From owner-chemistry@ccl.net Fri Apr 16 08:42:00 2010 From: "Mark Mackey mark]-[cresset-bmd.com" To: CCL Subject: CCL: Smiles convention for stereoisomers ? Message-Id: <-41669-100416044811-26391-Su6PSnpgL+44fomx1Q5LfQ]_[server.ccl.net> X-Original-From: Mark Mackey Content-Transfer-Encoding: 7bit Content-Type: text/plain; charset=ISO-8859-1; format=flowed Date: Fri, 16 Apr 2010 09:08:04 +0100 MIME-Version: 1.0 Sent to CCL by: Mark Mackey [mark-*-cresset-bmd.com] Hi Michel, Having just rewritten a SMILES parser Ive just fought my way through this, and can empathise with your confusion. The (in my mind) "obvious" way to do it isn't how Daylight actually specify it should be done. What the Daylight spec means is that the ordering of the atoms uses the position of the *ring closure digit*, not the atom itself. So, in the example from the Daylight web site: C[C-at-H]1CCCCO1 the order of the atoms is carbon, then the hydrogen, then the oxygen (because the '1' is next), then the other carbon. The position of the actual oxygen atom in the SMILES string is not relevant: it's the position of the '1' that counts. A number of parsers get this wrong, and it's not specified in the OpenSMILES spec (http://www.opensmiles.org/spec/open-smiles-3-input.html#3.9) what should happen here, but that's what Daylight do. In my experience this rule makes it rather more complicated than it ought to be to write a Daylight-compliant SMILES parser, but I suppose we're stuck with it. The CCL email-munging mechanism makes it very hard to sensibly discuss chiral SMILES. Jan, is there any chance it could be restricted to things matching an email address regexp, rather than all 'at' characters? Mark. -- Dr Mark Mackey Cresset Biomolecular Discovery Michel Petitjean petitjean.chiral%%gmail.com wrote: > Sent to CCL by: Michel Petitjean [petitjean.chiral_+_gmail.com] > Hi there, > > Does anybody know about the exact convention to specify atoms > positions from a SMILES having stereocenters in rings ? > It seems there is a difference in treatment for ring closure and other atoms ? > For instance for C[C]*[]*[H]1C[C]*[]*[H](O)CC(=O)O1 > For the second center, not a ring closure, we look from the CC bond, > and we have H,O,C clockwise. > For the first one how does one proceed ? > If one looks from first C to second C, then H, C, O should be > positioned clockwise, whereas actually it seems it is > countercloskwise. > > Idem from the example on their site : > http://www.daylight.com/dayhtml/doc/theory/theory.smiles.html > > C[C]*[H]1CCCCO1 > I could not understand the few sentences on SMILES theory related to > ring closure digit appearance. > > Thanks by advance > > Michel Petitjean.> > > -- Dr Mark Mackey Director, Development Cresset BioMolecular Discovery Ltd From owner-chemistry@ccl.net Fri Apr 16 09:21:00 2010 From: "Yang qiwu angiusf-x-gmail.com" To: CCL Subject: CCL:G: How to get the Q band in UV-Vis of tetraphenylporphyrin by gaussian Message-Id: <-41670-100415215446-5226-QFVkWDEHn2hdPvFzobcALA||server.ccl.net> X-Original-From: "Yang qiwu" Date: Thu, 15 Apr 2010 21:54:45 -0400 Sent to CCL by: "Yang qiwu" [angiusf|gmail.com] I calculated excited state of tetraphenylporphyrin in gaussian 09, the result is that the oscillator strengths of the first four state are zero. The four is in Q band range, so how can i obtain the Q band? input: # TD=NStates=6 upbe1pbe/6-31G* output: Excited State 1: 3.000-A 1.2665 eV 978.99 nm f=0.0000 =2.000 160A ->163A 0.31957 161A ->162A 0.64357 160B ->163B -0.31957 161B ->162B -0.64357 160A <-163A 0.11838 161A <-162A 0.17246 160B <-163B -0.11838 161B <-162B -0.17246 This state for optimization and/or second-order correction. Copying the excited state density for this state as the 1-particle RhoCI density. Excited State 2: 3.000-A 1.6843 eV 736.12 nm f=0.0000 =2.000 160A ->162A -0.19159 161A ->163A 0.67679 160B ->162B 0.19159 161B ->163B -0.67679 Excited State 3: 3.000-A 1.9938 eV 621.85 nm f=0.0000 =2.000 160A ->162A 0.10940 160A ->163A 0.62409 161A ->162A -0.30879 160B ->162B -0.10940 160B ->163B -0.62409 161B ->162B 0.30879 Excited State 4: 3.000-A 2.0085 eV 617.31 nm f=0.0000 =2.000 160A ->162A 0.66795 160A ->163A -0.10947 161A ->163A 0.19131 160B ->162B -0.66795 160B ->163B 0.10947 161B ->163B -0.19131 Excited State 5: 1.000-A 2.2015 eV 563.18 nm f=0.0157 =0.000 160A ->162A -0.42477 161A ->163A 0.56009 160B ->162B -0.42477 161B ->163B 0.56009 Excited State 6: 1.000-A 2.3499 eV 527.62 nm f=0.0373 =0.000 160A ->163A 0.42863 161A ->162A 0.55878 160B ->163B 0.42863 161B ->162B 0.55878 Thank you YangQiwu angiusf++gmail.com From owner-chemistry@ccl.net Fri Apr 16 11:01:00 2010 From: "Jens Spanget-Larsen spanget**ruc.dk" To: CCL Subject: CCL:G: How to get the Q band in UV-Vis of tetraphenylporphyrin by gaussian Message-Id: <-41671-100416110003-24468-WE2mu+tJVM9GNR4648WXaA . server.ccl.net> X-Original-From: Jens Spanget-Larsen Content-Transfer-Encoding: 7bit Content-Type: text/plain; charset=ISO-8859-1; format=flowed Date: Fri, 16 Apr 2010 16:59:37 +0200 MIME-Version: 1.0 Sent to CCL by: Jens Spanget-Larsen [spanget---ruc.dk] Dear YangQiwu, the first four excited states in your output are triplet states, and transitions from the ground state to these states are spin-forbidden. These transitions do not correspond to the Q band! Yours, Jens >--< ------------------------------------------------------ JENS SPANGET-LARSEN Office: +45 4674 2710 Dept. of Science (18.1) Fax: +45 4674 3011 Roskilde University Mobile: +45 2320 6246 P.O.Box 260 E-Mail: spanget!=!ruc.dk DK-4000 Roskilde, Denmark http://www.ruc.dk/~spanget ------------------------------------------------------ Yang qiwu angiusf-x-gmail.com wrote: > Sent to CCL by: "Yang qiwu" [angiusf|gmail.com] > I calculated excited state of tetraphenylporphyrin in gaussian 09, the result is that the oscillator strengths of the first four state are zero. The four is in Q band range, so how can i obtain the Q band? > > input: # TD=NStates=6 upbe1pbe/6-31G* > > output: > > Excited State 1: 3.000-A 1.2665 eV 978.99 nm f=0.0000 =2.000 > 160A ->163A 0.31957 > 161A ->162A 0.64357 > 160B ->163B -0.31957 > 161B ->162B -0.64357 > 160A <-163A 0.11838 > 161A <-162A 0.17246 > 160B <-163B -0.11838 > 161B <-162B -0.17246 > This state for optimization and/or second-order correction. > Copying the excited state density for this state as the 1-particle RhoCI density. > > Excited State 2: 3.000-A 1.6843 eV 736.12 nm f=0.0000 =2.000 > 160A ->162A -0.19159 > 161A ->163A 0.67679 > 160B ->162B 0.19159 > 161B ->163B -0.67679 > > Excited State 3: 3.000-A 1.9938 eV 621.85 nm f=0.0000 =2.000 > 160A ->162A 0.10940 > 160A ->163A 0.62409 > 161A ->162A -0.30879 > 160B ->162B -0.10940 > 160B ->163B -0.62409 > 161B ->162B 0.30879 > > Excited State 4: 3.000-A 2.0085 eV 617.31 nm f=0.0000 =2.000 > 160A ->162A 0.66795 > 160A ->163A -0.10947 > 161A ->163A 0.19131 > 160B ->162B -0.66795 > 160B ->163B 0.10947 > 161B ->163B -0.19131 > > Excited State 5: 1.000-A 2.2015 eV 563.18 nm f=0.0157 =0.000 > 160A ->162A -0.42477 > 161A ->163A 0.56009 > 160B ->162B -0.42477 > 161B ->163B 0.56009 > > Excited State 6: 1.000-A 2.3499 eV 527.62 nm f=0.0373 =0.000 > 160A ->163A 0.42863 > 161A ->162A 0.55878 > 160B ->163B 0.42863 > 161B ->162B 0.55878 > > > Thank you > > YangQiwu > angiusf^^^gmail.com> > > From owner-chemistry@ccl.net Fri Apr 16 14:27:01 2010 From: "Lydia Rhyman lydrhy%x%hotmail.com" To: CCL Subject: CCL: Rate constant Message-Id: <-41672-100416131826-1342-tRlRr7LyhrposhgyEt+6Mg]|[server.ccl.net> X-Original-From: "Lydia Rhyman" Date: Fri, 16 Apr 2010 13:18:25 -0400 Sent to CCL by: "Lydia Rhyman" [lydrhy**hotmail.com] Dear CClers, Greetings I have used the conventional transition state theory to calculate the rate constant of a reaction with the Wigner tunneling coefficient ( ) in the gas phase using the equation below: k=(KbT/h)(QtsNa/Q1Q2)exp(-Ea/RT) 1, 2 and TS have been fully optimised in the gas phase and Qs have been calculated from frequencies. I want to extend to solvent phase. Can the same procedure be used? Does the rate equation change? I will appreciate your response/hint. Kind regards Lydia Rhyman From owner-chemistry@ccl.net Fri Apr 16 21:51:01 2010 From: "Soren Eustis soreneustis ~~ gmail.com" To: CCL Subject: CCL: CCSD and MP2 Optimization error, but not for DFT?? Message-Id: <-41673-100416204839-22839-Tstdanudpsw4nN3dfAn4kw||server.ccl.net> X-Original-From: Soren Eustis Content-type: multipart/alternative; boundary="B_3354313478_463008" Date: Sat, 17 Apr 2010 01:44:36 +0200 Mime-version: 1.0 Sent to CCL by: Soren Eustis [soreneustis*gmail.com] > This message is in MIME format. Since your mail reader does not understand this format, some or all of this message may not be legible. --B_3354313478_463008 Content-type: text/plain; charset="ISO-8859-1" Content-transfer-encoding: quoted-printable Greetings,=20 I am working on a simple system: M3O- (M=3DLi, K, Na, etc...). I am able to get triplet and singlet ground states to converge fine with DFT, but whe= n I take those same geometries and submit them using MP2 or CCSD the job always fails after several (sometimes more) iterations. The error is that the coordinate system is inconsistent and =8Csmall interatomic distances=B9 wer= e encountered. The geometry at the final iteration is not even printed, and = I see NaN (empty set) for some RMS values. This is really odd. I have tried my normal geometry opt tricks (nrscale, maxstep), but no luck. This problem seems larger than that. Here is the top and bottom of the output: %mem=3D8gb %nprocshared=3D8 Will use up to 8 processors via shared memory. %CHK=3Doutput.chk ---------------------------------------------------------------------- #P CCSD/6-311++G(3d,3p) IOP(1/88=3D1) SCF(TIGHT,XQC) OPT(TIGHT,maxcycle=3D 300) FREQ(noraman) NOSYMMETRY ---------------------------------------------------------------------- ....... Berny optimization. Using GEDIIS/GDIIS optimizer. Internal Forces: Max 0.000930246 RMS 0.000664259 Search for a local minimum. Step number 3 out of a maximum of 100 All quantities printed in internal units (Hartrees-Bohrs-Radians) RMS Force =3D .66426D-03 SwitMx=3D.10000D-02 MixMth=3D 2 Mixed Optimization -- En-DIIS/RFO-DIIS Update second derivatives using D2CorX and points 1 2 3 DE=3D -7.87D-05 DEPred=3D-7.32D-05 R=3D 1.08D+00 SS=3D 1.41D+00 RLast=3D 3.79D-02 DXNew=3D 5.0454D-01 1.1371D-01 Trust test=3D 1.08D+00 RLast=3D 3.79D-02 DXMaxT set to 3.00D-01 The second derivative matrix: R1 R2 R3 R4 R5 R1 0.17194 R2 -0.02094 0.17194 R3 -0.02094 -0.02094 0.17194 R4 -0.00302 -0.00302 -0.00302 0.01693 R5 -0.00301 -0.00301 -0.00301 -0.00378 0.01694 R6 -0.00302 -0.00302 -0.00302 -0.00379 -0.00378 R6 R6 0.01693 Use linear search instead of GDIIS. Eigenvalues --- 0.00869 0.02071 0.02072 0.13074 0.19288 Eigenvalues --- 0.19288 RFO step: Lambda=3D-2.29742560D-04 EMin=3D 8.68925581D-03 Quartic linear search produced a step of 1.43713. Iteration 1 RMS(Cart)=3D 0.34299183 RMS(Int)=3D 0.11881741 Iteration 2 RMS(Cart)=3D 0.23882000 RMS(Int)=3D 0.04698067 New curvilinear step failed, DQL=3D 3.65D-02 SP=3D-1.00D+00. Iteration 1 RMS(Cart)=3D 0.30937004 RMS(Int)=3D 0.10049878 Iteration 2 RMS(Cart)=3D 0.22088439 RMS(Int)=3D 0.04067145 New curvilinear step failed, DQL=3D 5.98D-02 SP=3D-1.00D+00. Iteration 1 RMS(Cart)=3D 0.27574815 RMS(Int)=3D 0.08414942 Iteration 2 RMS(Cart)=3D 0.20316690 RMS(Int)=3D 0.03476852 New curvilinear step failed, DQL=3D 9.13D-02 SP=3D-1.00D+00. Iteration 1 RMS(Cart)=3D 0.24212704 RMS(Int)=3D 0.06983656 Iteration 2 RMS(Cart)=3D 0.18566499 RMS(Int)=3D 0.02929391 New curvilinear step failed, DQL=3D 1.42D-01 SP=3D-1.00D+00. Iteration 1 RMS(Cart)=3D 0.20850556 RMS(Int)=3D 0.05761178 Iteration 2 RMS(Cart)=3D 0.16838286 RMS(Int)=3D 0.02426886 New curvilinear step failed, DQL=3D 2.49D-01 SP=3D-1.00D+00. Iteration 1 RMS(Cart)=3D 0.17488479 RMS(Int)=3D 0.04748671 Iteration 2 RMS(Cart)=3D 0.15102309 RMS(Int)=3D 0.01967343 New curvilinear step failed, DQL=3D 6.18D-01 SP=3D-1.00D+00. Iteration 1 RMS(Cart)=3D 0.14126403 RMS(Int)=3D 0.03938524 Iteration 2 RMS(Cart)=3D 0.12626319 RMS(Int)=3D 0.01457652 New curvilinear step failed, DQL=3D 1.38D+00 SP=3D-9.86D-01. Iteration 1 RMS(Cart)=3D 0.10764312 RMS(Int)=3D 0.03308054 Iteration 2 RMS(Cart)=3D 0.10610184 RMS(Int)=3D 0.01052722 New curvilinear step failed, DQL=3D 5.81D+00 SP=3D-9.46D-01. Iteration 1 RMS(Cart)=3D 0.07402396 RMS(Int)=3D 0.02815003 Iteration 2 RMS(Cart)=3D 0.08995262 RMS(Int)=3D 0.00743084 New curvilinear step failed, DQL=3D 9.82D-02 SP=3D-8.35D-01. Iteration 1 RMS(Cart)=3D 0.04040832 RMS(Int)=3D 0.02400387 Iteration 2 RMS(Cart)=3D 0.07796541 RMS(Int)=3D 0.00532937 Iteration 3 RMS(Cart)=3D 0.02900701 RMS(Int)=3D 0.00400663 New curvilinear step failed, DQL=3D 6.68D-02 SP=3D-8.06D-01. Iteration 1 RMS(Cart)=3D 3.42991671 RMS(Int)=3D 4.96605092 Iteration 2 RMS(Cart)=3D447.15764271 RMS(Int)=3D898.91069919 Iteration 3 RMS(Cart)=3D************ RMS(Int)=3D************ Iteration 4 RMS(Cart)=3D************ RMS(Int)=3D************ Iteration 5 RMS(Cart)=3D************ RMS(Int)=3D************ Iteration 6 RMS(Cart)=3D************ RMS(Int)=3D************ Iteration 7 RMS(Cart)=3D************ RMS(Int)=3D************ Iteration 8 RMS(Cart)=3D************ RMS(Int)=3D************ Iteration 9 RMS(Cart)=3D************ RMS(Int)=3D************ Iteration 10 RMS(Cart)=3D************ RMS(Int)=3D************ Iteration 11 RMS(Cart)=3D************ RMS(Int)=3D************ Iteration 12 RMS(Cart)=3D************ RMS(Int)=3D************ Iteration 13 RMS(Cart)=3D************ RMS(Int)=3D************ Iteration 14 RMS(Cart)=3D************ RMS(Int)=3D************ Iteration 15 RMS(Cart)=3D************ RMS(Int)=3D************ Iteration 16 RMS(Cart)=3D************ RMS(Int)=3D************ Iteration 17 RMS(Cart)=3D************ RMS(Int)=3D************ Iteration 18 RMS(Cart)=3D************ RMS(Int)=3D************ Iteration 19 RMS(Cart)=3D************ RMS(Int)=3D************ Iteration 20 RMS(Cart)=3D************ RMS(Int)=3D************ Iteration 21 RMS(Cart)=3D************ RMS(Int)=3D************ Iteration 22 RMS(Cart)=3D************ RMS(Int)=3D************ Iteration 23 RMS(Cart)=3D************ RMS(Int)=3D************ Iteration 24 RMS(Cart)=3D************ RMS(Int)=3D************ Iteration 25 RMS(Cart)=3D************ RMS(Int)=3D************ Iteration 26 RMS(Cart)=3D************ RMS(Int)=3D************ Iteration 27 RMS(Cart)=3D************ RMS(Int)=3D************ Iteration 28 RMS(Cart)=3D************ RMS(Int)=3D************ Iteration 29 RMS(Cart)=3D************ RMS(Int)=3D************ Iteration 30 RMS(Cart)=3D************ RMS(Int)=3D************ Iteration 31 RMS(Cart)=3D************ RMS(Int)=3D************ Iteration 32 RMS(Cart)=3D************ RMS(Int)=3D************ Iteration 33 RMS(Cart)=3D************ RMS(Int)=3D************ Iteration 34 RMS(Cart)=3D************ RMS(Int)=3D************ Iteration 35 RMS(Cart)=3D************ RMS(Int)=3D************ Iteration 36 RMS(Cart)=3D************ RMS(Int)=3D************ Iteration 37 RMS(Cart)=3D************ RMS(Int)=3D************ Iteration 38 RMS(Cart)=3D************ RMS(Int)=3D************ Iteration 39 RMS(Cart)=3D************ RMS(Int)=3D************ Iteration 40 RMS(Cart)=3D************ RMS(Int)=3D************ Iteration 41 RMS(Cart)=3D************ RMS(Int)=3D************ Iteration 42 RMS(Cart)=3D************ RMS(Int)=3D************ Iteration 43 RMS(Cart)=3D************ RMS(Int)=3D************ Iteration 44 RMS(Cart)=3D************ RMS(Int)=3D************ Iteration 45 RMS(Cart)=3D************ RMS(Int)=3D************ Iteration 46 RMS(Cart)=3D************ RMS(Int)=3D************ Iteration 47 RMS(Cart)=3D************ RMS(Int)=3D************ Iteration 48 RMS(Cart)=3D************ RMS(Int)=3D************ Iteration 49 RMS(Cart)=3D************ RMS(Int)=3D************ Iteration 50 RMS(Cart)=3D************ RMS(Int)=3D************ Iteration 51 RMS(Cart)=3D************ RMS(Int)=3D************ Iteration 52 RMS(Cart)=3D************ RMS(Int)=3D************ Iteration 53 RMS(Cart)=3D************ RMS(Int)=3D************ Iteration 54 RMS(Cart)=3D************ RMS(Int)=3D************ Iteration 55 RMS(Cart)=3D************ RMS(Int)=3D************ Iteration 56 RMS(Cart)=3D************ RMS(Int)=3D************ Iteration 57 RMS(Cart)=3D************ RMS(Int)=3D************ Iteration 58 RMS(Cart)=3D************ RMS(Int)=3D************ Iteration 59 RMS(Cart)=3D************ RMS(Int)=3D************ Iteration 60 RMS(Cart)=3D************ RMS(Int)=3D************ Iteration 61 RMS(Cart)=3D************ RMS(Int)=3D************ Iteration 62 RMS(Cart)=3D************ RMS(Int)=3D************ Iteration 63 RMS(Cart)=3D************ RMS(Int)=3D************ Iteration 64 RMS(Cart)=3D************ RMS(Int)=3D************ Iteration 65 RMS(Cart)=3D************ RMS(Int)=3D************ Iteration 66 RMS(Cart)=3D************ RMS(Int)=3D************ Iteration 67 RMS(Cart)=3D************ RMS(Int)=3D************ Iteration 68 RMS(Cart)=3D************ RMS(Int)=3D************ Iteration 69 RMS(Cart)=3D Inf RMS(Int)=3D Inf Iteration 70 RMS(Cart)=3D NaN RMS(Int)=3D NaN TrRot=3D 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 Variable Old X -DE/DX Delta X Delta X Delta X New X (Linear) (Quad) (Total) R1 3.17933 0.00014 0.01492 -0.00622 NaN NaN R2 3.17933 0.00014 0.01492 -0.00622 NaN NaN R3 3.17934 0.00014 0.01492 -0.00622 NaN NaN R4 5.50652 0.00093 0.02770 0.08074 NaN NaN R5 5.50696 0.00093 0.02765 0.08060 NaN NaN R6 5.50657 0.00093 0.02770 0.08072 NaN NaN Item Value Threshold Converged? Maximum Force 0.000930 0.000015 NO RMS Force 0.000664 0.000010 NO Maximum Displacement NaN 0.000060 YES RMS Displacement NaN 0.000040 YES Predicted change in Energy=3D NaN GradGradGradGradGradGradGradGradGradGradGradGradGradGradGradGradGradGrad Leave Link 103 at Fri Apr 16 13:40:38 2010, MaxMem=3D 1073741824 cpu: 0.1 (Enter /home/soren/g09/l202.exe) Input orientation: --------------------------------------------------------------------- Center Atomic Atomic Coordinates (Angstroms) Number Number Type X Y Z --------------------------------------------------------------------- 1 8 0 NaN NaN NaN 2 3 0 NaN NaN NaN 3 3 0 NaN NaN NaN 4 3 0 NaN NaN NaN --------------------------------------------------------------------- Distance matrix (angstroms): 1 2 3 4 1 O 0.000000 2 Li 0.000000 0.000000 3 Li 0.000000 0.000000 0.000000 4 Li 0.000000 0.000000 0.000000 0.000000 Small interatomic distances encountered: 2 1 3 1 3 2 4 1 4 2 Small interatomic distances encountered: 4 3 Problem with the distance matrix. Error termination via Lnk1e in /home/soren/g09/l202.exe at Fri Apr 16 13:40:38 2010. Job cpu time: 0 days 6 hours 31 minutes 55.1 seconds. File lengths (MBytes): RWF=3D 3970 Int=3D 0 D2E=3D 0 Chk=3D 2 Scr=3D 1 Thanks in advance! Soren --=20 Dr. Soren N. Eustis ETH =AD Zurich Institute for Biogeochemistry and Pollutant Dynamics Universitatstrasse 16 8092 Zurich +41 44 632 93 48 (office) +41 44 632 14 38 (fax) soren:env.ethz.ch=20 --B_3354313478_463008 Content-type: text/html; charset="ISO-8859-1" Content-transfer-encoding: quoted-printable CCSD and MP2 Optimization error, but not for DFT?? Greetings,

  I am working on a simple system:  M3O- (M=3DLi, K, Na, etc..= .).  I am able to get triplet and singlet ground states to converge fin= e with DFT, but when I take those same geometries and submit them using MP2 = or CCSD the job always fails after several (sometimes more) iterations. &nbs= p;The error is that the coordinate system is inconsistent and ‘small i= nteratomic distances’ were encountered.  The geometry at the fina= l iteration is not even printed, and I see NaN (empty set) for some RMS valu= es.  

This is really odd.  I have tried my normal geometry opt tricks (nrsca= le, maxstep), but no luck.  This problem seems larger than that.  = Here is the top and bottom of the output:

%mem=3D8gb
 %nprocshared=3D8
 Will use up to    8 processors via shared memory.
 %CHK=3Doutput.chk
 ---------------------------------------------------------------------= -
 #P CCSD/6-311++G(3d,3p) IOP(1/88=3D1) SCF(TIGHT,XQC) OPT(TIGHT,maxcycle= =3D
 300) FREQ(noraman) NOSYMMETRY
 ---------------------------------------------------------------------= -



.......

Berny optimization.
 Using GEDIIS/GDIIS optimizer.
 Internal  Forces:  Max     0.000930246 = RMS     0.000664259
 Search for a local minimum.
 Step number   3 out of a maximum of  100
 All quantities printed in internal units (Hartrees-Bohrs-Radians)
 RMS Force =3D .66426D-03 SwitMx=3D.10000D-02 MixMth=3D 2
 Mixed Optimization -- En-DIIS/RFO-DIIS
 Update second derivatives using D2CorX and points    1=    2    3
 DE=3D -7.87D-05 DEPred=3D-7.32D-05 R=3D 1.08D+00
 SS=3D  1.41D+00  RLast=3D 3.79D-02 DXNew=3D 5.0454D-01 1.1371D-01=
 Trust test=3D 1.08D+00 RLast=3D 3.79D-02 DXMaxT set to 3.00D-01
 The second derivative matrix:
            &nb= sp;            &= nbsp;R1        R2     = ;   R3        R4  &nb= sp;     R5
           R1  =          0.17194
           R2  =         -0.02094   0.17194=
           R3  =         -0.02094  -0.02094 &nbs= p; 0.17194
           R4  =         -0.00302  -0.00302 &nbs= p;-0.00302   0.01693
           R5  =         -0.00301  -0.00301 &nbs= p;-0.00301  -0.00378   0.01694
           R6  =         -0.00302  -0.00302 &nbs= p;-0.00302  -0.00379  -0.00378
            &nb= sp;            &= nbsp;R6
           R6  =          0.01693
 Use linear search instead of GDIIS.
     Eigenvalues ---    0.00869 &nb= sp; 0.02071   0.02072   0.13074   0.19288=
     Eigenvalues ---    0.19288
 RFO step:  Lambda=3D-2.29742560D-04 EMin=3D 8.68925581D-03
 Quartic linear search produced a step of  1.43713.
 Iteration  1 RMS(Cart)=3D  0.34299183 RMS(Int)=3D  0.11881= 741
 Iteration  2 RMS(Cart)=3D  0.23882000 RMS(Int)=3D  0.04698= 067
 New curvilinear step failed, DQL=3D 3.65D-02 SP=3D-1.00D+00.
 Iteration  1 RMS(Cart)=3D  0.30937004 RMS(Int)=3D  0.10049= 878
 Iteration  2 RMS(Cart)=3D  0.22088439 RMS(Int)=3D  0.04067= 145
 New curvilinear step failed, DQL=3D 5.98D-02 SP=3D-1.00D+00.
 Iteration  1 RMS(Cart)=3D  0.27574815 RMS(Int)=3D  0.08414= 942
 Iteration  2 RMS(Cart)=3D  0.20316690 RMS(Int)=3D  0.03476= 852
 New curvilinear step failed, DQL=3D 9.13D-02 SP=3D-1.00D+00.
 Iteration  1 RMS(Cart)=3D  0.24212704 RMS(Int)=3D  0.06983= 656
 Iteration  2 RMS(Cart)=3D  0.18566499 RMS(Int)=3D  0.02929= 391
 New curvilinear step failed, DQL=3D 1.42D-01 SP=3D-1.00D+00.
 Iteration  1 RMS(Cart)=3D  0.20850556 RMS(Int)=3D  0.05761= 178
 Iteration  2 RMS(Cart)=3D  0.16838286 RMS(Int)=3D  0.02426= 886
 New curvilinear step failed, DQL=3D 2.49D-01 SP=3D-1.00D+00.
 Iteration  1 RMS(Cart)=3D  0.17488479 RMS(Int)=3D  0.04748= 671
 Iteration  2 RMS(Cart)=3D  0.15102309 RMS(Int)=3D  0.01967= 343
 New curvilinear step failed, DQL=3D 6.18D-01 SP=3D-1.00D+00.
 Iteration  1 RMS(Cart)=3D  0.14126403 RMS(Int)=3D  0.03938= 524
 Iteration  2 RMS(Cart)=3D  0.12626319 RMS(Int)=3D  0.01457= 652
 New curvilinear step failed, DQL=3D 1.38D+00 SP=3D-9.86D-01.
 Iteration  1 RMS(Cart)=3D  0.10764312 RMS(Int)=3D  0.03308= 054
 Iteration  2 RMS(Cart)=3D  0.10610184 RMS(Int)=3D  0.01052= 722
 New curvilinear step failed, DQL=3D 5.81D+00 SP=3D-9.46D-01.
 Iteration  1 RMS(Cart)=3D  0.07402396 RMS(Int)=3D  0.02815= 003
 Iteration  2 RMS(Cart)=3D  0.08995262 RMS(Int)=3D  0.00743= 084
 New curvilinear step failed, DQL=3D 9.82D-02 SP=3D-8.35D-01.
 Iteration  1 RMS(Cart)=3D  0.04040832 RMS(Int)=3D  0.02400= 387
 Iteration  2 RMS(Cart)=3D  0.07796541 RMS(Int)=3D  0.00532= 937
 Iteration  3 RMS(Cart)=3D  0.02900701 RMS(Int)=3D  0.00400= 663
 New curvilinear step failed, DQL=3D 6.68D-02 SP=3D-8.06D-01.
 Iteration  1 RMS(Cart)=3D  3.42991671 RMS(Int)=3D  4.96605= 092
 Iteration  2 RMS(Cart)=3D447.15764271 RMS(Int)=3D898.91069919
 Iteration  3 RMS(Cart)=3D************ RMS(Int)=3D************
 Iteration  4 RMS(Cart)=3D************ RMS(Int)=3D************
 Iteration  5 RMS(Cart)=3D************ RMS(Int)=3D************
 Iteration  6 RMS(Cart)=3D************ RMS(Int)=3D************
 Iteration  7 RMS(Cart)=3D************ RMS(Int)=3D************
 Iteration  8 RMS(Cart)=3D************ RMS(Int)=3D************
 Iteration  9 RMS(Cart)=3D************ RMS(Int)=3D************
 Iteration 10 RMS(Cart)=3D************ RMS(Int)=3D************
 Iteration 11 RMS(Cart)=3D************ RMS(Int)=3D************
 Iteration 12 RMS(Cart)=3D************ RMS(Int)=3D************
 Iteration 13 RMS(Cart)=3D************ RMS(Int)=3D************
 Iteration 14 RMS(Cart)=3D************ RMS(Int)=3D************
 Iteration 15 RMS(Cart)=3D************ RMS(Int)=3D************
 Iteration 16 RMS(Cart)=3D************ RMS(Int)=3D************
 Iteration 17 RMS(Cart)=3D************ RMS(Int)=3D************
 Iteration 18 RMS(Cart)=3D************ RMS(Int)=3D************
 Iteration 19 RMS(Cart)=3D************ RMS(Int)=3D************
 Iteration 20 RMS(Cart)=3D************ RMS(Int)=3D************
 Iteration 21 RMS(Cart)=3D************ RMS(Int)=3D************
 Iteration 22 RMS(Cart)=3D************ RMS(Int)=3D************
 Iteration 23 RMS(Cart)=3D************ RMS(Int)=3D************
 Iteration 24 RMS(Cart)=3D************ RMS(Int)=3D************
 Iteration 25 RMS(Cart)=3D************ RMS(Int)=3D************
 Iteration 26 RMS(Cart)=3D************ RMS(Int)=3D************
 Iteration 27 RMS(Cart)=3D************ RMS(Int)=3D************
 Iteration 28 RMS(Cart)=3D************ RMS(Int)=3D************
 Iteration 29 RMS(Cart)=3D************ RMS(Int)=3D************
 Iteration 30 RMS(Cart)=3D************ RMS(Int)=3D************
 Iteration 31 RMS(Cart)=3D************ RMS(Int)=3D************
 Iteration 32 RMS(Cart)=3D************ RMS(Int)=3D************
 Iteration 33 RMS(Cart)=3D************ RMS(Int)=3D************
 Iteration 34 RMS(Cart)=3D************ RMS(Int)=3D************
 Iteration 35 RMS(Cart)=3D************ RMS(Int)=3D************
 Iteration 36 RMS(Cart)=3D************ RMS(Int)=3D************
 Iteration 37 RMS(Cart)=3D************ RMS(Int)=3D************
 Iteration 38 RMS(Cart)=3D************ RMS(Int)=3D************
 Iteration 39 RMS(Cart)=3D************ RMS(Int)=3D************
 Iteration 40 RMS(Cart)=3D************ RMS(Int)=3D************
 Iteration 41 RMS(Cart)=3D************ RMS(Int)=3D************
 Iteration 42 RMS(Cart)=3D************ RMS(Int)=3D************
 Iteration 43 RMS(Cart)=3D************ RMS(Int)=3D************
 Iteration 44 RMS(Cart)=3D************ RMS(Int)=3D************
 Iteration 45 RMS(Cart)=3D************ RMS(Int)=3D************
 Iteration 46 RMS(Cart)=3D************ RMS(Int)=3D************
 Iteration 47 RMS(Cart)=3D************ RMS(Int)=3D************
 Iteration 48 RMS(Cart)=3D************ RMS(Int)=3D************
 Iteration 49 RMS(Cart)=3D************ RMS(Int)=3D************
 Iteration 50 RMS(Cart)=3D************ RMS(Int)=3D************
 Iteration 51 RMS(Cart)=3D************ RMS(Int)=3D************
 Iteration 52 RMS(Cart)=3D************ RMS(Int)=3D************
 Iteration 53 RMS(Cart)=3D************ RMS(Int)=3D************
 Iteration 54 RMS(Cart)=3D************ RMS(Int)=3D************
 Iteration 55 RMS(Cart)=3D************ RMS(Int)=3D************
 Iteration 56 RMS(Cart)=3D************ RMS(Int)=3D************
 Iteration 57 RMS(Cart)=3D************ RMS(Int)=3D************
 Iteration 58 RMS(Cart)=3D************ RMS(Int)=3D************
 Iteration 59 RMS(Cart)=3D************ RMS(Int)=3D************
 Iteration 60 RMS(Cart)=3D************ RMS(Int)=3D************
 Iteration 61 RMS(Cart)=3D************ RMS(Int)=3D************
 Iteration 62 RMS(Cart)=3D************ RMS(Int)=3D************
 Iteration 63 RMS(Cart)=3D************ RMS(Int)=3D************
 Iteration 64 RMS(Cart)=3D************ RMS(Int)=3D************
 Iteration 65 RMS(Cart)=3D************ RMS(Int)=3D************
 Iteration 66 RMS(Cart)=3D************ RMS(Int)=3D************
 Iteration 67 RMS(Cart)=3D************ RMS(Int)=3D************
 Iteration 68 RMS(Cart)=3D************ RMS(Int)=3D************
 Iteration 69 RMS(Cart)=3D        &nb= sp;Inf RMS(Int)=3D         Inf
 Iteration 70 RMS(Cart)=3D        &nb= sp;NaN RMS(Int)=3D         NaN
 TrRot=3D  0.000000  0.000000  0.000000  0.000000 &n= bsp;0.000000  0.000000
 Variable       Old X    = -DE/DX   Delta X   Delta X   Delta X  &nb= sp;  New X
            &nb= sp;            &= nbsp;       (Linear)    (Q= uad)   (Total)
    R1        3.1793= 3   0.00014   0.01492  -0.00622    &= nbsp;  NaN       NaN
    R2        3.1793= 3   0.00014   0.01492  -0.00622    &= nbsp;  NaN       NaN
    R3        3.1793= 4   0.00014   0.01492  -0.00622    &= nbsp;  NaN       NaN
    R4        5.5065= 2   0.00093   0.02770   0.08074   &n= bsp;   NaN       NaN
    R5        5.5069= 6   0.00093   0.02765   0.08060   &n= bsp;   NaN       NaN
    R6        5.5065= 7   0.00093   0.02770   0.08072   &n= bsp;   NaN       NaN
         Item   &nbs= p;           Value &n= bsp;   Threshold  Converged?
 Maximum Force          &= nbsp; 0.000930     0.000015     = ;NO
 RMS     Force       = ;     0.000664     0.000010 &nb= sp;   NO
 Maximum Displacement         =  NaN     0.000060     YES
 RMS     Displacement     &nbs= p;    NaN     0.000040   &= nbsp; YES
 Predicted change in Energy=3D        = ;  NaN
 GradGradGradGradGradGradGradGradGradGradGradGradGradGradGradGradGradG= rad

 Leave Link  103 at Fri Apr 16 13:40:38 2010, MaxMem=3D 1073741824 = cpu:       0.1
 (Enter /home/soren/g09/l202.exe)
            &nb= sp;            &= nbsp;Input orientation:         &nbs= p;            &n= bsp;   
 ---------------------------------------------------------------------=
 Center     Atomic      A= tomic            &nbs= p;Coordinates (Angstroms)
 Number     Number      &= nbsp;Type            =  X           Y  =          Z
 ---------------------------------------------------------------------=
      1       &= nbsp;  8          &nb= sp;0             = ;NaN         NaN    &= nbsp;    NaN
      2       &= nbsp;  3          &nb= sp;0             = ;NaN         NaN    &= nbsp;    NaN
      3       &= nbsp;  3          &nb= sp;0             = ;NaN         NaN    &= nbsp;    NaN
      4       &= nbsp;  3          &nb= sp;0             = ;NaN         NaN    &= nbsp;    NaN
 ---------------------------------------------------------------------=
            &nb= sp;       Distance matrix (angstroms):             &nb= sp;       1      = ;    2         &= nbsp;3          4
     1  O    0.000000
     2  Li   0.000000   0= .000000
     3  Li   0.000000   0= .000000   0.000000
     4  Li   0.000000   0= .000000   0.000000   0.000000
 Small interatomic distances encountered:     &nbs= p;2     1     3    &n= bsp;1     3     2    =  4     1     4   &nbs= p; 2
 Small interatomic distances encountered:     &nbs= p;4     3
 Problem with the distance matrix.
 Error termination via Lnk1e in /home/soren/g09/l202.exe at Fri Apr 16= 13:40:38 2010.
 Job cpu time:  0 days  6 hours 31 minutes 55.1 seconds.
 File lengths (MBytes):  RWF=3D   3970 Int=3D   &= nbsp;  0 D2E=3D      0 Chk=3D   &nb= sp;  2 Scr=3D      1





Thanks in advance!

Soren


--
Dr. Soren N. Eustis
ETH – Zurich
Institute for Biogeochemistry and Pollutant Dynamics
Universitatstrasse 16
8092 Zurich

+41 44 632 93 48 (office)
+41 44 632 14 38 (fax)

soren:env.ethz.ch

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