CCL:G: Antiferromagentism of dinulear transition metal complexes To: "Mesa, Sayed " Date: Sunday, November 7, 2010, 9:51 AM Dear Sayed My article=A0 Neese, F. Prediction of Molecular Spectra and Molecular Properties with Density Funct= ional Theory: from Fundamental Theory to Exchange Coupling Coord. Chem. Rev., 253,=A0526-563 (2009)=A0 Provides a discussion on broken symmetry and exchange coupling. The ORCA pr= ogram has built in recipes to calculate broken symmetry states.=A0 With my best regards, Frank NeeseVon meinem iPad gesendet Am 06.11.2010 um 17:49 schrieb "elsayed elmeselhy elsayed.elmes.|a|.yahoo.c= om" : Dear All Thanks for=A0 Adam Johannes for his useful reply. I have been optimized two= types of dinuclear cobalt complexes with different spin states (singlet, t= riplet, quintet and septet). For one complex, I find the septet state has t= he lowest energy. While for the other complex I found the singlet spin stat= e has the lowest energy. May questions are:=20 (i)=0A should I calculate the singlet broken asymmetry? (ii) What is the recipe to calculate=A0 broken asymmetry? Thanks in advance, Sayed --- On Thu, 11/4/10, Johannes Johansson johjo76*_*gmail.com wrote: > From: Johannes Johansson johjo76*_*gmail.com Subject: CCL:G: Antiferromagentism of dinulear transition metal complexes To: "Mesa, Sayed " Date: Thursday,=0A November 4, 2010, 3:18 PM Dear Sayed, please see the following discussion in the CCL archive:http://www.ccl.net/c= gi-bin/ccl/message-new?2009+07+10+011=0A For further reference:Adam Johannes Johansson, Holger Noack, Per E. M. Sieg= bahn, Genqiang Xue and Lawrence Que Jr.=0A=0ADalton Trans., 2009, 6741-6750 DOI:=A010.1039/B907263B =0ABest regards / Johannes =0A--=A0 =0AAdam Johannes Johansson Ph.D., M.Sc. Division of Physical Chemistry KTH (Royal Institute of Technology) Teknikringen 36 SE-100 44 Stockholm Sweden Office: 087908217 =0A =0A 2010/11/2 Sayed Mesa elsayed.elmes-,-yahoo.com =0A =0ASent to CCL by: "Sayed =A0Mesa" [elsayed.elmes##yahoo.com] =0A =0ADear All: =0A =0AI have measured the magnetism of some dinulear transition metal complexe= s, where transition metals are Co2+, Ni2+ & Cu2+. Some complexes shows stro= ng antiferromagentism and some others shows weak antiferromagentism while t= he remaining are ferromagentic. =0A=0A =0AI would like to optimize the geometries of these complexes with DFT (Gau= ssian), but I am confused how can I define the spin of the dinuclear comple= xs. By the way, the total number of eletrons of complexes is even in all ca= ses. =0A=0A =0AI know that diCobalet complex may have spin state of 1, 3, 5 or 7, while= diNikel complex have have spin states 1, 3 or 5. For dicopper, the spin st= ate may have 1 or 3. =0AMy question: Should I optimize the geometries of all probabilities of sp= in states and then choose the lowest energy among them. This scenario is va= lid? =0A =0AThanks in advance, =0ASayed =0A =0A =0A =0A-=3D This is automatically added to each message by the mailing script = =3D- =0A =0AE-mail to subscribers: CHEMISTRY[-]ccl.net or use: =0A =A0 =A0 =A0http://www.ccl.net/cgi-bin/ccl/send_ccl_message =0A =0AE-mail to administrators: CHEMISTRY-REQUEST[-]ccl.net or use =0A =A0 =A0 =A0http://www.ccl.net/cgi-bin/ccl/send_ccl_message =0A =0A=0A =A0 =A0 =A0http://www.ccl.net/chemistry/sub_unsub.shtml =0A =0A=0A =0A=0A=0A =0A=0A =0A =A0 =A0 =A0http://www.ccl.net/spammers.txt =0A =0A=0A =0A =0A =0A =0A=0A =0A=0A=0A --0-469450589-1289382066=:71656 Content-Type: text/html; charset=iso-8859-1 Content-Transfer-Encoding: quoted-printable
Dear All,

Thanks for Dr. Nesse for his= help and his excellent review which explain the concept. On the other hand= , for dinuclear cobalt complex, I have optimized the closed shell singlet s= tate and the open shell triplet, quintet and septet states, I found that th= e septet state has the lowest energy. To model the anti-ferromagnetic singl= et state, I have to start with the optimized geometry of septet state, righ= t?. Then divide the complex into three fragments (Co1, Co2 and the ligand).= The charge and multiplicities will be:
4 1, 2 3, 2 -3, 0 1 respectively= .  where

4 1 charge and multiplicity of  the whole comple= x
2 3 charge and multiplicity of  Co2+ with three alpha electron sp= in
=0A2 -3  charge and multiplicity of  Co2+ with three beta&n= bsp; electron spin
=0A1 0  charge and multiplicity of  the lig= and
=0A
Is this scenario is right or not?
Regards,

Sayed
--- On Sun, 11/7/10, Frank Neese neese%a%thch.uni-bonn.de <ow= ner-chemistry*|*ccl.net> wrote:

Fr= om: Frank Neese neese%a%thch.uni-bonn.de <owner-chemistry*|*ccl.net>Subject: CCL:G: Antiferromagentism of dinulear transition metal complexes<= br>To: "Mesa, Sayed " <elsayed.elmes*|*yahoo.com>
Date: Sund= ay, November 7, 2010, 9:51 AM

Dear Say= ed

My article 

<= tr valign=3D"TOP">
Neese, F.
Prediction of Molecular Spectra a= nd Molecular Properties with Density Functional Theory: from Fundamental Theory to Exch= ange Coupling
Coord. Chem. Rev., 253, 526-563 (2009)&nb= sp;

Provides a discussion on broken symmetry and exchange coupling. = The ORCA program has built in recipes to calculate broken symmetry states.&= nbsp;

With my best regards,
Frank Neese
= Von meinem iPad gesendet

Am 06.11.2010 um 17:49 schrie= b "elsayed elmeselhy elsayed.elmes.|a|.yahoo.com" <owner-chemistry|a|ccl.net>= ;:

Dear All

Thanks for  Adam Johannes for his useful reply. I have bee= n optimized two types of dinuclear cobalt complexes with different spin sta= tes (singlet, triplet, quintet and septet). For one complex, I find the sep= tet state has the lowest energy. While for the other complex I found the si= nglet spin state has the lowest energy. May questions are:

(i)=0A s= hould I calculate the singlet broken asymmetry?
(ii) What is the recipe = to calculate  broken asymmetry?
Thanks in advance,
Sayed

--- On Thu, 11/4/10, Johannes Johans= son johjo76*_*gmail.com <owner-chemistry:+:ccl.net> wrote:

From: Johannes Johansson johjo76*_*gmail.com <ow= ner-chemistry:+:ccl.net>
Subject: CCL:G: Antiferromagent= ism of dinulear transition metal complexes
To: "Mesa, Sayed " <elsaye= d.elmes:+:y= ahoo.com>
Date: Thursday,=0A November 4, 2010, 3:18 PM

Dear Sayed,

please see= the following discussion in the CCL archive:
=0A

For further reference:
Adam Johannes Joh= ansson, Holger Noack, Per E. M. Siegbahn, Genqiang Xue and Lawrence Que Jr.=
=0A
=0ADalton Trans., 2009, 6741-6750

DOI: 10.1039/B907263B
=0ABest regards / Johannes
=0A-- 
=0AAdam Johannes Johan= sson
Ph.D., M.Sc.
Division of Physical Chemistry
KTH (Royal Instit= ute of Technology)
Teknikringen 36
SE-100 44 Stockholm
Sweden
O= ffice: 087908217
=
=0A

=0A

2010/11/2 Sayed Mesa elsayed.elmes-,-yahoo.com <owner-chemistry[-]ccl.net>
=0A

= =0ASent to CCL by: "Sayed  Mesa" [elsayed.elmes##yahoo.com]
=0A
=0ADear All:=
=0A
=0AI have measured the magnetism of some dinulear transition met= al complexes, where transition metals are Co2+, Ni2+ & Cu2+. Some compl= exes shows strong antiferromagentism and some others shows weak antiferroma= gentism while the remaining are ferromagentic.
=0A=0A
=0AI would like= to optimize the geometries of these complexes with DFT (Gaussian), but I a= m confused how can I define the spin of the dinuclear complexs. By the way,= the total number of eletrons of complexes is even in all cases.
=0A=0A<= br>=0AI know that diCobalet complex may have spin state of 1, 3, 5 or 7, wh= ile diNikel complex have have spin states 1, 3 or 5. For dicopper, the spin= state may have 1 or 3.
=0AMy question: Should I optimize the geometries= of all probabilities of spin states and then choose the lowest energy amon= g them. This scenario is valid?
=0A
=0AThanks in advance,
=0ASayed=
=0A
=0A
=0A
=0A-=3D This is automatically added to each messag= e by the mailing script =3D-
=0A
=0AE-mail to subscribers: CHEMISTRY[-]ccl.net or use:
=0A      http://www.ccl.net/cgi-bin/ccl/send_c= cl_message
=0A
=0AE-mail to administrators: C= HEMISTRY-REQUEST[-]ccl.net or use
=0A      http://www.ccl.net/cgi-bin/ccl/send_ccl_m= essage
=0A
=0ASubscribe/Unsubscribe:
=0A      <= a rel=3D"nofollow" target=3D"_blank" href=3D"http://www.ccl.net/chemistry/s= ub_unsub.shtml">http://www.ccl.net/chemistry/sub_unsub= .shtml
=0A
=0ABefore posting, check wait time at: http://www.ccl.net
=0A=
=0AJob: http://www.ccl.net/jobs
=0AConferences: http://server.ccl.net/chemist= ry/announcements/conferences/
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=0ASearch Messages: http://www.ccl.net/chemistry/searchc= cl/index.shtml
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=0A
=0ARTFI: http://www.ccl.net/chemistry/aboutccl/instructions/
=0A
=0A
=0A




=0A=

=0A=0A

=0A=0A --0-469450589-1289382066=:71656-- From owner-chemistry@ccl.net Wed Nov 10 07:38:01 2010 From: "Frank Neese neese_-_thch.uni-bonn.de" To: CCL Subject: CCL: Antiferromagentism of dinulear transition metal complexes Message-Id: <-43122-101110073631-18952-udWxfgeDGRMi+fPSFdCxUA|server.ccl.net> X-Original-From: Frank Neese Content-Transfer-Encoding: 8bit Content-Type: text/plain; charset=us-ascii Date: Wed, 10 Nov 2010 13:36:23 +0100 Mime-Version: 1.0 (Apple Message framework v1081) Sent to CCL by: Frank Neese [neese!=!thch.uni-bonn.de] Dear Sayed, > I have to start with the optimized geometry of septet state, right?. > yes > > Then divide the complex into three fragments (Co1, Co2 and the ligand). The charge and multiplicities will be: > 4 1, 2 3, 2 -3, 0 1 respectively. where > > 4 1 charge and multiplicity of the whole complex > 2 3 charge and multiplicity of Co2+ with three alpha electron spin > 2 -3 charge and multiplicity of Co2+ with three beta electron spin > 1 0 charge and multiplicity of the ligand > > Is this scenario is right or not? > No, it is not correct. You simply state %scf brokensym 3,3 end and the program will (hopefully) find the correct broken symmetry state. Good luck! Best regards, FN From owner-chemistry@ccl.net Wed Nov 10 09:47:01 2010 From: "Maciej Maslyk maciejmarcin.maslyk:ceu.es" To: CCL Subject: CCL:G: Gaussian03 error: GetSCM: Allocation for FCRed failed: Message-Id: <-43123-101110084939-30609-cMw7IeFldX/VvJnlzQbL5w]![server.ccl.net> X-Original-From: "Maciej Maslyk" Date: Wed, 10 Nov 2010 08:49:38 -0500 Sent to CCL by: "Maciej Maslyk" [maciejmarcin.maslyk+/-ceu.es] Hi, I got this error doing QST3 with G03. Even if I put MaxDisc=10GB or 100GB and %RWF=loc1,size1,loc2,size2, the problem still appears. Help, please! GetSCM: Allocation for FCRed failed: Core=-2041361480 Need=241511221 GauSpace=2012942344 MaxMem=268435456 Avail=238352522. Error termination via Lnk1e in /usr/local/g03/l716.exe at Tue Nov 2 17:16:45 2010. Job cpu time: 0 days 5 hours 47 minutes 27.7 seconds. File lengths (MBytes): RWF= 1793 Int= 0 D2E= 0 Chk= 154 Scr= 1 From owner-chemistry@ccl.net Wed Nov 10 10:22:01 2010 From: "Italo Anjos italocurvelo!^!gmail.com" To: CCL Subject: CCL: Imaginary frequencies Message-Id: <-43124-101110094223-15841-sNJ1RYg7iYXabE68OhbORg : server.ccl.net> X-Original-From: Italo Anjos Content-Type: multipart/alternative; boundary=0016e6d5fc5f02d3820494b3dd5b Date: Wed, 10 Nov 2010 11:42:14 -0300 MIME-Version: 1.0 Sent to CCL by: Italo Anjos [italocurvelo%%gmail.com] --0016e6d5fc5f02d3820494b3dd5b Content-Type: text/plain; charset=ISO-8859-1 Hi all, I'm facing some troubles with imaginary frequencies. But I noticed those frequencies seem to be related to free rotation of methyl groups. I tried using a low-level theory and basis and then using a higher-level one but for some molecules the imaginary frequencies still persist. How can I get rid of these '*rotational*' imaginary frequencies? Do they really mean the molecule is not in a minimum or can only the *vibrational* frequencies confirm that? I appreciate any help. With regards, Italo --0016e6d5fc5f02d3820494b3dd5b Content-Type: text/html; charset=ISO-8859-1 Hi all,

I'm facing some troubles with imaginary frequencies. But I noticed those frequencies seem to be related to free rotation of methyl groups. I tried using a low-level theory and basis and then using a higher-level one but for some molecules the imaginary frequencies still persist. How can I get rid of these 'rotational' imaginary frequencies? Do they really mean the molecule is not in a minimum or can only the vibrational frequencies confirm that?

I appreciate any help.

With regards,

Italo
--0016e6d5fc5f02d3820494b3dd5b-- From owner-chemistry@ccl.net Wed Nov 10 10:56:00 2010 From: "baljinder grewal baljinder7_._gmail.com" To: CCL Subject: CCL:G: NBO analysis Message-Id: <-43125-101110095538-24430-/rJwuiT2qHQsfhrt6tZFCQ-*-server.ccl.net> X-Original-From: "baljinder grewal" Date: Wed, 10 Nov 2010 09:55:37 -0500 Sent to CCL by: "baljinder grewal" [baljinder7/a\gmail.com] Dear all, I am new user of gaussian software.To study the electron density distribution of series of compounds, i had done NBO analysis using opt=nbo as keyword in g03.Job had run sucessfuly to completion, generating very long log file but i dont know where to look for NBO output.Kindly suggest me how to interprete the NBO analysis. Thanks in advance From owner-chemistry@ccl.net Wed Nov 10 11:33:00 2010 From: "elsayed elmeselhy elsayed.elmes---yahoo.com" To: CCL Subject: CCL:G: Antiferromagentism of dinulear transition metal complexes Message-Id: <-43126-101110113132-7768-/8cA/TxNXNVgWE7irnnJsg ~~ server.ccl.net> X-Original-From: elsayed elmeselhy Content-Type: multipart/alternative; boundary="0-725497414-1289406685=:48686" Date: Wed, 10 Nov 2010 08:31:25 -0800 (PST) MIME-Version: 1.0 Sent to CCL by: elsayed elmeselhy [elsayed.elmes ~~ yahoo.com] --0-725497414-1289406685=:48686 Content-Type: text/plain; charset=iso-8859-1 Content-Transfer-Encoding: quoted-printable Dear Dr. Neese and all Thanks for your reply. I am Gaussian user, so could I calculate the broken = symmetry state using Gaussian 09. If yes please give a hint about the recip= e. On the other hand, the experiment told us that the complex is antiferromage= ntic. So do I need to determine which the broken symmetry state for this mo= lecule or work directly as antiferromagentic state?=20 Thanks in advance Sayed --- On Wed, 11/10/10, Frank Neese neese_-_thch.uni-bonn.de wrote: > From: Frank Neese neese_-_thch.uni-bonn.de Subject: CCL: Antiferromagentism of dinulear transition metal complexes To: "Mesa, Sayed " Date: Wednesday, November 10, 2010, 2:36 PM Sent to CCL by: Frank Neese [neese!=3D!thch.uni-bonn.de] Dear Sayed, > I have to start with the optimized geometry of septet state, right?.=20 > yes >=20 > Then divide the complex into three fragments (Co1, Co2 and the ligand). T= he charge and multiplicities will be: > 4 1, 2 3, 2 -3, 0 1 respectively.=A0 where=20 >=20 > 4 1 charge and multiplicity of=A0 the whole complex > 2 3 charge and multiplicity of=A0 Co2+ with three alpha electron spin > 2 -3=A0 charge and multiplicity of=A0 Co2+ with three beta=A0 electron sp= in > 1 0=A0 charge and multiplicity of=A0 the ligand >=20 > Is this scenario is right or not? >=20 No, it is not correct. You simply state %scf brokensym 3,3 end and the program will (hopefully) find the correct broken symmetry state. Go= od luck!=20 Best regards, FN -=3D This is automatically added to each message by the mailing script =3D-=A0 =A0 =A0=A0 =A0 =A0Subscribe/Unsubscribe:=20 =A0 =A0 =A0Job: http://www.ccl.net/jobs=20=A0 =A0 =A0=0A=0A=0A --0-725497414-1289406685=:48686 Content-Type: text/html; charset=iso-8859-1 Content-Transfer-Encoding: quoted-printable
Dear Dr. Neese and all

Thanks for your= reply. I am Gaussian user, so could I calculate the broken symmetry state = using Gaussian 09. If yes please give a hint about the recipe.

On th= e other hand, the experiment told us that the complex is antiferromagentic.= So do I need to determine which the broken symmetry state for this molecul= e or work directly as antiferromagentic state?

Thanks in advanceSayed

--- On Wed, 11/10/10, Frank Neese neese_-_thch.uni-bonn.de= <owner-chemistry * ccl.net> wrote:

From: Frank Neese neese_-_thch.uni-bonn.de <owner-chemistry * ccl.= net>
Subject: CCL: Antiferromagentism of dinulear transition metal co= mplexes
To: "Mesa, Sayed " <elsayed.elmes * yahoo.com>
Da= te: Wednesday, November 10, 2010, 2:36 PM


= Sent to CCL by: Frank Neese [neese!=3D!thch.uni-bonn.de]
Dear Sayed,
=
> I have to start with the optimized geometry of septet state, right= ?.
> yes
>
> Then divide the complex into three fragmen= ts (Co1, Co2 and the ligand). The charge and multiplicities will be:
>= ; 4 1, 2 3, 2 -3, 0 1 respectively.  where
>
> 4 1 charg= e and multiplicity of  the whole complex
> 2 3 charge and multip= licity of  Co2+ with three alpha electron spin
> 2 -3  char= ge and multiplicity of  Co2+ with three beta  electron spin
&g= t; 1 0  charge and multiplicity of  the ligand
>
> I= s this scenario is right or not?
>

No, it is not correct. You= simply state

%scf brokensym 3,3 end

and the program will (ho= pefully) find the correct broken symmetry state. Good luck!
Best regards,
FN



-=3D This is automatically added to each mes= sage by the mailing script =3D-
To recover the email address of the auth= or of the message, please change
the strange characters on the top line = to the * sign. You can also
look up the X-Original-From: line in the mai= l header.

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

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RTFI: http://www.ccl.net/chemistry/aboutccl/instructions/<= br>


=0A=0A --0-725497414-1289406685=:48686-- From owner-chemistry@ccl.net Wed Nov 10 12:08:00 2010 From: "=?ISO-8859-1?Q?Ulf_Ekstr=F6m?= ulfek~!~few.vu.nl" To: CCL Subject: CCL: Imaginary frequencies Message-Id: <-43127-101110113135-7841-mRUrwddZPKD1zs/G7shebA]![server.ccl.net> X-Original-From: =?ISO-8859-1?Q?Ulf_Ekstr=F6m?= Content-Type: text/plain; charset=ISO-8859-1 Date: Wed, 10 Nov 2010 17:31:28 +0100 MIME-Version: 1.0 Sent to CCL by: =?ISO-8859-1?Q?Ulf_Ekstr=F6m?= [ulfek:few.vu.nl] If you have any groups that are free to rotate you will get frequencies that are very small, or imaginary. You should only worry if these frequencies have large magnitude. Using analytical calculation of the frequencies can also help you to get a clearer picture if you are not doing that already. If you want more detailed help please upload your output file somewhere and send us a link to it. Sincerely, Ulf Ekstrom From owner-chemistry@ccl.net Wed Nov 10 14:12:00 2010 From: "Michael Dimitrov mich.dimitrov^^gmail.com" To: CCL Subject: CCL: Separation of steric and electronic effects Message-Id: <-43128-101110140832-4997-k8H7I556PnWddTvRqKS7pQ]*[server.ccl.net> X-Original-From: Michael Dimitrov Content-Type: text/plain; charset=ISO-8859-1 Date: Wed, 10 Nov 2010 22:08:22 +0300 MIME-Version: 1.0 Sent to CCL by: Michael Dimitrov [mich.dimitrov,+,gmail.com] Hi, I am interested in the procedure of computational separation of steric and electronic effects as described in Scheme 3 of the article Eur. J. Inorg. Chem. 2007, 5390 ( http://dx.doi.org/10.1002/ejic.200700850 ) I doubt if B3LYP level is good enough to take into account steric and electronic factors? Perhaps it would be better to use MP2, CCSD or another density functional for accurate description of both steric and electronic factors? Best regards, Michael Dimitrov. From owner-chemistry@ccl.net Wed Nov 10 14:47:00 2010 From: "Jon Heinz goeeoe*|*hotmail.com" To: CCL Subject: CCL: Randomization Message-Id: <-43129-101110114803-24797-0VWsJTv4lzsK8bcFsMsvJA[a]server.ccl.net> X-Original-From: "Jon Heinz" Date: Wed, 10 Nov 2010 11:48:01 -0500 Sent to CCL by: "Jon Heinz" [goeeoe!A!hotmail.com] Hello, I am trying to validate my QSAR models and I have read about Y- randomisation method. I do not understand what this technique means OR why it is important to carry it out. Are there any other suitable validation studies I can perform on my models, apart from cross validation? thank you Jon Heinz goeeoe*hotmail.com Portsmouth UK From owner-chemistry@ccl.net Wed Nov 10 15:22:00 2010 From: "Yi (Yves) Wang yves.wang%duke.edu" To: CCL Subject: CCL:G: NBO analysis Message-Id: <-43130-101110115025-27480-kzgbH9MUCpv1LUJ44RrEUg|*|server.ccl.net> X-Original-From: "Yi (Yves) Wang" Content-Type: multipart/alternative; boundary=Apple-Mail-2--284510954 Date: Wed, 10 Nov 2010 11:50:17 -0500 Mime-Version: 1.0 (Apple Message framework v1081) Sent to CCL by: "Yi (Yves) Wang" [yves.wang .. duke.edu] --Apple-Mail-2--284510954 Content-Transfer-Encoding: quoted-printable Content-Type: text/plain; charset=GB2312 http://www.gaussian.com/g_tech/g_ur/k_population.htm http://www.chem.wisc.edu/~nbo5/ Usually you should you pop=3DNBO, not opt. = __________________________________________________________________________= ___ Yi (Yves) Wang Department of Biochemistry Structural Biology & Biophysics Program Duke University BS: University of Science and Technology of China School of Life Sciences, National Laboratory for Physical Sciences at = Microscale Tel: +1-919-236-3307 (Cell) +1-919-684-0235 (Lab 1) +1-919-660-1634 (Lab 2) Office: A20 LSRC / 5301 FFSC E-Mail: yves.wang,duke.edu Mail: Box 90317, Chemistry Department =D4=DA 2010-11-10=A3=AC=C9=CF=CE=E79:55=A3=AC baljinder grewal = baljinder7_._gmail.com =D0=B4=B5=C0=A3=BA >=20 > Sent to CCL by: "baljinder grewal" [baljinder7/a\gmail.com] > Dear all, > I am new user of gaussian software.To study the electron density = distribution of series of compounds, i had done NBO analysis using = opt=3Dnbo as keyword in g03.Job had run sucessfuly to completion, = generating very long log file but i dont know where to look for NBO = output.Kindly suggest me how to interprete the NBO analysis. >=20 > Thanks in advance >=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-2--284510954 Content-Transfer-Encoding: quoted-printable Content-Type: text/html; charset=GB2312 http://www.g= aussian.com/g_tech/g_ur/k_population.htm
http://www.chem.wisc.edu/= ~nbo5/

Usually you should you pop=3DNBO, not = opt.


Yi (Yves) Wang
Department of Biochemistry
Structural Biology & Biophysics = Program
Duke = University
BS: University = of Science and Technology of China
   +1-919-660-1634 (Lab 2)
Office: A20 LSRC / 5301 = FFSC
Mail: Box 90317, Chemistry = Department


=D4=DA 2010-11-10=A3=AC=C9=CF=CE=E79:55=A3=AC baljinder = grewal baljinder7_._gmail.com =D0=B4=B5=C0=A3=BA


Sent to CCL by: "baljinder  grewal" = [baljinder7/a\gmail.com]
Dear all,
I am new user of gaussian = software.To study the electron density distribution of series of = compounds, i had done NBO analysis using opt=3Dnbo as keyword in g03.Job = had run sucessfuly to completion, generating very long log file but i = dont know where to look for NBO output.Kindly suggest me how to = interprete the NBO analysis.

Thanks in advance



-=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
the strange characters on the top line to the , sign. = You can also
look up the X-Original-From: line in the mail = header.
=      http://www.ccl.net/cgi-bin/ccl/send_ccl_mess= age

E-mail to administrators: CHEMISTRY-REQUEST,ccl.net or = use
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Before posting, check wait time at: = http://www.ccl.net
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= --Apple-Mail-2--284510954-- From owner-chemistry@ccl.net Wed Nov 10 16:37:00 2010 From: "Sebastian Kozuch kozuchs,,yahoo.com" To: CCL Subject: CCL: Separation of steric and electronic effects Message-Id: <-43131-101110162817-13291-g+3iEiTj97mLdIi6YyzI3Q^server.ccl.net> X-Original-From: Sebastian Kozuch Content-Type: multipart/alternative; boundary="0-1455235642-1289424485=:365" Date: Wed, 10 Nov 2010 13:28:05 -0800 (PST) MIME-Version: 1.0 Sent to CCL by: Sebastian Kozuch [kozuchs]=[yahoo.com] --0-1455235642-1289424485=:365 Content-Type: text/plain; charset=us-ascii B3LYP models electronic and repulsivesteric effects quite well (although I would go for some other functional when having transition metals). But as most of the DFT methods, it does not work well with dispersive forces. If you add a dispersion correction add on (for instance check: http://jcp.aip.org/resource/1/jcpsa6/v132/i15/p154104_s1 ) the results will be much better (look at http://pubs.rsc.org/en/Content/ArticleLanding/2010/DT/C0DT00778A ). But, if you work with a QM/MM type of method, do not add dispersion forces. You should choose an outer layer that can manage dispersion forces by itself, (like an MM method). MP2 may be OK, but not advisable with transition metals. You can forget CCSD, unless you have a quantum computer. Now, one of the biggest problem with the separation of steric and electronic effects is that you will loose accuracy everywhere, and you will have to work with qualitative values. One of the problems will be the solvation model, that does not work with ONIOM (unless there is some update I am not aware off). And you will have lots of artifacts from the separation scheme. You may want to have a look at J. Mol. Cat. A 2010 , 324 , 120-126. In there we tried to tackle some of those problems. Best, xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx ..........Sebastian Kozuch........... xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx ....Weizmann Institute of Science.... ...........Rehovot, Israel........... .. sebastian.kozuch#,#weizmann.ac.il .. http://yfaat.ch.huji.ac.il/kozuch.htm xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx ________________________________ > From: Michael Dimitrov mich.dimitrov^^gmail.com To: "Kozuch, Sebastian " Sent: Wed, November 10, 2010 9:08:22 PM Subject: CCL: Separation of steric and electronic effects Sent to CCL by: Michael Dimitrov [mich.dimitrov,+,gmail.com] Hi, I am interested in the procedure of computational separation of steric and electronic effects as described in Scheme 3 of the article Eur. J. Inorg. Chem. 2007, 5390 ( http://dx.doi.org/10.1002/ejic.200700850 ) I doubt if B3LYP level is good enough to take into account steric and electronic factors? Perhaps it would be better to use MP2, CCSD or another density functional for accurate description of both steric and electronic factors? Best regards, Michael Dimitrov.http://www.ccl.net/cgi-bin/ccl/send_ccl_messagehttp://www.ccl.net/chemistry/sub_unsub.shtmlhttp://www.ccl.net/spammers.txt--0-1455235642-1289424485=:365 Content-Type: text/html; charset=us-ascii
B3LYP models electronic and repulsive steric effects quite well (although I would go for some other functional when having transition metals). But as most of the DFT methods, it does not work well with dispersive forces. If you add a dispersion correction add on (for instance check: http://jcp.aip.org/resource/1/jcpsa6/v132/i15/p154104_s1 ) the results will be much better (look at http://pubs.rsc.org/en/Content/ArticleLanding/2010/DT/C0DT00778A ). But, if you work with a QM/MM type of method, do not add dispersion forces. You should choose an outer layer that can manage dispersion forces by itself, (like an MM method).
MP2 may be OK, but not advisable with transition metals. You can forget CCSD, unless you have a quantum computer.
Now, one of the biggest problem with the separation of steric and electronic effects is that you will loose accuracy everywhere, and you will have to work with qualitative values. One of the problems will be the solvation model, that does not work with ONIOM (unless there is some update I am not aware off). And you will have lots of artifacts from the separation scheme.
You may want to have a look at J. Mol. Cat. A 2010 , 324 , 120-126. In there we tried to tackle some of those problems.

Best,
 
xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx
..........Sebastian Kozuch...........
xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx
....Weizmann Institute of Science....
...........Rehovot, Israel...........
.. sebastian.kozuch#,#weizmann.ac.il ..
http://yfaat.ch.huji.ac.il/kozuch.htm
xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx


From: Michael Dimitrov mich.dimitrov^^gmail.com <owner-chemistry#,#ccl.net>
To: "Kozuch, Sebastian " <kozuchs#,#yahoo.com>
Sent: Wed, November 10, 2010 9:08:22 PM
Subject: CCL: Separation of steric and electronic effects


Sent to CCL by: Michael Dimitrov [mich.dimitrov,+,gmail.com]
Hi,

I am interested in the procedure of computational separation of steric
and electronic effects as described in Scheme 3 of the article Eur. J.
Inorg. Chem. 2007, 5390 ( http://dx.doi.org/10.1002/ejic.200700850 )

I doubt if  B3LYP level is good enough to take into account steric and
electronic factors? Perhaps it would be better to use MP2, CCSD or
another density functional for accurate description of both steric and
electronic factors?

Best regards,
Michael Dimitrov.



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--0-1455235642-1289424485=:365-- From owner-chemistry@ccl.net Wed Nov 10 17:11:00 2010 From: "Hamdy El Sheshtawy h.elsheshtawy a jacobs-university.de" To: CCL Subject: CCL: Thermochemistry calculations Message-Id: <-43132-101110164650-17605-vVbHBel6tzNtxpHD/CYtqA() server.ccl.net> X-Original-From: Hamdy El Sheshtawy Content-Transfer-Encoding: 7bit Content-Type: text/plain; charset="US-ASCII"; format=flowed; delsp=yes Date: Wed, 10 Nov 2010 22:46:35 +0100 MIME-Version: 1.0 (Apple Message framework v936) Sent to CCL by: Hamdy El Sheshtawy [h.elsheshtawy]![jacobs-university.de] Dear all, I am doing solvent effect calculations with B3LYP/6-311G** on radicals and I want to know how to extract the Delta G and DH and DS solvations > from the frequency output. For eample in the output file I have these informations: Zero-point correction= 0.288623 (Hartree/ Particle) Thermal correction to Energy= 0.303786 Thermal correction to Enthalpy= 0.304731 Thermal correction to Gibbs Free Energy= 0.243475 Sum of electronic and zero-point Energies= -657.083380 Sum of electronic and thermal Energies= -657.068216 Sum of electronic and thermal Enthalpies= -657.067272 Sum of electronic and thermal Free Energies= -657.128527 E (Thermal) CV S KCal/Mol Cal/Mol-Kelvin Cal/Mol-Kelvin Total 190.629 57.627 128.923 Electronic 0.000 0.000 1.377 Translational 0.889 2.981 41.889 Rotational 0.889 2.981 32.465 Vibrational 188.851 51.665 53.191 best Hamdy From owner-chemistry@ccl.net Wed Nov 10 18:23:01 2010 From: "David Jay Anick david.anick^^^rcn.com" To: CCL Subject: CCL: (Para)Magnetic susceptibility Message-Id: <-43133-101110181657-5402-my73Je21t6eP4e5xM0fHQA+*+server.ccl.net> X-Original-From: "David Jay Anick" Date: Wed, 10 Nov 2010 18:16:56 -0500 Sent to CCL by: "David Jay Anick" [david.anick-x-rcn.com] Dear CCL, I am studying small molecule and clusters whose ground state is triplet (two unpaired electrons) and are therefore presumably paramagnetic. How can the (para)magnetic susceptibility of triplet molecules or clusters be predicted with ab initio methods? If the parameters needed for the computation are uncommon ones, what program(s) can you recommend to calculate them? Thank you to all responders! David Anick From owner-chemistry@ccl.net Wed Nov 10 20:41:01 2010 From: "xunlei ding dingxunlei.(~).gmail.com" To: CCL Subject: CCL: Imaginary frequencies Message-Id: <-43134-101110203848-17844-2MTQrrCjPpMNMDctfVFAzQ(~)server.ccl.net> X-Original-From: xunlei ding Content-Transfer-Encoding: 8bit Content-Type: text/plain; charset=ISO-8859-1 Date: Thu, 11 Nov 2010 09:38:40 +0800 MIME-Version: 1.0 Sent to CCL by: xunlei ding [dingxunlei|gmail.com] Sometims "int(ultrafine)" may solve this problem. Good luck! ding 2010/11/11 Ulf Ekström ulfek~!~few.vu.nl : > > Sent to CCL by: =?ISO-8859-1?Q?Ulf_Ekstr=F6m?= [ulfek:few.vu.nl] > If you have any groups that are free to rotate you will get frequencies that > are very small, or imaginary. You should only worry if these frequencies have > large magnitude. Using analytical calculation of the frequencies can also help > you to get a clearer picture if you are not doing that already. > > If you want more detailed help please upload your output file somewhere > and send us a link to it. > > Sincerely, > Ulf Ekstrom>      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> > > From owner-chemistry@ccl.net Wed Nov 10 21:51:00 2010 From: "baljinder baljinder7^-^gmail.com" To: CCL Subject: CCL:G: NBO analysis Message-Id: <-43135-101110213245-5534-+oDO7YHSS+xBWwf2EYRiIg*server.ccl.net> X-Original-From: baljinder Content-Type: multipart/alternative; boundary=0016e65ae1f69e5eb40494bdc99f Date: Thu, 11 Nov 2010 08:02:39 +0530 MIME-Version: 1.0 Sent to CCL by: baljinder [baljinder7]![gmail.com] --0016e65ae1f69e5eb40494bdc99f Content-Type: text/plain; charset=GB2312 Content-Transfer-Encoding: quoted-printable Thank You Yi (Yves) Wang for correction and sending informative links 2010/11/10 Yi (Yves) Wang yves.wang%duke.edu > http://www.gaussian.com/g_tech/g_ur/k_population.htm > http://www.chem.wisc.edu/~nbo5/ > > Usually you should you pop=3DNBO, not opt. > > > _________________________________________________________________________= ____ > > Yi (Yves) Wang > Department of Biochemistry > Structural Biology & Biophysics Program > Duke University > BS: University of Science and Technology of China > School of Life Sciences, National Laboratory for Physical Sciences at > Microscale > Tel: +1-919-236-3307 (Cell) > +1-919-684-0235 (Lab 1) > +1-919-660-1634 (Lab 2) > Office: A20 LSRC / 5301 FFSC > E-Mail: yves.wang. .. .duke.edu > Mail: Box 90317, Chemistry Department > > > =D4=DA 2010-11-10=A3=AC=C9=CF=CE=E79:55=A3=AC baljinder grewal baljinder7= _._gmail.com =D0=B4=B5=C0=A3=BA > > > Sent to CCL by: "baljinder grewal" [baljinder7/a\gmail.com] > Dear all, > I am new user of gaussian software.To study the electron density > distribution of series of compounds, i had done NBO analysis using opt=3D= nbo > as keyword in g03.Job had run sucessfuly to completion, generating very l= ong > log file but i dont know where to look for NBO output.Kindly suggest me h= ow > to interprete the NBO analysis. > > Thanks in advance > > > > -=3D This is automatically added to each message by the mailing script = =3D-> the strange characters on the top line to the . .. . sign. You can also> > E-mail to administrators: CHEMISTRY-REQUEST. .. .ccl.net or use> > > > --0016e65ae1f69e5eb40494bdc99f Content-Type: text/html; charset=GB2312 Content-Transfer-Encoding: quoted-printable
Thank You Yi (Yves) Wang for correction and sending inform= ative links

2010/11/10 Yi (Yves) Wang yve= s.wang%duke.edu <owner-chemistry .. ccl.net>
http://www.gaussian.com/g_tech/g_ur/k_populati= on.htm

Usually you should you po= p=3DNBO, not opt.
=

___________________________________________________________________________= __

Yi (Yves) Wang
Department of Biochemistry
Structural Biology & Biophysics Program
Duke University
BS: University of Science and Technology of China
School of Life Sciences, National Laborato= ry for Physical Sciences at Microscale
Tel: +1-919-236-3307 (Cell)
   +1-919-684-0235 (Lab 1)
   +1-919-660-1634 (Lab = 2)
Office: A20 LSRC / 5301 FFSC
Mail: Box 90317, Chemistry Department


=D4=DA 2010-11-10=A3=AC=C9=CF=CE=E79:55=A3=AC baljinder grewa= l baljinder7_._gmail.com= =D0=B4=B5=C0=A3=BA


Sent to CCL by: "baljinder  grewal" [baljinder7/a\gmail.com]
Dear all,
I am new user of gaussian software.To study the electron densi= ty distribution of series of compounds, i had done NBO analysis using opt= =3Dnbo as keyword in g03.Job had run sucessfuly to completion, generating v= ery long log file but i dont know where to look for NBO output.Kindly sugge= st me how to interprete the NBO analysis.

Thanks in advance



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