From owner-chemistry@ccl.net Thu Jan 5 01:27:00 2017 From: "Arthur Zalevsky aozalevsky],[gmail.com" To: CCL Subject: CCL: Protein structures Message-Id: <-52584-170105012536-22103-wsnC1oRmKSkmT5b0vLTfnQ ~~ server.ccl.net> X-Original-From: Arthur Zalevsky Content-Type: multipart/alternative; boundary=001a113971aacbb942054552f75d Date: Thu, 05 Jan 2017 06:25:20 +0000 MIME-Version: 1.0 Sent to CCL by: Arthur Zalevsky [aozalevsky=gmail.com] --001a113971aacbb942054552f75d Content-Type: text/plain; charset=UTF-8 Content-Transfer-Encoding: quoted-printable Hi John, Paper by Kuzmanic et al also may be of interest for you: "X-ray refinement significantly underestimates the level of microscopic heterogeneity in biomolecular crystals" Nature Communications 5, Article number: 3220 (2014) http://www.nature.com/articles/ncomms4220 Regards, Arthur -- Ph.D student Virtual Structural Biology Group Faculty of Bioengineering and Bioinformatics Lomonosov Moscow State University =E2=80=8E email: aozalevsky===fbb.msu.ru email: aozalevsky===gmail.com web: http://vsb.fbb.msu.ru=E2=80=8E cell: +79268299066 <+7%20926%20829-90-66> =D1=87=D1=82, 5 =D1=8F=D0=BD=D0=B2. 2017 =D0=B3. =D0=B2 8:47, Lars Goerigk = lars.goerigk#unimelb.edu.au < owner-chemistry===ccl.net>: > Hi John, > > not sure if this is helpful as a starting point, but an analysis of commo= n > methods for geometry optimisations in periodic boundary conditions, incl.= a > comparison with a crystal structure and free R-factors, has been publishe= d > in > > J. Phys Chem B 2014, *118*, 14612-14626. Therein you can also find a > literature review and a summary of the work by Ryde and Thiel in the area > of quantum refinement of protein X-ray structures with QM/MM. > > Best wishes, > > Lars > > > *Dr Lars Goerigk *| Lecturer & ARC DECRA Fellow > School of Chemistry | The University of Melbourne > Victoria 3010 | Australia > *Website: *goerigk.chemistry.unimelb.edu.au > > *Follow me on Twitter: *https://twitter.com/lgoer_compchem > > On 5 Jan 2017, at 8:42 am, Jim Kress jimkress35.-$-.gmail.com < > owner-chemistry-$-ccl.net> wrote: > > > Ignoring hardware and software demands for the moment is it > preferable/practical/wise to optimize such a structure? > > > It depends on whether it is intrinsically disordered or not. It also > depends on whether you want an in vivo representation or if you think the > in-vacuo representation is representative of the actual structure in vivo= . > > Jim > > > *From:* owner-chemistry+jimkress35=3D=3Dgmail.com]![ccl.net [mailto: > owner-chemistry+jimkress35=3D=3Dgmail.com]![ccl.net] *On Behalf Of *John > McKelvey jmmckel*gmail.com > *Sent:* Wednesday, January 04, 2017 12:17 PM > > > *To:* Kress, Jim > > *Subject:* CCL: Protein structures > > > > Folks, > > I realize that over time development of technology may have an impact on > reliability or accuracy of protein XRAY structures. How does one determi= ne > accuracy or reliability of such structures? Ignoring hardware and softwa= re > demands for the moment is it preferable/practical/wise to optimize such a > structure? > > Many thanks! > John > > -- > John McKelvey > 545 Legacy Pointe Dr > O'Fallon, MO 63376 > 636-294-5203 <(636)%20294-5203> > jmmckel{:}gmail.com > > --001a113971aacbb942054552f75d Content-Type: text/html; charset=UTF-8 Content-Transfer-Encoding: quoted-printable
Hi John,=C2=A0

Paper by Kuzmanic = et al also may be of interest for you:

"X-ray refinement= significantly underestimates the level of microscopic heterogeneity in bio= molecular crystals"=C2=A0Nature Communications 5, Article number: 3220= (2014)

Regards,<= /div>
Arthur=C2=A0

--
Ph.D studentVirtual Structural Biology Group
Faculty of Bioengineering and Bioinfor= matics
Lomonosov Moscow State University
=E2=80=8E
email: aozalevsky===fbb.msu.ru
email: aozalevsky===gmail.com
web: http://vsb.fbb.msu.ru=E2=80=8E
cell: +79268299066


<= div class=3D"gmail_quote">
=D1=87=D1=82, 5 =D1=8F=D0=BD=D0= =B2. 2017 =D0=B3. =D0=B2 8:47, Lars Goerigk lars.goerigk#unimelb.edu.au <owner-chemistry===ccl.net>:
Hi John,

not sure if this is helpful as a starting point, b= ut an analysis of common methods for geometry optimisations in periodic bou= ndary conditions, incl. a comparison with a crystal structure and free R-fa= ctors, has been published in

J. Phys Chem B 2014,=C2=A0= 118, 14612-14626. Therein you can also find a literature review and a = summary of the work by Ryde and Thiel in the area of quantum refinement of = =C2=A0protein X-ray structures with QM/MM.

Best wishes,

Lars


D= r Lars Goerigk=C2=A0|=C2=A0= Lecturer & ARC DECRA= Fellow
School of Chemistry | The University of Melbourne
Victoria 3010 | Australia
Website:=C2=A0goerigk= .chemistry.unimelb.edu.au
Follow me on Twitter:=C2=A0https://twitter.com/lgoer_compch= em

On 5 Jan 2017, at 8:42 am, Jim Kress jimkress35.-$= -.gmail.= com <owner-chemistry-$-ccl.net> wrote:

<= div class=3D"gmail_msg">
> Ignoring hardware and software demands for the moment is it pre= ferable/practical/wise to optimize such a structure?=
=C2=A0
<= blockquote type=3D"cite" class=3D"gmail_msg">
It depends on whether it is intrinsically disordered or not.=C2=A0 I= t also depends on whether you want an in vivo representation or if you thin= k the in-vacuo representation is representative of the actual structure in vivo.
=C2=A0
Jim
=C2=A0
<= blockquote type=3D"cite" class=3D"gmail_msg">
From:=C2=A0owner-chemistry= +jimkress35=3D=3Dgmail.com]![= ccl.net=C2=A0[mailto:owner-chemistry+jimkress35=3D=3Dgmail.com]![ccl.net]= =C2=A0= On Behalf Of=C2=A0John McKelvey jmmckel*gmail.com
Sent:=C2=A0Wednesday, January 04, 2017 12:17 PM=

To:=C2=A0Kress, Jim <jimkress35]![gmail.com>
Subject:=C2=A0CCL: Prot= ein structures=
=C2=A0

Folks,

I realize that over time development of technology may have an impact on re= liability or accuracy of protein XRAY structures.=C2=A0 How does one determ= ine accuracy or reliability of such structures?=C2=A0 Ignoring hardware and= software demands for the moment is it preferable/practical/wise to optimize such a structure?

Many thanks!

John

--
John McKelvey
545 Legacy Pointe Dr<= /div>
O'Fallon, MO 63376
636-294-5203
jmmckel{:}gmail.com<= /a>
--001a113971aacbb942054552f75d-- From owner-chemistry@ccl.net Thu Jan 5 11:57:01 2017 From: "Neus Aguilera neusaguilera,+,yahoo.com" To: CCL Subject: CCL:G: Understading the nature of molecular orbital (non bonding or sigma) Message-Id: <-52585-170105043544-29198-C85t6km/arj/+S/oavk9/g{:}server.ccl.net> X-Original-From: Neus Aguilera Content-Type: multipart/alternative; boundary="Apple-Mail=_1A51EF67-3C69-4EA8-A3AE-E12862E53435" Date: Thu, 5 Jan 2017 09:32:49 +0000 Mime-Version: 1.0 (Mac OS X Mail 10.2 \(3259\)) Sent to CCL by: Neus Aguilera [neusaguilera#%#yahoo.com] --Apple-Mail=_1A51EF67-3C69-4EA8-A3AE-E12862E53435 Content-Transfer-Encoding: quoted-printable Content-Type: text/plain; charset=us-ascii Dear Utpal, I would consider relaunching the calculations with some extra keywords = to be able to use a molecular orbital visualizer, as MOLDEN #P gfinput gfprint IOP(6/7=3D1) (source:http://www.cmbi.ru.nl/molden/gauss.html = ) Then you will be able to open the .out with MOLDEN. Please let me know if this worked for you, Have a nice day, Neus Aguilera-Porta > El 4 gen 2017, a les 11:47, Utpal Sarkar utpalchemiitkgp]~[gmail.com = va escriure: >=20 >=20 > Sent to CCL by: "Utpal Sarkar" [utpalchemiitkgp(0)gmail.com] > Dear Gaussian users, >=20 > I am trying to identify the molecular orbital transition for a = particular peak of UV visible spectrum from Gaussian output. My question = is how can I recognize weather a particular orbital is non bonding n = orbital or sigma orbital? >=20 > In my case, I have found for a particular peak at 237.93 nm with = oscillator strength f=3D0.1806 and the responsible transitions are=20 >=20 > 41 -> 44 0.32998 > 41 -> 46 0.16625 > 42 -> 45 -0.21871 > 42 -> 47 0.19689 > 42 -> 48 0.29232 > 42 -> 50 -0.22757 > 42 -> 52 -0.14040 > 43 -> 46 -0.12852 > 43 -> 49 0.27673 >=20 >=20 > Now I want to identify weather orbital number 42 is sigma or = nonbonding n orbital.=20 >=20 >=20 > The coefficients of orbital number 42 is given below : >=20 >=20 > 41 42 43 44 45 > O O O V V >=20 > Eigenvalues -- -0.27285 -0.24084 -0.23213 -0.05116 -0.04261 >=20 > 1 1 C 1S 0.00000 -0.00420 0.00000 0.00001 -0.00829 > 2 2S 0.00000 -0.00653 0.00000 0.00002 -0.01337 > 3 2PX 0.00000 -0.02012 -0.00001 0.00001 0.00289 > 4 2PY -0.00001 -0.00168 0.00000 -0.00002 0.01821 > 5 2PZ -0.13793 0.00001 0.02323 0.08393 0.00016 >=20 > 6 3S -0.00001 0.01777 0.00001 -0.00006 0.04398 > 7 3PX 0.00000 -0.02621 0.00000 0.00002 -0.00073 >=20 > 8 3PY -0.00001 -0.00037 0.00000 -0.00002 0.02348 > 9 3PZ -0.21271 0.00002 0.03355 0.12668 0.00024 >=20 > 10 4S 0.00001 0.04010 0.00010 -0.00041 0.13704 > 11 4PX -0.00001 -0.03987 -0.00012 -0.00001 -0.00228 > 12 4PY -0.00003 0.00962 0.00003 0.00003 0.06605 > 13 4PZ -0.20444 0.00003 0.04608 0.20909 0.00040 >=20 > 14 5S 0.00115 -0.35581 0.00042 0.00562 -2.59840 > 15 5PX -0.00036 0.37640 -0.00053 0.00004 -0.46640 >=20 > 16 5PY -0.00011 0.03293 0.00005 -0.00263 1.81287 > 17 5PZ -0.00891 0.00007 -0.01617 0.11613 0.00054 > 18 6D 0 0.00000 0.00022 0.00000 0.00000 -0.00167 > 19 6D+1 -0.00349 0.00000 -0.01518 -0.01160 -0.00002 > 20 6D-1 0.00841 0.00000 -0.00111 0.00349 0.00001 > 21 6D+2 0.00000 -0.00233 0.00000 0.00000 0.00518 > 22 6D-2 0.00000 0.00204 0.00000 0.00000 0.00069 > 23 2 C 1S 0.00000 0.00418 0.00000 0.00002 -0.00937 > 24 2S 0.00000 0.00682 0.00000 0.00003 -0.01539 > 25 2PX 0.00001 0.02532 0.00000 0.00003 -0.01284 > 26 2PY -0.00001 -0.00688 0.00001 -0.00001 0.00125 > 27 2PZ -0.03567 0.00001 0.08391 0.01761 -0.00001 > 28 3S -0.00002 -0.01999 0.00000 -0.00010 0.05218 > 29 3PX 0.00002 0.04132 0.00001 0.00005 -0.02390 > 30 3PY -0.00001 -0.00767 0.00002 -0.00002 0.00704 > 31 3PZ -0.05659 0.00002 0.13408 0.02588 -0.00002 > 32 4S -0.00002 -0.03998 -0.00006 -0.00023 0.17293 > 33 4PX -0.00002 0.05482 -0.00005 0.00033 -0.09711 > 34 4PY 0.00000 -0.07317 -0.00016 0.00003 -0.07289 > 35 4PZ -0.03986 0.00001 0.12373 0.02282 -0.00003 >=20 > 36 5S -0.00032 -0.11569 -0.00081 -0.01228 6.78260 >=20 > 37 5PX -0.00042 0.05717 -0.00013 0.00494 -1.60116 >=20 > 38 5PY -0.00059 0.44119 -0.00063 -0.00072 -1.24950 >=20 > 39 5PZ -0.02588 -0.00006 0.04361 0.17297 -0.00036 > 40 6D 0 0.00000 0.00018 0.00000 0.00001 -0.00208 > 41 6D+1 -0.02147 0.00000 0.00844 0.01814 0.00003 > 42 6D-1 -0.00727 0.00000 -0.01096 0.00789 0.00002 > 43 6D+2 -0.00001 0.00459 0.00000 -0.00001 0.00141 > 44 6D-2 0.00000 0.00783 0.00000 0.00000 0.00323 > 45 3 C 1S 0.00000 -0.00250 0.00001 0.00000 -0.00307 > 46 2S -0.00001 -0.00394 0.00001 0.00001 -0.00527 > 47 2PX 0.00000 -0.02120 0.00002 0.00000 -0.00284 > 48 2PY 0.00001 -0.00889 -0.00001 0.00001 -0.00383 > 49 2PZ 0.04067 0.00002 0.07965 -0.05872 -0.00012 > 50 3S 0.00002 0.00920 -0.00002 -0.00003 0.02598 > 51 3PX -0.00001 -0.03375 0.00006 0.00000 -0.00496 > 52 3PY 0.00002 -0.01359 -0.00002 0.00002 -0.00541 > 53 3PZ 0.06382 0.00003 0.12680 -0.09881 -0.00020 > 54 4S 0.00020 0.01844 -0.00050 0.00003 -0.00626 >=20 > 55 4PX 0.00001 -0.10072 0.00008 -0.00023 0.03817 >=20 > 56 4PY -0.00005 -0.02876 -0.00003 0.00013 -0.11338 > 57 4PZ 0.06310 0.00004 0.13146 -0.10786 -0.00029 >=20 > 58 5S -0.00091 1.35401 -0.00060 -0.00343 1.95224 >=20 > 59 5PX 0.00011 -0.07907 -0.00052 -0.01066 4.45406 >=20 > 60 5PY -0.00021 0.25218 -0.00015 0.00362 -2.43405 >=20 > 61 5PZ 0.02754 0.00003 -0.00041 -0.30749 -0.00068 > 62 6D 0 0.00000 -0.00126 0.00000 0.00001 -0.00313 > 63 6D+1 0.02091 0.00000 0.01506 0.02310 0.00003 > 64 6D-1 -0.00972 0.00000 0.00984 0.00010 -0.00001 > 65 6D+2 0.00001 0.00092 0.00000 0.00001 -0.00749 > 66 6D-2 0.00000 0.00700 -0.00001 0.00000 -0.00141 > 67 4 C 1S 0.00000 0.00209 0.00000 0.00002 -0.01205 > 68 2S 0.00000 0.00332 -0.00001 0.00003 -0.01967 > 69 2PX 0.00000 0.01269 -0.00001 0.00001 -0.00401 > 70 2PY -0.00001 -0.00223 0.00001 0.00002 -0.02944 > 71 2PZ 0.13807 -0.00001 0.03273 0.09279 0.00016 > 72 3S -0.00001 -0.01048 0.00002 -0.00011 0.07052 > 73 3PX 0.00001 0.01699 -0.00002 0.00003 -0.00983 > 74 3PY -0.00002 -0.00209 0.00001 0.00002 -0.03833 > 75 3PZ 0.21444 -0.00001 0.04852 0.14133 0.00025 > 76 4S -0.00007 0.03587 0.00010 0.00012 0.02042 > 77 4PX 0.00005 0.01075 -0.00004 -0.00013 0.06745 > 78 4PY -0.00002 0.03088 0.00003 0.00014 -0.08716 >=20 > 79 4PZ 0.19966 -0.00001 0.05466 0.21749 0.00040 >=20 > 80 5S 0.00048 0.24000 0.00046 0.01370 -6.29902 > 81 5PX 0.00014 0.15294 0.00022 -0.00038 0.95984 >=20 > 82 5PY 0.00016 0.03045 -0.00005 0.00288 -2.02375 > 83 5PZ 0.02481 -0.00001 0.02389 0.30485 0.00041 > 84 6D 0 0.00000 -0.00014 0.00000 0.00000 -0.00113 > 85 6D+1 0.00307 0.00000 -0.01335 0.00485 0.00001 > 86 6D-1 0.00725 0.00000 0.00326 -0.00480 -0.00001 > 87 6D+2 0.00000 0.00252 0.00000 0.00000 0.00556 > 88 6D-2 0.00000 0.00085 0.00000 0.00000 -0.00282 > 89 5 C 1S 0.00000 -0.00128 0.00000 0.00000 -0.00810 > 90 2S 0.00000 -0.00204 0.00000 0.00001 -0.01317 > 91 2PX 0.00000 -0.00832 0.00001 -0.00002 0.02313 > 92 2PY 0.00000 -0.00240 0.00001 0.00000 -0.01084 > 93 2PZ 0.06902 -0.00002 -0.06649 -0.02215 -0.00004 > 94 3S -0.00001 0.00606 0.00000 -0.00002 0.04591 > 95 3PX 0.00000 -0.01115 0.00001 -0.00003 0.03168 > 96 3PY -0.00001 -0.00283 0.00001 0.00001 -0.01523 > 97 3PZ 0.10653 -0.00003 -0.10344 -0.03512 -0.00007 > 98 4S 0.00000 -0.01037 -0.00002 -0.00007 0.04618 > 99 4PX 0.00000 0.00126 0.00003 -0.00004 0.05818 > 100 4PY 0.00002 -0.00822 0.00000 -0.00002 -0.01083 > 101 4PZ 0.09937 -0.00003 -0.10252 -0.04632 -0.00010 >=20 > 102 5S -0.00035 -0.82701 0.00051 0.00144 0.52163 > 103 5PX 0.00017 0.10769 0.00005 -0.00063 0.66730 >=20 > 104 5PY 0.00005 -0.08692 0.00039 0.00162 -0.24277 > 105 5PZ 0.01608 0.00001 -0.03265 -0.08881 -0.00014 > 106 6D 0 0.00000 -0.00007 0.00000 0.00000 -0.00241 > 107 6D+1 -0.01473 0.00000 -0.00471 -0.01392 -0.00002 > 108 6D-1 -0.01513 0.00000 -0.00919 -0.01697 -0.00003 > 109 6D+2 0.00000 -0.00040 0.00000 0.00000 -0.00226 > 110 6D-2 0.00000 0.00182 0.00000 -0.00001 0.00809 > 111 6 C 1S 0.00000 0.00206 0.00000 0.00001 -0.00756 > 112 2S 0.00000 0.00328 0.00000 0.00001 -0.01224 > 113 2PX 0.00000 0.01042 0.00000 -0.00002 0.01938 > 114 2PY 0.00000 -0.00458 0.00000 0.00000 0.00515 > 115 2PZ -0.08000 -0.00001 -0.07284 -0.07944 -0.00013 > 116 3S 0.00000 -0.00969 -0.00001 -0.00003 0.04258 > 117 3PX 0.00000 0.01483 0.00000 -0.00003 0.02922 > 118 3PY 0.00001 -0.00640 0.00000 0.00001 0.00699 > 119 3PZ -0.12304 -0.00001 -0.11316 -0.12197 -0.00020 > 120 4S -0.00002 0.00460 0.00005 0.00008 0.05411 > 121 4PX 0.00001 0.00771 -0.00002 -0.00004 0.01724 > 122 4PY 0.00001 -0.00624 0.00003 0.00001 0.01256 > 123 4PZ -0.11495 -0.00001 -0.11594 -0.18994 -0.00033 >=20 > 124 5S -0.00009 0.16872 -0.00011 -0.00994 4.64091 > 125 5PX 0.00005 -0.06078 -0.00020 0.00194 -0.77473 >=20 > 126 5PY 0.00014 -0.25334 0.00036 0.00074 0.22739 >=20 > 127 5PZ -0.02468 -0.00005 -0.01066 -0.15953 -0.00042 > 128 6D 0 0.00000 0.00004 0.00000 0.00000 -0.00184 > 129 6D+1 0.01185 0.00000 -0.00198 -0.01019 -0.00002 > 130 6D-1 -0.01584 0.00000 0.00844 0.00961 0.00002 > 131 6D+2 0.00000 0.00150 0.00000 0.00000 -0.00427 > 132 6D-2 0.00000 0.00180 0.00000 0.00001 -0.00663 > 133 7 H 1S 0.00000 0.00276 0.00000 -0.00001 -0.00016 > 134 2S 0.00000 0.00033 -0.00002 -0.00001 -0.01090 > 135 3S 0.00001 -0.00344 -0.00001 0.00012 -0.13711 > 136 4S 0.00003 -0.06299 -0.00001 0.00187 -1.54608 > 137 5PX 0.00000 -0.00055 0.00000 0.00000 -0.00001 > 138 5PY 0.00000 0.00060 0.00000 0.00001 -0.00575 > 139 5PZ -0.01251 0.00000 0.00163 0.00961 0.00002 > 140 8 H 1S 0.00001 -0.00311 0.00000 0.00000 0.00078 > 141 2S 0.00002 0.00008 -0.00001 -0.00001 -0.00098 > 142 3S 0.00002 0.01171 -0.00001 0.00021 -0.15692 > 143 4S 0.00005 -0.02814 -0.00004 0.00174 -1.97399 > 144 5PX 0.00000 0.00049 0.00000 0.00000 0.00052 > 145 5PY 0.00000 0.00042 0.00000 -0.00001 0.01084 > 146 5PZ 0.01269 0.00000 0.00269 0.01163 0.00002 > 147 9 H 1S 0.00000 -0.00582 0.00000 0.00000 -0.00246 > 148 2S 0.00001 -0.01106 0.00000 0.00000 -0.01231 > 149 3S 0.00000 -0.01276 0.00001 0.00008 -0.10144 > 150 4S -0.00004 -0.03749 0.00007 0.00121 -1.35734 > 151 5PX 0.00000 -0.00017 0.00000 0.00000 -0.00629 > 152 5PY 0.00000 -0.00055 0.00000 0.00000 0.00507 > 153 5PZ 0.00639 0.00000 -0.00659 -0.00303 -0.00001 > 154 10 H 1S 0.00000 0.00742 0.00000 0.00000 -0.00369 > 155 2S 0.00000 0.01212 0.00000 0.00000 -0.01105 > 156 3S -0.00001 0.01434 0.00002 0.00005 -0.06846 > 157 4S -0.00004 0.05825 0.00006 0.00002 -0.75096 > 158 5PX 0.00000 0.00023 0.00000 0.00000 -0.00645 > 159 5PY 0.00000 -0.00057 0.00000 0.00000 -0.00321 > 160 5PZ -0.00740 0.00000 -0.00708 -0.01018 -0.00002 > 161 11 N 1S 0.00000 0.01372 -0.00001 0.00003 -0.00782 > 162 2S -0.00001 0.02167 -0.00001 0.00006 -0.01277 > 163 2PX -0.00002 0.04387 -0.00004 0.00005 -0.01666 > 164 2PY 0.00003 -0.02001 0.00003 0.00001 -0.01927 > 165 2PZ -0.09681 0.00000 -0.09374 -0.07140 -0.00005 > 166 3S 0.00002 -0.05881 0.00002 -0.00018 0.04236 > 167 3PX -0.00002 0.06205 -0.00006 0.00007 -0.02270 > 168 3PY 0.00005 -0.02060 0.00004 0.00001 -0.03001 > 169 3PZ -0.14942 0.00001 -0.14256 -0.10704 -0.00008 >=20 > 170 4S 0.00002 -0.25348 0.00023 -0.00037 0.09649 >=20 > 171 4PX -0.00010 0.07780 0.00005 0.00005 -0.05391 > 172 4PY 0.00002 -0.07692 0.00024 -0.00010 0.00907 > 173 4PZ -0.16396 -0.00005 -0.17391 -0.16705 -0.00011 > 174 5S 0.00008 -0.31318 0.00020 -0.00140 0.89693 > 175 5PX -0.00024 -0.09505 0.00045 -0.00043 -0.21030 >=20 > 176 5PY -0.00024 -0.15548 0.00046 0.00029 -0.33094 >=20 > 177 5PZ -0.05292 0.00003 -0.05002 -0.17772 -0.00018 > 178 6D 0 0.00000 -0.00185 0.00000 0.00002 -0.00149 > 179 6D+1 0.00364 0.00000 0.00520 -0.02009 -0.00003 > 180 6D-1 -0.00039 0.00000 -0.00057 0.01129 0.00001 > 181 6D+2 0.00000 0.00150 0.00000 -0.00001 0.00611 > 182 6D-2 0.00000 -0.00183 0.00000 0.00000 0.00022 > 183 12 S 1S 0.00000 0.00290 0.00000 -0.00001 0.00163 > 184 2S 0.00000 0.00837 0.00000 -0.00003 0.00464 > 185 3S 0.00000 -0.01879 -0.00001 0.00006 -0.00998 > 186 4S 0.00000 -0.03107 -0.00001 0.00011 -0.01976 > 187 5S 0.00000 0.06171 0.00001 -0.00029 0.05265 >=20 > 188 6S -0.00006 0.14997 0.00031 0.00004 -0.02952 > 189 7S -0.00086 -0.63601 0.00275 0.00698 -2.70572 >=20 > 190 7PX 0.00011 0.08675 -0.00009 0.00205 -0.38791 > 191 7PY 0.00022 0.16721 -0.00061 -0.00068 0.46445 >=20 > 192 7PZ -0.02854 -0.00013 0.04463 -0.19770 -0.00015 > 193 8PX 0.00000 0.01606 0.00000 -0.00004 0.01283 > 194 8PY -0.00003 0.01951 0.00002 -0.00003 0.00473 > 195 8PZ -0.04816 0.00002 0.04326 0.02805 0.00002 > 196 9PX 0.00000 0.03105 0.00000 -0.00008 0.02428 > 197 9PY -0.00006 0.03729 0.00004 -0.00006 0.00882 > 198 9PZ -0.09209 0.00003 0.08258 0.05304 0.00004 > 199 10PX 0.00000 -0.04744 -0.00001 0.00011 -0.03405 > 200 10PY 0.00008 -0.05379 -0.00005 0.00009 -0.01131 > 201 10PZ 0.13230 -0.00004 -0.11935 -0.07694 -0.00007 > 202 11PX 0.00001 -0.08915 -0.00001 0.00029 -0.09302 >=20 > 203 11PY 0.00018 -0.12713 -0.00019 0.00022 -0.04127 >=20 > 204 11PZ 0.28539 -0.00008 -0.26406 -0.19142 -0.00016 > 205 12PX 0.00005 -0.03524 0.00007 0.00081 -0.22530 > 206 12PY 0.00014 -0.09592 -0.00016 0.00003 0.02799 > 207 12PZ 0.15826 -0.00003 -0.19006 -0.20245 -0.00022 > 208 13D 0 0.00001 0.00601 -0.00001 0.00005 -0.00229 > 209 13D+1 -0.00454 -0.00001 0.00983 -0.02539 -0.00003 > 210 13D-1 -0.00987 -0.00001 0.00459 -0.04352 -0.00003 > 211 13D+2 0.00000 -0.01900 -0.00002 -0.00003 0.01677 > 212 13D-2 0.00000 0.00397 0.00000 0.00003 -0.01970 > 213 13 C 1S 0.00000 -0.00054 0.00001 -0.00007 0.00707 > 214 2S 0.00000 -0.00087 0.00001 -0.00011 0.01133 > 215 2PX 0.00000 0.00412 0.00000 0.00002 -0.01209 > 216 2PY 0.00000 0.00413 0.00000 0.00006 -0.01879 > 217 2PZ 0.00044 0.00001 0.00137 0.19642 0.0002 > 218 3S 0.00000 -0.00105 -0.00002 0.00032 -0.02794 > 219 3PX 0.00000 0.00728 0.00001 0.00004 -0.02614 > 220 3PY 0.00000 0.01138 0.00001 0.00009 -0.03399 > 221 3PZ 0.00049 0.00002 0.00146 0.30948 0.00035 >=20 > 222 4S -0.00002 0.11622 -0.00015 0.00089 -0.17612 > 223 4PX 0.00009 0.10208 -0.00035 0.00019 -0.04885 > 224 4PY 0.00008 -0.15266 -0.00010 0.00015 -0.00317 >=20 > 225 4PZ 0.02778 0.00000 0.02512 0.47540 0.00056 > 226 5S -0.00002 0.24610 -0.00057 -0.00686 2.55118 >=20 > 227 5PX 0.00063 0.06008 -0.00196 -0.00210 0.82602 > 228 5PY 0.00056 0.32064 -0.00117 0.00218 -0.06420 >=20 > 229 5PZ 0.00365 -0.00003 0.00989 0.49364 -0.00012 > 230 6D 0 0.00000 0.00053 0.00000 0.00002 -0.00347 > 231 6D+1 -0.00533 -0.00001 -0.03539 0.00094 0.00000 > 232 6D-1 0.01987 0.00000 -0.00369 0.00682 0.00000 > 233 6D+2 0.00000 -0.01008 0.00002 0.00001 -0.00922 > 234 6D-2 0.00001 0.04164 0.00000 0.00000 0.00012 > 235 14 S 1S 0.00000 -0.00023 0.00000 -0.00001 0.00057 > 236 2S 0.00000 -0.00066 0.00000 -0.00002 0.00160 > 237 3S 0.00000 0.00144 0.00000 0.00004 -0.00315 > 238 4S 0.00000 0.00259 0.00000 0.00008 -0.00798 > 239 5S 0.00000 -0.00662 0.00001 -0.00018 0.02430 > 240 6S 0.00011 0.01941 -0.00027 0.00004 -0.03475 >=20 > 241 7S 0.00088 0.10246 -0.00234 0.00077 0.12869 >=20 > 242 7PX 0.00021 0.01705 -0.00053 0.00011 0.07181 > 243 7PY 0.00000 0.04548 -0.00001 -0.00031 0.05435 > 244 7PZ 0.00797 0.00000 -0.04975 -0.23449 -0.00012 > 245 8PX 0.00000 -0.01267 0.00005 0.00001 0.00038 > 246 8PY 0.00002 0.09670 -0.00002 0.00000 0.00285 > 247 8PZ -0.00531 -0.00001 -0.07103 0.04261 0.00005 > 248 9PX 0.00001 -0.02407 0.00009 0.00003 0.00077 >=20 > 249 9PY 0.00003 0.18538 -0.00003 0.00000 0.00564 >=20 > 250 9PZ -0.01020 -0.00003 -0.13601 0.08045 0.00009 > 251 10PX -0.00001 0.03338 -0.00012 -0.00004 -0.00168 >=20 > 252 10PY -0.00004 -0.26602 0.00004 0.00001 -0.00954 >=20 > 253 10PZ 0.01444 0.00004 0.19208 -0.11091 -0.00012 > 254 11PX 0.00002 0.07699 -0.00034 -0.00006 0.00332 >=20 > 255 11PY -0.00009 -0.53528 0.00009 0.00002 -0.01279 >=20 > 256 11PZ 0.02904 0.00009 0.41149 -0.29074 -0.00033 > 257 12PX 0.00003 0.06051 -0.00024 0.00035 -0.11187 >=20 > 258 12PY -0.00008 -0.36514 0.00009 -0.00007 -0.02518 >=20 > 259 12PZ 0.00517 0.00006 0.25799 -0.27088 -0.00028 > 260 13D 0 0.00000 0.00005 0.00002 0.00006 -0.00304 > 261 13D+1 0.00124 0.00001 0.01518 0.05558 0.00007 > 262 13D-1 0.00295 -0.00001 0.00167 0.00834 0.00001 > 263 13D+2 0.00000 0.00432 -0.00001 -0.00002 0.00215 > 264 13D-2 -0.00001 -0.02106 0.00000 0.00000 -0.00360 > 265 15 H 1S 0.00000 0.00080 0.00001 0.00002 -0.00804 > 266 2S -0.00002 0.01162 0.00008 0.00001 -0.00684 > 267 3S -0.00015 -0.02440 0.00023 0.00024 -0.29261 >=20 > 268 4S 0.00000 0.10929 0.00001 0.00126 -0.61549 >=20 > 269 5PX 0.00000 -0.00083 0.00000 0.00000 -0.00002 > 270 5PY 0.00000 0.00011 0.00001 -0.00002 0.01104 > 271 5PZ -0.00915 0.00000 -0.00861 -0.00943 0.00000 >=20 > Any type of help is highly appreciated. > regards > utpal >=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=_1A51EF67-3C69-4EA8-A3AE-E12862E53435 Content-Transfer-Encoding: quoted-printable Content-Type: text/html; charset=us-ascii
Dear Utpal,

I = would consider relaunching the calculations with some extra keywords to = be able to use a molecular orbital visualizer, as MOLDEN

#P gfinput = gfprint IOP(6/7=3D1)
(source:http://www.cmbi.ru.nl/molden/gauss.html)

Then you will be able to = open the .out with MOLDEN.

Please let me know if this worked for you,
Have a nice day,


Neus = Aguilera-Porta







El 4 gen 2017, a les 11:47, = Utpal Sarkar utpalchemiitkgp]~[gmail.com <owner-chemistry++ccl.net> va escriure:


Sent to CCL by: "Utpal  Sarkar" [utpalchemiitkgp(0)gmail.com]
Dear = Gaussian users,

I am trying to identify the = molecular orbital transition for a particular peak of UV visible = spectrum from Gaussian output. My question is how can I recognize = weather a particular orbital is non bonding n orbital or sigma = orbital?

In my case, I have found for a = particular peak at 237.93 nm with oscillator strength f=3D0.1806 =   and the responsible transitions are

     41 -> 44 =         0.32998
=      41 -> 46 =         0.16625
=      42 -> 45 =        -0.21871
=      42 -> 47 =         0.19689
=      42 -> 48 =         0.29232
=      42 -> 50 =        -0.22757
=      42 -> 52 =        -0.14040
=      43 -> 46 =        -0.12852
=      43 -> 49 =         0.27673


Now I want to identify weather orbital number = 42 is sigma or nonbonding n orbital.


The coefficients of orbital number 42 is given below :


=             &n= bsp;           &nbs= p;41        42 =        43 =        44 =        45
=             &n= bsp;           &nbs= p; O         O =         O =         V =         V

    Eigenvalues -- =    -0.27285  -0.24084  -0.23213  -0.05116 =  -0.04261

  1 1 =   C  1S =          0.00000 =  -0.00420   0.00000   0.00001  -0.00829
  2        2S =          0.00000 =  -0.00653   0.00000   0.00002  -0.01337
  3        2PX =         0.00000  -0.02012 =  -0.00001   0.00001   0.00289
=   4        2PY =        -0.00001  -0.00168 =   0.00000  -0.00002   0.01821
=   5        2PZ =        -0.13793   0.00001 =   0.02323   0.08393   0.00016

  6 =        3S =         -0.00001 =   0.01777   0.00001  -0.00006 =   0.04398
  7 =        3PX =         0.00000  -0.02621 =   0.00000   0.00002  -0.00073

  8        3PY =        -0.00001  -0.00037 =   0.00000  -0.00002   0.02348
=   9        3PZ =        -0.21271   0.00002 =   0.03355   0.12668   0.00024

 10 =        4S =          0.00001 =   0.04010   0.00010  -0.00041 =   0.13704
 11 =        4PX =        -0.00001  -0.03987 =  -0.00012  -0.00001  -0.00228
 12 =        4PY =        -0.00003   0.00962 =   0.00003   0.00003   0.06605
=  13        4PZ =        -0.20444   0.00003 =   0.04608   0.20909   0.00040

 14 =        5S =          0.00115 =  -0.35581   0.00042   0.00562  -2.59840
 15        5PX =        -0.00036   0.37640 =  -0.00053   0.00004  -0.46640

 16        5PY =        -0.00011   0.03293 =   0.00005  -0.00263   1.81287
=  17        5PZ =        -0.00891   0.00007 =  -0.01617   0.11613   0.00054
=  18        6D 0 =        0.00000   0.00022 =   0.00000   0.00000  -0.00167
=  19        6D+1 =       -0.00349   0.00000 =  -0.01518  -0.01160  -0.00002
 20 =        6D-1 =        0.00841   0.00000 =  -0.00111   0.00349   0.00001
=  21        6D+2 =        0.00000  -0.00233 =   0.00000   0.00000   0.00518
=  22        6D-2 =        0.00000   0.00204 =   0.00000   0.00000   0.00069
=  23 2   C  1S =          0.00000 =   0.00418   0.00000   0.00002 =  -0.00937
 24 =        2S =          0.00000 =   0.00682   0.00000   0.00003 =  -0.01539
 25 =        2PX =         0.00001 =   0.02532   0.00000   0.00003 =  -0.01284
 26 =        2PY =        -0.00001  -0.00688 =   0.00001  -0.00001   0.00125
=  27        2PZ =        -0.03567   0.00001 =   0.08391   0.01761  -0.00001
=  28        3S =         -0.00002  -0.01999 =   0.00000  -0.00010   0.05218
=  29        3PX =         0.00002 =   0.04132   0.00001   0.00005 =  -0.02390
 30 =        3PY =        -0.00001  -0.00767 =   0.00002  -0.00002   0.00704
=  31        3PZ =        -0.05659   0.00002 =   0.13408   0.02588  -0.00002
=  32        4S =         -0.00002  -0.03998 =  -0.00006  -0.00023   0.17293
=  33        4PX =        -0.00002   0.05482 =  -0.00005   0.00033  -0.09711
=  34        4PY =         0.00000  -0.07317 =  -0.00016   0.00003  -0.07289
=  35        4PZ =        -0.03986   0.00001 =   0.12373   0.02282  -0.00003

 36        5S =         -0.00032  -0.11569 =  -0.00081  -0.01228   6.78260

 37        5PX =        -0.00042   0.05717 =  -0.00013   0.00494  -1.60116

 38        5PY =        -0.00059   0.44119 =  -0.00063  -0.00072  -1.24950

=  39        5PZ =        -0.02588  -0.00006 =   0.04361   0.17297  -0.00036
=  40        6D 0 =        0.00000   0.00018 =   0.00000   0.00001  -0.00208
=  41        6D+1 =       -0.02147   0.00000 =   0.00844   0.01814   0.00003
=  42        6D-1 =       -0.00727   0.00000 =  -0.01096   0.00789   0.00002
=  43        6D+2 =       -0.00001   0.00459 =   0.00000  -0.00001   0.00141
=  44        6D-2 =        0.00000   0.00783 =   0.00000   0.00000   0.00323
=  45 3   C  1S =          0.00000 =  -0.00250   0.00001   0.00000  -0.00307
 46        2S =         -0.00001  -0.00394 =   0.00001   0.00001  -0.00527
=  47        2PX =         0.00000  -0.02120 =   0.00002   0.00000  -0.00284
=  48        2PY =         0.00001  -0.00889 =  -0.00001   0.00001  -0.00383
=  49        2PZ =         0.04067 =   0.00002   0.07965  -0.05872  -0.00012
 50        3S =          0.00002 =   0.00920  -0.00002  -0.00003   0.02598
 51        3PX =        -0.00001  -0.03375 =   0.00006   0.00000  -0.00496
=  52        3PY =         0.00002  -0.01359 =  -0.00002   0.00002  -0.00541
=  53        3PZ =         0.06382 =   0.00003   0.12680  -0.09881  -0.00020
 54        4S =          0.00020 =   0.01844  -0.00050   0.00003  -0.00626

 55 =        4PX =         0.00001  -0.10072 =   0.00008  -0.00023   0.03817

 56        4PY =        -0.00005  -0.02876 =  -0.00003   0.00013  -0.11338
=  57        4PZ =         0.06310 =   0.00004   0.13146  -0.10786  -0.00029

 58 =        5S =         -0.00091 =   1.35401  -0.00060  -0.00343   1.95224

 59 =        5PX =         0.00011  -0.07907 =  -0.00052  -0.01066   4.45406

 60        5PY =        -0.00021   0.25218 =  -0.00015   0.00362  -2.43405

 61        5PZ =         0.02754 =   0.00003  -0.00041  -0.30749  -0.00068
 62        6D 0 =        0.00000  -0.00126 =   0.00000   0.00001  -0.00313
=  63        6D+1 =        0.02091   0.00000 =   0.01506   0.02310   0.00003
=  64        6D-1 =       -0.00972   0.00000 =   0.00984   0.00010  -0.00001
=  65        6D+2 =        0.00001   0.00092 =   0.00000   0.00001  -0.00749
=  66        6D-2 =        0.00000   0.00700 =  -0.00001   0.00000  -0.00141
=  67 4   C  1S =          0.00000 =   0.00209   0.00000   0.00002 =  -0.01205
 68 =        2S =          0.00000 =   0.00332  -0.00001   0.00003  -0.01967
 69        2PX =         0.00000 =   0.01269  -0.00001   0.00001  -0.00401
 70        2PY =        -0.00001  -0.00223 =   0.00001   0.00002  -0.02944
=  71        2PZ =         0.13807  -0.00001 =   0.03273   0.09279   0.00016
=  72        3S =         -0.00001  -0.01048 =   0.00002  -0.00011   0.07052
=  73        3PX =         0.00001 =   0.01699  -0.00002   0.00003  -0.00983
 74        3PY =        -0.00002  -0.00209 =   0.00001   0.00002  -0.03833
=  75        3PZ =         0.21444  -0.00001 =   0.04852   0.14133   0.00025
=  76        4S =         -0.00007 =   0.03587   0.00010   0.00012 =   0.02042
 77 =        4PX =         0.00005 =   0.01075  -0.00004  -0.00013   0.06745
 78        4PY =        -0.00002   0.03088 =   0.00003   0.00014  -0.08716

 79        4PZ =         0.19966  -0.00001 =   0.05466   0.21749   0.00040

 80 =        5S =          0.00048 =   0.24000   0.00046   0.01370 =  -6.29902
 81 =        5PX =         0.00014 =   0.15294   0.00022  -0.00038 =   0.95984

 82 =        5PY =         0.00016 =   0.03045  -0.00005   0.00288  -2.02375
 83        5PZ =         0.02481  -0.00001 =   0.02389   0.30485   0.00041
=  84        6D 0 =        0.00000  -0.00014 =   0.00000   0.00000  -0.00113
=  85        6D+1 =        0.00307   0.00000 =  -0.01335   0.00485   0.00001
=  86        6D-1 =        0.00725   0.00000 =   0.00326  -0.00480  -0.00001
=  87        6D+2 =        0.00000   0.00252 =   0.00000   0.00000   0.00556
=  88        6D-2 =        0.00000   0.00085 =   0.00000   0.00000  -0.00282
=  89 5   C  1S =          0.00000 =  -0.00128   0.00000   0.00000  -0.00810
 90        2S =          0.00000 =  -0.00204   0.00000   0.00001  -0.01317
 91        2PX =         0.00000  -0.00832 =   0.00001  -0.00002   0.02313
=  92        2PY =         0.00000  -0.00240 =   0.00001   0.00000  -0.01084
=  93        2PZ =         0.06902  -0.00002 =  -0.06649  -0.02215  -0.00004
 94 =        3S =         -0.00001 =   0.00606   0.00000  -0.00002 =   0.04591
 95 =        3PX =         0.00000  -0.01115 =   0.00001  -0.00003   0.03168
=  96        3PY =        -0.00001  -0.00283 =   0.00001   0.00001  -0.01523
=  97        3PZ =         0.10653  -0.00003 =  -0.10344  -0.03512  -0.00007
 98 =        4S =          0.00000 =  -0.01037  -0.00002  -0.00007   0.04618
 99        4PX =         0.00000 =   0.00126   0.00003  -0.00004 =   0.05818
100 =        4PY =         0.00002  -0.00822 =   0.00000  -0.00002  -0.01083
101 =        4PZ =         0.09937  -0.00003 =  -0.10252  -0.04632  -0.00010

= 102        5S =         -0.00035  -0.82701 =   0.00051   0.00144   0.52163
= 103        5PX =         0.00017 =   0.10769   0.00005  -0.00063 =   0.66730

104 =        5PY =         0.00005  -0.08692 =   0.00039   0.00162  -0.24277
= 105        5PZ =         0.01608 =   0.00001  -0.03265  -0.08881  -0.00014
106        6D 0 =        0.00000  -0.00007 =   0.00000   0.00000  -0.00241
= 107        6D+1 =       -0.01473   0.00000 =  -0.00471  -0.01392  -0.00002
108 =        6D-1 =       -0.01513   0.00000 =  -0.00919  -0.01697  -0.00003
109 =        6D+2 =        0.00000  -0.00040 =   0.00000   0.00000  -0.00226
= 110        6D-2 =        0.00000   0.00182 =   0.00000  -0.00001   0.00809
= 111 6   C  1S =          0.00000 =   0.00206   0.00000   0.00001 =  -0.00756
112 =        2S =          0.00000 =   0.00328   0.00000   0.00001 =  -0.01224
113 =        2PX =         0.00000 =   0.01042   0.00000  -0.00002 =   0.01938
114 =        2PY =         0.00000  -0.00458 =   0.00000   0.00000   0.00515
= 115        2PZ =        -0.08000  -0.00001 =  -0.07284  -0.07944  -0.00013
116 =        3S =          0.00000 =  -0.00969  -0.00001  -0.00003   0.04258
117        3PX =         0.00000 =   0.01483   0.00000  -0.00003 =   0.02922
118 =        3PY =         0.00001  -0.00640 =   0.00000   0.00001   0.00699
= 119        3PZ =        -0.12304  -0.00001 =  -0.11316  -0.12197  -0.00020
120 =        4S =         -0.00002 =   0.00460   0.00005   0.00008 =   0.05411
121 =        4PX =         0.00001 =   0.00771  -0.00002  -0.00004   0.01724
122        4PY =         0.00001  -0.00624 =   0.00003   0.00001   0.01256
= 123        4PZ =        -0.11495  -0.00001 =  -0.11594  -0.18994  -0.00033

= 124        5S =         -0.00009 =   0.16872  -0.00011  -0.00994   4.64091
125        5PX =         0.00005  -0.06078 =  -0.00020   0.00194  -0.77473

126        5PY =         0.00014  -0.25334 =   0.00036   0.00074   0.22739

127 =        5PZ =        -0.02468  -0.00005 =  -0.01066  -0.15953  -0.00042
128 =        6D 0 =        0.00000   0.00004 =   0.00000   0.00000  -0.00184
= 129        6D+1 =        0.01185   0.00000 =  -0.00198  -0.01019  -0.00002
130 =        6D-1 =       -0.01584   0.00000 =   0.00844   0.00961   0.00002
= 131        6D+2 =        0.00000   0.00150 =   0.00000   0.00000  -0.00427
= 132        6D-2 =        0.00000   0.00180 =   0.00000   0.00001  -0.00663
= 133 7   H  1S =          0.00000 =   0.00276   0.00000  -0.00001  -0.00016
134        2S =          0.00000 =   0.00033  -0.00002  -0.00001  -0.01090
135        3S =          0.00001 =  -0.00344  -0.00001   0.00012  -0.13711
136        4S =          0.00003 =  -0.06299  -0.00001   0.00187  -1.54608
137        5PX =         0.00000  -0.00055 =   0.00000   0.00000  -0.00001
= 138        5PY =         0.00000 =   0.00060   0.00000   0.00001 =  -0.00575
139 =        5PZ =        -0.01251   0.00000 =   0.00163   0.00961   0.00002
= 140 8   H  1S =          0.00001 =  -0.00311   0.00000   0.00000 =   0.00078
141 =        2S =          0.00002 =   0.00008  -0.00001  -0.00001  -0.00098
142        3S =          0.00002 =   0.01171  -0.00001   0.00021  -0.15692
143        4S =          0.00005 =  -0.02814  -0.00004   0.00174  -1.97399
144        5PX =         0.00000 =   0.00049   0.00000   0.00000 =   0.00052
145 =        5PY =         0.00000 =   0.00042   0.00000  -0.00001 =   0.01084
146 =        5PZ =         0.01269 =   0.00000   0.00269   0.01163 =   0.00002
147 9   H  1S =          0.00000 =  -0.00582   0.00000   0.00000  -0.00246
148        2S =          0.00001 =  -0.01106   0.00000   0.00000  -0.01231
149        3S =          0.00000 =  -0.01276   0.00001   0.00008  -0.10144
150        4S =         -0.00004  -0.03749 =   0.00007   0.00121  -1.35734
= 151        5PX =         0.00000  -0.00017 =   0.00000   0.00000  -0.00629
= 152        5PY =         0.00000  -0.00055 =   0.00000   0.00000   0.00507
= 153        5PZ =         0.00639 =   0.00000  -0.00659  -0.00303  -0.00001
154 10  H  1S =          0.00000 =   0.00742   0.00000   0.00000 =  -0.00369
155 =        2S =          0.00000 =   0.01212   0.00000   0.00000 =  -0.01105
156 =        3S =         -0.00001 =   0.01434   0.00002   0.00005 =  -0.06846
157 =        4S =         -0.00004 =   0.05825   0.00006   0.00002 =  -0.75096
158 =        5PX =         0.00000 =   0.00023   0.00000   0.00000 =  -0.00645
159 =        5PY =         0.00000  -0.00057 =   0.00000   0.00000  -0.00321
= 160        5PZ =        -0.00740   0.00000 =  -0.00708  -0.01018  -0.00002
161 11 =  N  1S =          0.00000 =   0.01372  -0.00001   0.00003  -0.00782
162        2S =         -0.00001 =   0.02167  -0.00001   0.00006  -0.01277
163        2PX =        -0.00002   0.04387 =  -0.00004   0.00005  -0.01666
164 =        2PY =         0.00003  -0.02001 =   0.00003   0.00001  -0.01927
= 165        2PZ =        -0.09681   0.00000 =  -0.09374  -0.07140  -0.00005
166 =        3S =          0.00002 =  -0.05881   0.00002  -0.00018   0.04236
167        3PX =        -0.00002   0.06205 =  -0.00006   0.00007  -0.02270
168 =        3PY =         0.00005  -0.02060 =   0.00004   0.00001  -0.03001
= 169        3PZ =        -0.14942   0.00001 =  -0.14256  -0.10704  -0.00008

= 170        4S =          0.00002 =  -0.25348   0.00023  -0.00037   0.09649

171 =        4PX =        -0.00010   0.07780 =   0.00005   0.00005  -0.05391
= 172        4PY =         0.00002  -0.07692 =   0.00024  -0.00010   0.00907
= 173        4PZ =        -0.16396  -0.00005 =  -0.17391  -0.16705  -0.00011
174 =        5S =          0.00008 =  -0.31318   0.00020  -0.00140   0.89693
175        5PX =        -0.00024  -0.09505 =   0.00045  -0.00043  -0.21030

176        5PY =        -0.00024  -0.15548 =   0.00046   0.00029  -0.33094

177        5PZ =        -0.05292   0.00003 =  -0.05002  -0.17772  -0.00018
178 =        6D 0 =        0.00000  -0.00185 =   0.00000   0.00002  -0.00149
= 179        6D+1 =        0.00364   0.00000 =   0.00520  -0.02009  -0.00003
180 =        6D-1 =       -0.00039   0.00000 =  -0.00057   0.01129   0.00001
= 181        6D+2 =        0.00000   0.00150 =   0.00000  -0.00001   0.00611
= 182        6D-2 =        0.00000  -0.00183 =   0.00000   0.00000   0.00022
= 183 12  S  1S =          0.00000 =   0.00290   0.00000  -0.00001 =   0.00163
184 =        2S =          0.00000 =   0.00837   0.00000  -0.00003 =   0.00464
185 =        3S =          0.00000 =  -0.01879  -0.00001   0.00006  -0.00998
186        4S =          0.00000 =  -0.03107  -0.00001   0.00011  -0.01976
187        5S =          0.00000 =   0.06171   0.00001  -0.00029 =   0.05265

188 =        6S =         -0.00006 =   0.14997   0.00031   0.00004 =  -0.02952
189 =        7S =         -0.00086  -0.63601 =   0.00275   0.00698  -2.70572

190        7PX =         0.00011 =   0.08675  -0.00009   0.00205  -0.38791
191        7PY =         0.00022 =   0.16721  -0.00061  -0.00068   0.46445

192 =        7PZ =        -0.02854  -0.00013 =   0.04463  -0.19770  -0.00015
193 =        8PX =         0.00000 =   0.01606   0.00000  -0.00004 =   0.01283
194 =        8PY =        -0.00003   0.01951 =   0.00002  -0.00003   0.00473
= 195        8PZ =        -0.04816   0.00002 =   0.04326   0.02805   0.00002
= 196        9PX =         0.00000 =   0.03105   0.00000  -0.00008 =   0.02428
197 =        9PY =        -0.00006   0.03729 =   0.00004  -0.00006   0.00882
= 198        9PZ =        -0.09209   0.00003 =   0.08258   0.05304   0.00004
= 199       10PX =         0.00000  -0.04744 =  -0.00001   0.00011  -0.03405
200 =       10PY =         0.00008  -0.05379 =  -0.00005   0.00009  -0.01131
201 =       10PZ =         0.13230  -0.00004 =  -0.11935  -0.07694  -0.00007
202 =       11PX =         0.00001  -0.08915 =  -0.00001   0.00029  -0.09302

203       11PY =         0.00018  -0.12713 =  -0.00019   0.00022  -0.04127

204       11PZ =         0.28539  -0.00008 =  -0.26406  -0.19142  -0.00016
205 =       12PX =         0.00005  -0.03524 =   0.00007   0.00081  -0.22530
= 206       12PY =         0.00014  -0.09592 =  -0.00016   0.00003   0.02799
= 207       12PZ =         0.15826  -0.00003 =  -0.19006  -0.20245  -0.00022
208 =       13D 0 =        0.00001   0.00601 =  -0.00001   0.00005  -0.00229
209 =       13D+1 =       -0.00454  -0.00001 =   0.00983  -0.02539  -0.00003
210 =       13D-1 =       -0.00987  -0.00001 =   0.00459  -0.04352  -0.00003
211 =       13D+2 =        0.00000  -0.01900 =  -0.00002  -0.00003   0.01677
212 =       13D-2 =        0.00000   0.00397 =   0.00000   0.00003  -0.01970
= 213 13  C  1S =          0.00000 =  -0.00054   0.00001  -0.00007   0.00707
214        2S =          0.00000 =  -0.00087   0.00001  -0.00011   0.01133
215        2PX =         0.00000 =   0.00412   0.00000   0.00002 =  -0.01209
216 =        2PY =         0.00000 =   0.00413   0.00000   0.00006 =  -0.01879
217 =        2PZ =         0.00044 =   0.00001   0.00137   0.19642 =   0.0002
218 =        3S =          0.00000 =  -0.00105  -0.00002   0.00032  -0.02794
219        3PX =         0.00000 =   0.00728   0.00001   0.00004 =  -0.02614
220 =        3PY =         0.00000 =   0.01138   0.00001   0.00009 =  -0.03399
221 =        3PZ =         0.00049 =   0.00002   0.00146   0.30948 =   0.00035

222 =        4S =         -0.00002 =   0.11622  -0.00015   0.00089  -0.17612
223        4PX =         0.00009 =   0.10208  -0.00035   0.00019  -0.04885
224        4PY =         0.00008  -0.15266 =  -0.00010   0.00015  -0.00317

225        4PZ =         0.02778 =   0.00000   0.02512   0.47540 =   0.00056
226 =        5S =         -0.00002 =   0.24610  -0.00057  -0.00686   2.55118

227 =        5PX =         0.00063 =   0.06008  -0.00196  -0.00210   0.82602
228        5PY =         0.00056 =   0.32064  -0.00117   0.00218  -0.06420

229 =        5PZ =         0.00365  -0.00003 =   0.00989   0.49364  -0.00012
= 230        6D 0 =        0.00000   0.00053 =   0.00000   0.00002  -0.00347
= 231        6D+1 =       -0.00533  -0.00001 =  -0.03539   0.00094   0.00000
= 232        6D-1 =        0.01987   0.00000 =  -0.00369   0.00682   0.00000
= 233        6D+2 =        0.00000  -0.01008 =   0.00002   0.00001  -0.00922
= 234        6D-2 =        0.00001   0.04164 =   0.00000   0.00000   0.00012
= 235 14  S  1S =          0.00000 =  -0.00023   0.00000  -0.00001   0.00057
236        2S =          0.00000 =  -0.00066   0.00000  -0.00002   0.00160
237        3S =          0.00000 =   0.00144   0.00000   0.00004 =  -0.00315
238 =        4S =          0.00000 =   0.00259   0.00000   0.00008 =  -0.00798
239 =        5S =          0.00000 =  -0.00662   0.00001  -0.00018   0.02430
240        6S =          0.00011 =   0.01941  -0.00027   0.00004  -0.03475

241 =        7S =          0.00088 =   0.10246  -0.00234   0.00077 =   0.12869

242 =        7PX =         0.00021 =   0.01705  -0.00053   0.00011 =   0.07181
243 =        7PY =         0.00000 =   0.04548  -0.00001  -0.00031   0.05435
244        7PZ =         0.00797 =   0.00000  -0.04975  -0.23449  -0.00012
245        8PX =         0.00000  -0.01267 =   0.00005   0.00001   0.00038
= 246        8PY =         0.00002 =   0.09670  -0.00002   0.00000 =   0.00285
247 =        8PZ =        -0.00531  -0.00001 =  -0.07103   0.04261   0.00005
= 248        9PX =         0.00001  -0.02407 =   0.00009   0.00003   0.00077

249 =        9PY =         0.00003 =   0.18538  -0.00003   0.00000 =   0.00564

250 =        9PZ =        -0.01020  -0.00003 =  -0.13601   0.08045   0.00009
= 251       10PX =        -0.00001   0.03338 =  -0.00012  -0.00004  -0.00168

= 252       10PY =        -0.00004  -0.26602 =   0.00004   0.00001  -0.00954

253       10PZ =         0.01444 =   0.00004   0.19208  -0.11091  -0.00012
254       11PX =         0.00002 =   0.07699  -0.00034  -0.00006   0.00332

255       11PY =        -0.00009  -0.53528 =   0.00009   0.00002  -0.01279

256       11PZ =         0.02904 =   0.00009   0.41149  -0.29074  -0.00033
257       12PX =         0.00003 =   0.06051  -0.00024   0.00035  -0.11187

258       12PY =        -0.00008  -0.36514 =   0.00009  -0.00007  -0.02518

259       12PZ =         0.00517 =   0.00006   0.25799  -0.27088  -0.00028
260       13D 0 =        0.00000   0.00005 =   0.00002   0.00006  -0.00304
= 261       13D+1 =        0.00124   0.00001 =   0.01518   0.05558   0.00007
= 262       13D-1 =        0.00295  -0.00001 =   0.00167   0.00834   0.00001
= 263       13D+2 =        0.00000   0.00432 =  -0.00001  -0.00002   0.00215
264 =       13D-2 =       -0.00001  -0.02106 =   0.00000   0.00000  -0.00360
= 265 15  H  1S =          0.00000 =   0.00080   0.00001   0.00002 =  -0.00804
266 =        2S =         -0.00002 =   0.01162   0.00008   0.00001 =  -0.00684
267 =        3S =         -0.00015  -0.02440 =   0.00023   0.00024  -0.29261

268        4S =          0.00000 =   0.10929   0.00001   0.00126 =  -0.61549

269 =        5PX =         0.00000  -0.00083 =   0.00000   0.00000  -0.00002
= 270        5PY =         0.00000 =   0.00011   0.00001  -0.00002 =   0.01104
271 =        5PZ =        -0.00915   0.00000 =  -0.00861  -0.00943   0.00000

Any type of help is highly appreciated.
regards
utpal



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= --Apple-Mail=_1A51EF67-3C69-4EA8-A3AE-E12862E53435-- From owner-chemistry@ccl.net Thu Jan 5 12:32:01 2017 From: "Anuj Tripathi tranuj%a%gmail.com" To: CCL Subject: CCL: query Message-Id: <-52586-170105104527-30281-SmfhNwi/Ma9GmfntPqeQhg]_[server.ccl.net> X-Original-From: "Anuj Tripathi" Date: Thu, 5 Jan 2017 10:45:26 -0500 Sent to CCL by: "Anuj Tripathi" [tranuj*gmail.com] which are the best functionals for H-bonding and charge transfer? From owner-chemistry@ccl.net Thu Jan 5 14:08:01 2017 From: "Igors Mihailovs igorsm*o*cfi.lu.lv" To: CCL Subject: CCL:G: Understading the nature of molecular orbital (non bonding or sigma) Message-Id: <-52587-170105131814-2454-SUS4YwTzjYDAT42n+ksySQ[A]server.ccl.net> X-Original-From: Igors Mihailovs Content-Type: multipart/alternative; boundary="------------45FB059704A67A6E497FEE81" Date: Thu, 5 Jan 2017 20:18:40 +0200 MIME-Version: 1.0 Sent to CCL by: Igors Mihailovs [igorsm.#,#.cfi.lu.lv] This is a multi-part message in MIME format. --------------45FB059704A67A6E497FEE81 Content-Type: text/plain; charset=UTF-8; format=flowed Content-Transfer-Encoding: 8bit Dear Utpal, If the problem was that answered by Neus, then you should probably use formatted checkpoint file which you can generate from the checkpoint (.chk) of the calculation you already have (no need to rerun) by the *formchk* command. The .fchk (or .fch) file can be opened by all of commonly used molecular visualizers (e.g., Avogadro or Gabedit). But to me, it appears that your transition is quite of mixed character. Wouldn't it be better to calculate and later visualize Natural Transition Orbitals? See Gaussian reference for their description. For example, if Your excited state calculation was done with checkpoint file //home/igors/darba/IN18_438_TPSSh_6311_tolu.chk/, and You are interested in the 3rd transition, you can run the following job: /%OldChk=/home/igors/darba/IN18_438_TPSSh_6311_tolu.chk// //%Chk=/home/igors/darba/IN18_438_TPSSh_6311_tolu_S3.chk// // //# TPSSh/6-311G(d,p) Guess=(Only,Read) Geom=Check Density=(Check,Transition=3) Pop=SaveNTO// // //Natural Transition Orbitals job example// // //0 1/ (end of file) And then run in console or command prompt the following: $> formchk /home/igors/darba/IN18_438_TPSSh_6311_tolu_S3.chk With best regards, Igors Mihailovs ISSP University of Latvia/ Riga Technical University On 05/01/17 11:32, Neus Aguilera neusaguilera,+,yahoo.com wrote: > Dear Utpal, > > I would consider relaunching the calculations with some extra keywords > to be able to use a molecular orbital visualizer, as MOLDEN > > *#P gfinput gfprint IOP(6/7=1)* > (source:http://www.cmbi.ru.nl/molden/gauss.html) > > Then you will be able to open the .out with MOLDEN. > > Please let me know if this worked for you, > Have a nice day, > > > Neus Aguilera-Porta > > > > > > > >> El 4 gen 2017, a les 11:47, Utpal Sarkar utpalchemiitkgp]~[gmail.com >> > > va escriure: >> >> >> Sent to CCL by: "Utpal Sarkar" [utpalchemiitkgp(0)gmail.com >> ] >> Dear Gaussian users, >> >> I am trying to identify the molecular orbital transition for a >> particular peak of UV visible spectrum from Gaussian output. My >> question is how can I recognize weather a particular orbital is non >> bonding n orbital or sigma orbital? >> >> In my case, I have found for a particular peak at 237.93 nm with >> oscillator strength f=0.1806 and the responsible transitions are >> >> 41 -> 44 0.32998 >> 41 -> 46 0.16625 >> 42 -> 45 -0.21871 >> 42 -> 47 0.19689 >> 42 -> 48 0.29232 >> 42 -> 50 -0.22757 >> 42 -> 52 -0.14040 >> 43 -> 46 -0.12852 >> 43 -> 49 0.27673 >> >> >> Now I want to identify weather orbital number 42 is sigma or >> nonbonding n orbital. >> >> >> The coefficients of orbital number 42 is given below : >> >> >> 41 42 43 44 45 >> O O O V V >> >> Eigenvalues -- -0.27285 -0.24084 -0.23213 -0.05116 -0.04261 >> >> 1 1 C 1S 0.00000 -0.00420 0.00000 0.00001 -0.00829 >> 2 2S 0.00000 -0.00653 0.00000 0.00002 -0.01337 >> 3 2PX 0.00000 -0.02012 -0.00001 0.00001 0.00289 >> 4 2PY -0.00001 -0.00168 0.00000 -0.00002 0.01821 >> 5 2PZ -0.13793 0.00001 0.02323 0.08393 0.00016 >> >> 6 3S -0.00001 0.01777 0.00001 -0.00006 0.04398 >> 7 3PX 0.00000 -0.02621 0.00000 0.00002 -0.00073 >> >> 8 3PY -0.00001 -0.00037 0.00000 -0.00002 0.02348 >> 9 3PZ -0.21271 0.00002 0.03355 0.12668 0.00024 >> >> 10 4S 0.00001 0.04010 0.00010 -0.00041 0.13704 >> 11 4PX -0.00001 -0.03987 -0.00012 -0.00001 -0.00228 >> 12 4PY -0.00003 0.00962 0.00003 0.00003 0.06605 >> 13 4PZ -0.20444 0.00003 0.04608 0.20909 0.00040 >> >> 14 5S 0.00115 -0.35581 0.00042 0.00562 -2.59840 >> 15 5PX -0.00036 0.37640 -0.00053 0.00004 -0.46640 >> >> 16 5PY -0.00011 0.03293 0.00005 -0.00263 1.81287 >> 17 5PZ -0.00891 0.00007 -0.01617 0.11613 0.00054 >> 18 6D 0 0.00000 0.00022 0.00000 0.00000 -0.00167 >> 19 6D+1 -0.00349 0.00000 -0.01518 -0.01160 -0.00002 >> 20 6D-1 0.00841 0.00000 -0.00111 0.00349 0.00001 >> 21 6D+2 0.00000 -0.00233 0.00000 0.00000 0.00518 >> 22 6D-2 0.00000 0.00204 0.00000 0.00000 0.00069 >> 23 2 C 1S 0.00000 0.00418 0.00000 0.00002 -0.00937 >> 24 2S 0.00000 0.00682 0.00000 0.00003 -0.01539 >> 25 2PX 0.00001 0.02532 0.00000 0.00003 -0.01284 >> 26 2PY -0.00001 -0.00688 0.00001 -0.00001 0.00125 >> 27 2PZ -0.03567 0.00001 0.08391 0.01761 -0.00001 >> 28 3S -0.00002 -0.01999 0.00000 -0.00010 0.05218 >> 29 3PX 0.00002 0.04132 0.00001 0.00005 -0.02390 >> 30 3PY -0.00001 -0.00767 0.00002 -0.00002 0.00704 >> 31 3PZ -0.05659 0.00002 0.13408 0.02588 -0.00002 >> 32 4S -0.00002 -0.03998 -0.00006 -0.00023 0.17293 >> 33 4PX -0.00002 0.05482 -0.00005 0.00033 -0.09711 >> 34 4PY 0.00000 -0.07317 -0.00016 0.00003 -0.07289 >> 35 4PZ -0.03986 0.00001 0.12373 0.02282 -0.00003 >> >> 36 5S -0.00032 -0.11569 -0.00081 -0.01228 6.78260 >> >> 37 5PX -0.00042 0.05717 -0.00013 0.00494 -1.60116 >> >> 38 5PY -0.00059 0.44119 -0.00063 -0.00072 -1.24950 >> >> 39 5PZ -0.02588 -0.00006 0.04361 0.17297 -0.00036 >> 40 6D 0 0.00000 0.00018 0.00000 0.00001 -0.00208 >> 41 6D+1 -0.02147 0.00000 0.00844 0.01814 0.00003 >> 42 6D-1 -0.00727 0.00000 -0.01096 0.00789 0.00002 >> 43 6D+2 -0.00001 0.00459 0.00000 -0.00001 0.00141 >> 44 6D-2 0.00000 0.00783 0.00000 0.00000 0.00323 >> 45 3 C 1S 0.00000 -0.00250 0.00001 0.00000 -0.00307 >> 46 2S -0.00001 -0.00394 0.00001 0.00001 -0.00527 >> 47 2PX 0.00000 -0.02120 0.00002 0.00000 -0.00284 >> 48 2PY 0.00001 -0.00889 -0.00001 0.00001 -0.00383 >> 49 2PZ 0.04067 0.00002 0.07965 -0.05872 -0.00012 >> 50 3S 0.00002 0.00920 -0.00002 -0.00003 0.02598 >> 51 3PX -0.00001 -0.03375 0.00006 0.00000 -0.00496 >> 52 3PY 0.00002 -0.01359 -0.00002 0.00002 -0.00541 >> 53 3PZ 0.06382 0.00003 0.12680 -0.09881 -0.00020 >> 54 4S 0.00020 0.01844 -0.00050 0.00003 -0.00626 >> >> 55 4PX 0.00001 -0.10072 0.00008 -0.00023 0.03817 >> >> 56 4PY -0.00005 -0.02876 -0.00003 0.00013 -0.11338 >> 57 4PZ 0.06310 0.00004 0.13146 -0.10786 -0.00029 >> >> 58 5S -0.00091 1.35401 -0.00060 -0.00343 1.95224 >> >> 59 5PX 0.00011 -0.07907 -0.00052 -0.01066 4.45406 >> >> 60 5PY -0.00021 0.25218 -0.00015 0.00362 -2.43405 >> >> 61 5PZ 0.02754 0.00003 -0.00041 -0.30749 -0.00068 >> 62 6D 0 0.00000 -0.00126 0.00000 0.00001 -0.00313 >> 63 6D+1 0.02091 0.00000 0.01506 0.02310 0.00003 >> 64 6D-1 -0.00972 0.00000 0.00984 0.00010 -0.00001 >> 65 6D+2 0.00001 0.00092 0.00000 0.00001 -0.00749 >> 66 6D-2 0.00000 0.00700 -0.00001 0.00000 -0.00141 >> 67 4 C 1S 0.00000 0.00209 0.00000 0.00002 -0.01205 >> 68 2S 0.00000 0.00332 -0.00001 0.00003 -0.01967 >> 69 2PX 0.00000 0.01269 -0.00001 0.00001 -0.00401 >> 70 2PY -0.00001 -0.00223 0.00001 0.00002 -0.02944 >> 71 2PZ 0.13807 -0.00001 0.03273 0.09279 0.00016 >> 72 3S -0.00001 -0.01048 0.00002 -0.00011 0.07052 >> 73 3PX 0.00001 0.01699 -0.00002 0.00003 -0.00983 >> 74 3PY -0.00002 -0.00209 0.00001 0.00002 -0.03833 >> 75 3PZ 0.21444 -0.00001 0.04852 0.14133 0.00025 >> 76 4S -0.00007 0.03587 0.00010 0.00012 0.02042 >> 77 4PX 0.00005 0.01075 -0.00004 -0.00013 0.06745 >> 78 4PY -0.00002 0.03088 0.00003 0.00014 -0.08716 >> >> 79 4PZ 0.19966 -0.00001 0.05466 0.21749 0.00040 >> >> 80 5S 0.00048 0.24000 0.00046 0.01370 -6.29902 >> 81 5PX 0.00014 0.15294 0.00022 -0.00038 0.95984 >> >> 82 5PY 0.00016 0.03045 -0.00005 0.00288 -2.02375 >> 83 5PZ 0.02481 -0.00001 0.02389 0.30485 0.00041 >> 84 6D 0 0.00000 -0.00014 0.00000 0.00000 -0.00113 >> 85 6D+1 0.00307 0.00000 -0.01335 0.00485 0.00001 >> 86 6D-1 0.00725 0.00000 0.00326 -0.00480 -0.00001 >> 87 6D+2 0.00000 0.00252 0.00000 0.00000 0.00556 >> 88 6D-2 0.00000 0.00085 0.00000 0.00000 -0.00282 >> 89 5 C 1S 0.00000 -0.00128 0.00000 0.00000 -0.00810 >> 90 2S 0.00000 -0.00204 0.00000 0.00001 -0.01317 >> 91 2PX 0.00000 -0.00832 0.00001 -0.00002 0.02313 >> 92 2PY 0.00000 -0.00240 0.00001 0.00000 -0.01084 >> 93 2PZ 0.06902 -0.00002 -0.06649 -0.02215 -0.00004 >> 94 3S -0.00001 0.00606 0.00000 -0.00002 0.04591 >> 95 3PX 0.00000 -0.01115 0.00001 -0.00003 0.03168 >> 96 3PY -0.00001 -0.00283 0.00001 0.00001 -0.01523 >> 97 3PZ 0.10653 -0.00003 -0.10344 -0.03512 -0.00007 >> 98 4S 0.00000 -0.01037 -0.00002 -0.00007 0.04618 >> 99 4PX 0.00000 0.00126 0.00003 -0.00004 0.05818 >> 100 4PY 0.00002 -0.00822 0.00000 -0.00002 -0.01083 >> 101 4PZ 0.09937 -0.00003 -0.10252 -0.04632 -0.00010 >> >> 102 5S -0.00035 -0.82701 0.00051 0.00144 0.52163 >> 103 5PX 0.00017 0.10769 0.00005 -0.00063 0.66730 >> >> 104 5PY 0.00005 -0.08692 0.00039 0.00162 -0.24277 >> 105 5PZ 0.01608 0.00001 -0.03265 -0.08881 -0.00014 >> 106 6D 0 0.00000 -0.00007 0.00000 0.00000 -0.00241 >> 107 6D+1 -0.01473 0.00000 -0.00471 -0.01392 -0.00002 >> 108 6D-1 -0.01513 0.00000 -0.00919 -0.01697 -0.00003 >> 109 6D+2 0.00000 -0.00040 0.00000 0.00000 -0.00226 >> 110 6D-2 0.00000 0.00182 0.00000 -0.00001 0.00809 >> 111 6 C 1S 0.00000 0.00206 0.00000 0.00001 -0.00756 >> 112 2S 0.00000 0.00328 0.00000 0.00001 -0.01224 >> 113 2PX 0.00000 0.01042 0.00000 -0.00002 0.01938 >> 114 2PY 0.00000 -0.00458 0.00000 0.00000 0.00515 >> 115 2PZ -0.08000 -0.00001 -0.07284 -0.07944 -0.00013 >> 116 3S 0.00000 -0.00969 -0.00001 -0.00003 0.04258 >> 117 3PX 0.00000 0.01483 0.00000 -0.00003 0.02922 >> 118 3PY 0.00001 -0.00640 0.00000 0.00001 0.00699 >> 119 3PZ -0.12304 -0.00001 -0.11316 -0.12197 -0.00020 >> 120 4S -0.00002 0.00460 0.00005 0.00008 0.05411 >> 121 4PX 0.00001 0.00771 -0.00002 -0.00004 0.01724 >> 122 4PY 0.00001 -0.00624 0.00003 0.00001 0.01256 >> 123 4PZ -0.11495 -0.00001 -0.11594 -0.18994 -0.00033 >> >> 124 5S -0.00009 0.16872 -0.00011 -0.00994 4.64091 >> 125 5PX 0.00005 -0.06078 -0.00020 0.00194 -0.77473 >> >> 126 5PY 0.00014 -0.25334 0.00036 0.00074 0.22739 >> >> 127 5PZ -0.02468 -0.00005 -0.01066 -0.15953 -0.00042 >> 128 6D 0 0.00000 0.00004 0.00000 0.00000 -0.00184 >> 129 6D+1 0.01185 0.00000 -0.00198 -0.01019 -0.00002 >> 130 6D-1 -0.01584 0.00000 0.00844 0.00961 0.00002 >> 131 6D+2 0.00000 0.00150 0.00000 0.00000 -0.00427 >> 132 6D-2 0.00000 0.00180 0.00000 0.00001 -0.00663 >> 133 7 H 1S 0.00000 0.00276 0.00000 -0.00001 -0.00016 >> 134 2S 0.00000 0.00033 -0.00002 -0.00001 -0.01090 >> 135 3S 0.00001 -0.00344 -0.00001 0.00012 -0.13711 >> 136 4S 0.00003 -0.06299 -0.00001 0.00187 -1.54608 >> 137 5PX 0.00000 -0.00055 0.00000 0.00000 -0.00001 >> 138 5PY 0.00000 0.00060 0.00000 0.00001 -0.00575 >> 139 5PZ -0.01251 0.00000 0.00163 0.00961 0.00002 >> 140 8 H 1S 0.00001 -0.00311 0.00000 0.00000 0.00078 >> 141 2S 0.00002 0.00008 -0.00001 -0.00001 -0.00098 >> 142 3S 0.00002 0.01171 -0.00001 0.00021 -0.15692 >> 143 4S 0.00005 -0.02814 -0.00004 0.00174 -1.97399 >> 144 5PX 0.00000 0.00049 0.00000 0.00000 0.00052 >> 145 5PY 0.00000 0.00042 0.00000 -0.00001 0.01084 >> 146 5PZ 0.01269 0.00000 0.00269 0.01163 0.00002 >> 147 9 H 1S 0.00000 -0.00582 0.00000 0.00000 -0.00246 >> 148 2S 0.00001 -0.01106 0.00000 0.00000 -0.01231 >> 149 3S 0.00000 -0.01276 0.00001 0.00008 -0.10144 >> 150 4S -0.00004 -0.03749 0.00007 0.00121 -1.35734 >> 151 5PX 0.00000 -0.00017 0.00000 0.00000 -0.00629 >> 152 5PY 0.00000 -0.00055 0.00000 0.00000 0.00507 >> 153 5PZ 0.00639 0.00000 -0.00659 -0.00303 -0.00001 >> 154 10 H 1S 0.00000 0.00742 0.00000 0.00000 -0.00369 >> 155 2S 0.00000 0.01212 0.00000 0.00000 -0.01105 >> 156 3S -0.00001 0.01434 0.00002 0.00005 -0.06846 >> 157 4S -0.00004 0.05825 0.00006 0.00002 -0.75096 >> 158 5PX 0.00000 0.00023 0.00000 0.00000 -0.00645 >> 159 5PY 0.00000 -0.00057 0.00000 0.00000 -0.00321 >> 160 5PZ -0.00740 0.00000 -0.00708 -0.01018 -0.00002 >> 161 11 N 1S 0.00000 0.01372 -0.00001 0.00003 -0.00782 >> 162 2S -0.00001 0.02167 -0.00001 0.00006 -0.01277 >> 163 2PX -0.00002 0.04387 -0.00004 0.00005 -0.01666 >> 164 2PY 0.00003 -0.02001 0.00003 0.00001 -0.01927 >> 165 2PZ -0.09681 0.00000 -0.09374 -0.07140 -0.00005 >> 166 3S 0.00002 -0.05881 0.00002 -0.00018 0.04236 >> 167 3PX -0.00002 0.06205 -0.00006 0.00007 -0.02270 >> 168 3PY 0.00005 -0.02060 0.00004 0.00001 -0.03001 >> 169 3PZ -0.14942 0.00001 -0.14256 -0.10704 -0.00008 >> >> 170 4S 0.00002 -0.25348 0.00023 -0.00037 0.09649 >> >> 171 4PX -0.00010 0.07780 0.00005 0.00005 -0.05391 >> 172 4PY 0.00002 -0.07692 0.00024 -0.00010 0.00907 >> 173 4PZ -0.16396 -0.00005 -0.17391 -0.16705 -0.00011 >> 174 5S 0.00008 -0.31318 0.00020 -0.00140 0.89693 >> 175 5PX -0.00024 -0.09505 0.00045 -0.00043 -0.21030 >> >> 176 5PY -0.00024 -0.15548 0.00046 0.00029 -0.33094 >> >> 177 5PZ -0.05292 0.00003 -0.05002 -0.17772 -0.00018 >> 178 6D 0 0.00000 -0.00185 0.00000 0.00002 -0.00149 >> 179 6D+1 0.00364 0.00000 0.00520 -0.02009 -0.00003 >> 180 6D-1 -0.00039 0.00000 -0.00057 0.01129 0.00001 >> 181 6D+2 0.00000 0.00150 0.00000 -0.00001 0.00611 >> 182 6D-2 0.00000 -0.00183 0.00000 0.00000 0.00022 >> 183 12 S 1S 0.00000 0.00290 0.00000 -0.00001 0.00163 >> 184 2S 0.00000 0.00837 0.00000 -0.00003 0.00464 >> 185 3S 0.00000 -0.01879 -0.00001 0.00006 -0.00998 >> 186 4S 0.00000 -0.03107 -0.00001 0.00011 -0.01976 >> 187 5S 0.00000 0.06171 0.00001 -0.00029 0.05265 >> >> 188 6S -0.00006 0.14997 0.00031 0.00004 -0.02952 >> 189 7S -0.00086 -0.63601 0.00275 0.00698 -2.70572 >> >> 190 7PX 0.00011 0.08675 -0.00009 0.00205 -0.38791 >> 191 7PY 0.00022 0.16721 -0.00061 -0.00068 0.46445 >> >> 192 7PZ -0.02854 -0.00013 0.04463 -0.19770 -0.00015 >> 193 8PX 0.00000 0.01606 0.00000 -0.00004 0.01283 >> 194 8PY -0.00003 0.01951 0.00002 -0.00003 0.00473 >> 195 8PZ -0.04816 0.00002 0.04326 0.02805 0.00002 >> 196 9PX 0.00000 0.03105 0.00000 -0.00008 0.02428 >> 197 9PY -0.00006 0.03729 0.00004 -0.00006 0.00882 >> 198 9PZ -0.09209 0.00003 0.08258 0.05304 0.00004 >> 199 10PX 0.00000 -0.04744 -0.00001 0.00011 -0.03405 >> 200 10PY 0.00008 -0.05379 -0.00005 0.00009 -0.01131 >> 201 10PZ 0.13230 -0.00004 -0.11935 -0.07694 -0.00007 >> 202 11PX 0.00001 -0.08915 -0.00001 0.00029 -0.09302 >> >> 203 11PY 0.00018 -0.12713 -0.00019 0.00022 -0.04127 >> >> 204 11PZ 0.28539 -0.00008 -0.26406 -0.19142 -0.00016 >> 205 12PX 0.00005 -0.03524 0.00007 0.00081 -0.22530 >> 206 12PY 0.00014 -0.09592 -0.00016 0.00003 0.02799 >> 207 12PZ 0.15826 -0.00003 -0.19006 -0.20245 -0.00022 >> 208 13D 0 0.00001 0.00601 -0.00001 0.00005 -0.00229 >> 209 13D+1 -0.00454 -0.00001 0.00983 -0.02539 -0.00003 >> 210 13D-1 -0.00987 -0.00001 0.00459 -0.04352 -0.00003 >> 211 13D+2 0.00000 -0.01900 -0.00002 -0.00003 0.01677 >> 212 13D-2 0.00000 0.00397 0.00000 0.00003 -0.01970 >> 213 13 C 1S 0.00000 -0.00054 0.00001 -0.00007 0.00707 >> 214 2S 0.00000 -0.00087 0.00001 -0.00011 0.01133 >> 215 2PX 0.00000 0.00412 0.00000 0.00002 -0.01209 >> 216 2PY 0.00000 0.00413 0.00000 0.00006 -0.01879 >> 217 2PZ 0.00044 0.00001 0.00137 0.19642 0.0002 >> 218 3S 0.00000 -0.00105 -0.00002 0.00032 -0.02794 >> 219 3PX 0.00000 0.00728 0.00001 0.00004 -0.02614 >> 220 3PY 0.00000 0.01138 0.00001 0.00009 -0.03399 >> 221 3PZ 0.00049 0.00002 0.00146 0.30948 0.00035 >> >> 222 4S -0.00002 0.11622 -0.00015 0.00089 -0.17612 >> 223 4PX 0.00009 0.10208 -0.00035 0.00019 -0.04885 >> 224 4PY 0.00008 -0.15266 -0.00010 0.00015 -0.00317 >> >> 225 4PZ 0.02778 0.00000 0.02512 0.47540 0.00056 >> 226 5S -0.00002 0.24610 -0.00057 -0.00686 2.55118 >> >> 227 5PX 0.00063 0.06008 -0.00196 -0.00210 0.82602 >> 228 5PY 0.00056 0.32064 -0.00117 0.00218 -0.06420 >> >> 229 5PZ 0.00365 -0.00003 0.00989 0.49364 -0.00012 >> 230 6D 0 0.00000 0.00053 0.00000 0.00002 -0.00347 >> 231 6D+1 -0.00533 -0.00001 -0.03539 0.00094 0.00000 >> 232 6D-1 0.01987 0.00000 -0.00369 0.00682 0.00000 >> 233 6D+2 0.00000 -0.01008 0.00002 0.00001 -0.00922 >> 234 6D-2 0.00001 0.04164 0.00000 0.00000 0.00012 >> 235 14 S 1S 0.00000 -0.00023 0.00000 -0.00001 0.00057 >> 236 2S 0.00000 -0.00066 0.00000 -0.00002 0.00160 >> 237 3S 0.00000 0.00144 0.00000 0.00004 -0.00315 >> 238 4S 0.00000 0.00259 0.00000 0.00008 -0.00798 >> 239 5S 0.00000 -0.00662 0.00001 -0.00018 0.02430 >> 240 6S 0.00011 0.01941 -0.00027 0.00004 -0.03475 >> >> 241 7S 0.00088 0.10246 -0.00234 0.00077 0.12869 >> >> 242 7PX 0.00021 0.01705 -0.00053 0.00011 0.07181 >> 243 7PY 0.00000 0.04548 -0.00001 -0.00031 0.05435 >> 244 7PZ 0.00797 0.00000 -0.04975 -0.23449 -0.00012 >> 245 8PX 0.00000 -0.01267 0.00005 0.00001 0.00038 >> 246 8PY 0.00002 0.09670 -0.00002 0.00000 0.00285 >> 247 8PZ -0.00531 -0.00001 -0.07103 0.04261 0.00005 >> 248 9PX 0.00001 -0.02407 0.00009 0.00003 0.00077 >> >> 249 9PY 0.00003 0.18538 -0.00003 0.00000 0.00564 >> >> 250 9PZ -0.01020 -0.00003 -0.13601 0.08045 0.00009 >> 251 10PX -0.00001 0.03338 -0.00012 -0.00004 -0.00168 >> >> 252 10PY -0.00004 -0.26602 0.00004 0.00001 -0.00954 >> >> 253 10PZ 0.01444 0.00004 0.19208 -0.11091 -0.00012 >> 254 11PX 0.00002 0.07699 -0.00034 -0.00006 0.00332 >> >> 255 11PY -0.00009 -0.53528 0.00009 0.00002 -0.01279 >> >> 256 11PZ 0.02904 0.00009 0.41149 -0.29074 -0.00033 >> 257 12PX 0.00003 0.06051 -0.00024 0.00035 -0.11187 >> >> 258 12PY -0.00008 -0.36514 0.00009 -0.00007 -0.02518 >> >> 259 12PZ 0.00517 0.00006 0.25799 -0.27088 -0.00028 >> 260 13D 0 0.00000 0.00005 0.00002 0.00006 -0.00304 >> 261 13D+1 0.00124 0.00001 0.01518 0.05558 0.00007 >> 262 13D-1 0.00295 -0.00001 0.00167 0.00834 0.00001 >> 263 13D+2 0.00000 0.00432 -0.00001 -0.00002 0.00215 >> 264 13D-2 -0.00001 -0.02106 0.00000 0.00000 -0.00360 >> 265 15 H 1S 0.00000 0.00080 0.00001 0.00002 -0.00804 >> 266 2S -0.00002 0.01162 0.00008 0.00001 -0.00684 >> 267 3S -0.00015 -0.02440 0.00023 0.00024 -0.29261 >> >> 268 4S 0.00000 0.10929 0.00001 0.00126 -0.61549 >> >> 269 5PX 0.00000 -0.00083 0.00000 0.00000 -0.00002 >> 270 5PY 0.00000 0.00011 0.00001 -0.00002 0.01104 >> 271 5PZ -0.00915 0.00000 -0.00861 -0.00943 0.00000 >> >> Any type of help is highly appreciated. >> regards >> utpal>> the strange characters on the top line to the %% sign. You can also >> >> E-mail to subscribers: CHEMISTRY%%ccl.net >> or use:>> >> E-mail to administrators: CHEMISTRY-REQUEST%%ccl.net >> or use>> >> > -- Ar cieņu, Igors Mihailovs Organisko materiālu laboratorija LU CFI --------------45FB059704A67A6E497FEE81 Content-Type: text/html; charset=UTF-8 Content-Transfer-Encoding: 8bit Dear Utpal,

If the problem was that answered by Neus, then you should probably use formatted checkpoint file which you can generate from the checkpoint (.chk) of the calculation you already have (no need to rerun) by the formchk command. The .fchk (or .fch) file can be opened by all of commonly used molecular visualizers (e.g., Avogadro or Gabedit).

But to me, it appears that your transition is quite of mixed character. Wouldn't it be better to calculate and later visualize Natural Transition Orbitals? See Gaussian reference for their description.

For example, if Your excited state calculation was done with checkpoint file /home/igors/darba/IN18_438_TPSSh_6311_tolu.chk, and You are interested in the 3rd transition, you can run the following job:


%OldChk=/home/igors/darba/IN18_438_TPSSh_6311_tolu.chk
%Chk=/home/igors/darba/IN18_438_TPSSh_6311_tolu_S3.chk

# TPSSh/6-311G(d,p) Guess=(Only,Read) Geom=Check Density=(Check,Transition=3) Pop=SaveNTO

Natural Transition Orbitals job example

0 1

(end of file)

And then run in console or command prompt the following:
$> formchk /home/igors/darba/IN18_438_TPSSh_6311_tolu_S3.chk

With best regards,
Igors Mihailovs
ISSP University of Latvia/ Riga Technical University

On 05/01/17 11:32, Neus Aguilera neusaguilera,+,yahoo.com wrote:
Dear Utpal,

I would consider relaunching the calculations with some extra keywords to be able to use a molecular orbital visualizer, as MOLDEN

#P gfinput gfprint IOP(6/7=1)

Then you will be able to open the .out with MOLDEN.

Please let me know if this worked for you,
Have a nice day,


Neus Aguilera-Porta







El 4 gen 2017, a les 11:47, Utpal Sarkar utpalchemiitkgp]~[gmail.com <owner-chemistry%%ccl.net> va escriure:


Sent to CCL by: "Utpal  Sarkar" [utpalchemiitkgp(0)gmail.com]
Dear Gaussian users,

I am trying to identify the molecular orbital transition for a particular peak of UV visible spectrum from Gaussian output. My question is how can I recognize weather a particular orbital is non bonding n orbital or sigma orbital?

In my case, I have found for a particular peak at 237.93 nm with oscillator strength f=0.1806   and the responsible transitions are

     41 -> 44         0.32998
     41 -> 46         0.16625
     42 -> 45        -0.21871
     42 -> 47         0.19689
     42 -> 48         0.29232
     42 -> 50        -0.22757
     42 -> 52        -0.14040
     43 -> 46        -0.12852
     43 -> 49         0.27673


Now I want to identify weather orbital number 42 is sigma or nonbonding n orbital.


The coefficients of orbital number 42 is given below :


                         41        42        43        44        45
                          O         O         O         V         V

    Eigenvalues --    -0.27285  -0.24084  -0.23213  -0.05116  -0.04261

  1 1   C  1S          0.00000  -0.00420   0.00000   0.00001  -0.00829
  2        2S          0.00000  -0.00653   0.00000   0.00002  -0.01337
  3        2PX         0.00000  -0.02012  -0.00001   0.00001   0.00289
  4        2PY        -0.00001  -0.00168   0.00000  -0.00002   0.01821
  5        2PZ        -0.13793   0.00001   0.02323   0.08393   0.00016

  6        3S         -0.00001   0.01777   0.00001  -0.00006   0.04398
  7        3PX         0.00000  -0.02621   0.00000   0.00002  -0.00073

  8        3PY        -0.00001  -0.00037   0.00000  -0.00002   0.02348
  9        3PZ        -0.21271   0.00002   0.03355   0.12668   0.00024

 10        4S          0.00001   0.04010   0.00010  -0.00041   0.13704
 11        4PX        -0.00001  -0.03987  -0.00012  -0.00001  -0.00228
 12        4PY        -0.00003   0.00962   0.00003   0.00003   0.06605
 13        4PZ        -0.20444   0.00003   0.04608   0.20909   0.00040

 14        5S          0.00115  -0.35581   0.00042   0.00562  -2.59840
 15        5PX        -0.00036   0.37640  -0.00053   0.00004  -0.46640

 16        5PY        -0.00011   0.03293   0.00005  -0.00263   1.81287
 17        5PZ        -0.00891   0.00007  -0.01617   0.11613   0.00054
 18        6D 0        0.00000   0.00022   0.00000   0.00000  -0.00167
 19        6D+1       -0.00349   0.00000  -0.01518  -0.01160  -0.00002
 20        6D-1        0.00841   0.00000  -0.00111   0.00349   0.00001
 21        6D+2        0.00000  -0.00233   0.00000   0.00000   0.00518
 22        6D-2        0.00000   0.00204   0.00000   0.00000   0.00069
 23 2   C  1S          0.00000   0.00418   0.00000   0.00002  -0.00937
 24        2S          0.00000   0.00682   0.00000   0.00003  -0.01539
 25        2PX         0.00001   0.02532   0.00000   0.00003  -0.01284
 26        2PY        -0.00001  -0.00688   0.00001  -0.00001   0.00125
 27        2PZ        -0.03567   0.00001   0.08391   0.01761  -0.00001
 28        3S         -0.00002  -0.01999   0.00000  -0.00010   0.05218
 29        3PX         0.00002   0.04132   0.00001   0.00005  -0.02390
 30        3PY        -0.00001  -0.00767   0.00002  -0.00002   0.00704
 31        3PZ        -0.05659   0.00002   0.13408   0.02588  -0.00002
 32        4S         -0.00002  -0.03998  -0.00006  -0.00023   0.17293
 33        4PX        -0.00002   0.05482  -0.00005   0.00033  -0.09711
 34        4PY         0.00000  -0.07317  -0.00016   0.00003  -0.07289
 35        4PZ        -0.03986   0.00001   0.12373   0.02282  -0.00003

 36        5S         -0.00032  -0.11569  -0.00081  -0.01228   6.78260

 37        5PX        -0.00042   0.05717  -0.00013   0.00494  -1.60116

 38        5PY        -0.00059   0.44119  -0.00063  -0.00072  -1.24950

 39        5PZ        -0.02588  -0.00006   0.04361   0.17297  -0.00036
 40        6D 0        0.00000   0.00018   0.00000   0.00001  -0.00208
 41        6D+1       -0.02147   0.00000   0.00844   0.01814   0.00003
 42        6D-1       -0.00727   0.00000  -0.01096   0.00789   0.00002
 43        6D+2       -0.00001   0.00459   0.00000  -0.00001   0.00141
 44        6D-2        0.00000   0.00783   0.00000   0.00000   0.00323
 45 3   C  1S          0.00000  -0.00250   0.00001   0.00000  -0.00307
 46        2S         -0.00001  -0.00394   0.00001   0.00001  -0.00527
 47        2PX         0.00000  -0.02120   0.00002   0.00000  -0.00284
 48        2PY         0.00001  -0.00889  -0.00001   0.00001  -0.00383
 49        2PZ         0.04067   0.00002   0.07965  -0.05872  -0.00012
 50        3S          0.00002   0.00920  -0.00002  -0.00003   0.02598
 51        3PX        -0.00001  -0.03375   0.00006   0.00000  -0.00496
 52        3PY         0.00002  -0.01359  -0.00002   0.00002  -0.00541
 53        3PZ         0.06382   0.00003   0.12680  -0.09881  -0.00020
 54        4S          0.00020   0.01844  -0.00050   0.00003  -0.00626

 55        4PX         0.00001  -0.10072   0.00008  -0.00023   0.03817

 56        4PY        -0.00005  -0.02876  -0.00003   0.00013  -0.11338
 57        4PZ         0.06310   0.00004   0.13146  -0.10786  -0.00029

 58        5S         -0.00091   1.35401  -0.00060  -0.00343   1.95224

 59        5PX         0.00011  -0.07907  -0.00052  -0.01066   4.45406

 60        5PY        -0.00021   0.25218  -0.00015   0.00362  -2.43405

 61        5PZ         0.02754   0.00003  -0.00041  -0.30749  -0.00068
 62        6D 0        0.00000  -0.00126   0.00000   0.00001  -0.00313
 63        6D+1        0.02091   0.00000   0.01506   0.02310   0.00003
 64        6D-1       -0.00972   0.00000   0.00984   0.00010  -0.00001
 65        6D+2        0.00001   0.00092   0.00000   0.00001  -0.00749
 66        6D-2        0.00000   0.00700  -0.00001   0.00000  -0.00141
 67 4   C  1S          0.00000   0.00209   0.00000   0.00002  -0.01205
 68        2S          0.00000   0.00332  -0.00001   0.00003  -0.01967
 69        2PX         0.00000   0.01269  -0.00001   0.00001  -0.00401
 70        2PY        -0.00001  -0.00223   0.00001   0.00002  -0.02944
 71        2PZ         0.13807  -0.00001   0.03273   0.09279   0.00016
 72        3S         -0.00001  -0.01048   0.00002  -0.00011   0.07052
 73        3PX         0.00001   0.01699  -0.00002   0.00003  -0.00983
 74        3PY        -0.00002  -0.00209   0.00001   0.00002  -0.03833
 75        3PZ         0.21444  -0.00001   0.04852   0.14133   0.00025
 76        4S         -0.00007   0.03587   0.00010   0.00012   0.02042
 77        4PX         0.00005   0.01075  -0.00004  -0.00013   0.06745
 78        4PY        -0.00002   0.03088   0.00003   0.00014  -0.08716

 79        4PZ         0.19966  -0.00001   0.05466   0.21749   0.00040

 80        5S          0.00048   0.24000   0.00046   0.01370  -6.29902
 81        5PX         0.00014   0.15294   0.00022  -0.00038   0.95984

 82        5PY         0.00016   0.03045  -0.00005   0.00288  -2.02375
 83        5PZ         0.02481  -0.00001   0.02389   0.30485   0.00041
 84        6D 0        0.00000  -0.00014   0.00000   0.00000  -0.00113
 85        6D+1        0.00307   0.00000  -0.01335   0.00485   0.00001
 86        6D-1        0.00725   0.00000   0.00326  -0.00480  -0.00001
 87        6D+2        0.00000   0.00252   0.00000   0.00000   0.00556
 88        6D-2        0.00000   0.00085   0.00000   0.00000  -0.00282
 89 5   C  1S          0.00000  -0.00128   0.00000   0.00000  -0.00810
 90        2S          0.00000  -0.00204   0.00000   0.00001  -0.01317
 91        2PX         0.00000  -0.00832   0.00001  -0.00002   0.02313
 92        2PY         0.00000  -0.00240   0.00001   0.00000  -0.01084
 93        2PZ         0.06902  -0.00002  -0.06649  -0.02215  -0.00004
 94        3S         -0.00001   0.00606   0.00000  -0.00002   0.04591
 95        3PX         0.00000  -0.01115   0.00001  -0.00003   0.03168
 96        3PY        -0.00001  -0.00283   0.00001   0.00001  -0.01523
 97        3PZ         0.10653  -0.00003  -0.10344  -0.03512  -0.00007
 98        4S          0.00000  -0.01037  -0.00002  -0.00007   0.04618
 99        4PX         0.00000   0.00126   0.00003  -0.00004   0.05818
100        4PY         0.00002  -0.00822   0.00000  -0.00002  -0.01083
101        4PZ         0.09937  -0.00003  -0.10252  -0.04632  -0.00010

102        5S         -0.00035  -0.82701   0.00051   0.00144   0.52163
103        5PX         0.00017   0.10769   0.00005  -0.00063   0.66730

104        5PY         0.00005  -0.08692   0.00039   0.00162  -0.24277
105        5PZ         0.01608   0.00001  -0.03265  -0.08881  -0.00014
106        6D 0        0.00000  -0.00007   0.00000   0.00000  -0.00241
107        6D+1       -0.01473   0.00000  -0.00471  -0.01392  -0.00002
108        6D-1       -0.01513   0.00000  -0.00919  -0.01697  -0.00003
109        6D+2        0.00000  -0.00040   0.00000   0.00000  -0.00226
110        6D-2        0.00000   0.00182   0.00000  -0.00001   0.00809
111 6   C  1S          0.00000   0.00206   0.00000   0.00001  -0.00756
112        2S          0.00000   0.00328   0.00000   0.00001  -0.01224
113        2PX         0.00000   0.01042   0.00000  -0.00002   0.01938
114        2PY         0.00000  -0.00458   0.00000   0.00000   0.00515
115        2PZ        -0.08000  -0.00001  -0.07284  -0.07944  -0.00013
116        3S          0.00000  -0.00969  -0.00001  -0.00003   0.04258
117        3PX         0.00000   0.01483   0.00000  -0.00003   0.02922
118        3PY         0.00001  -0.00640   0.00000   0.00001   0.00699
119        3PZ        -0.12304  -0.00001  -0.11316  -0.12197  -0.00020
120        4S         -0.00002   0.00460   0.00005   0.00008   0.05411
121        4PX         0.00001   0.00771  -0.00002  -0.00004   0.01724
122        4PY         0.00001  -0.00624   0.00003   0.00001   0.01256
123        4PZ        -0.11495  -0.00001  -0.11594  -0.18994  -0.00033

124        5S         -0.00009   0.16872  -0.00011  -0.00994   4.64091
125        5PX         0.00005  -0.06078  -0.00020   0.00194  -0.77473

126        5PY         0.00014  -0.25334   0.00036   0.00074   0.22739

127        5PZ        -0.02468  -0.00005  -0.01066  -0.15953  -0.00042
128        6D 0        0.00000   0.00004   0.00000   0.00000  -0.00184
129        6D+1        0.01185   0.00000  -0.00198  -0.01019  -0.00002
130        6D-1       -0.01584   0.00000   0.00844   0.00961   0.00002
131        6D+2        0.00000   0.00150   0.00000   0.00000  -0.00427
132        6D-2        0.00000   0.00180   0.00000   0.00001  -0.00663
133 7   H  1S          0.00000   0.00276   0.00000  -0.00001  -0.00016
134        2S          0.00000   0.00033  -0.00002  -0.00001  -0.01090
135        3S          0.00001  -0.00344  -0.00001   0.00012  -0.13711
136        4S          0.00003  -0.06299  -0.00001   0.00187  -1.54608
137        5PX         0.00000  -0.00055   0.00000   0.00000  -0.00001
138        5PY         0.00000   0.00060   0.00000   0.00001  -0.00575
139        5PZ        -0.01251   0.00000   0.00163   0.00961   0.00002
140 8   H  1S          0.00001  -0.00311   0.00000   0.00000   0.00078
141        2S          0.00002   0.00008  -0.00001  -0.00001  -0.00098
142        3S          0.00002   0.01171  -0.00001   0.00021  -0.15692
143        4S          0.00005  -0.02814  -0.00004   0.00174  -1.97399
144        5PX         0.00000   0.00049   0.00000   0.00000   0.00052
145        5PY         0.00000   0.00042   0.00000  -0.00001   0.01084
146        5PZ         0.01269   0.00000   0.00269   0.01163   0.00002
147 9   H  1S          0.00000  -0.00582   0.00000   0.00000  -0.00246
148        2S          0.00001  -0.01106   0.00000   0.00000  -0.01231
149        3S          0.00000  -0.01276   0.00001   0.00008  -0.10144
150        4S         -0.00004  -0.03749   0.00007   0.00121  -1.35734
151        5PX         0.00000  -0.00017   0.00000   0.00000  -0.00629
152        5PY         0.00000  -0.00055   0.00000   0.00000   0.00507
153        5PZ         0.00639   0.00000  -0.00659  -0.00303  -0.00001
154 10  H  1S          0.00000   0.00742   0.00000   0.00000  -0.00369
155        2S          0.00000   0.01212   0.00000   0.00000  -0.01105
156        3S         -0.00001   0.01434   0.00002   0.00005  -0.06846
157        4S         -0.00004   0.05825   0.00006   0.00002  -0.75096
158        5PX         0.00000   0.00023   0.00000   0.00000  -0.00645
159        5PY         0.00000  -0.00057   0.00000   0.00000  -0.00321
160        5PZ        -0.00740   0.00000  -0.00708  -0.01018  -0.00002
161 11  N  1S          0.00000   0.01372  -0.00001   0.00003  -0.00782
162        2S         -0.00001   0.02167  -0.00001   0.00006  -0.01277
163        2PX        -0.00002   0.04387  -0.00004   0.00005  -0.01666
164        2PY         0.00003  -0.02001   0.00003   0.00001  -0.01927
165        2PZ        -0.09681   0.00000  -0.09374  -0.07140  -0.00005
166        3S          0.00002  -0.05881   0.00002  -0.00018   0.04236
167        3PX        -0.00002   0.06205  -0.00006   0.00007  -0.02270
168        3PY         0.00005  -0.02060   0.00004   0.00001  -0.03001
169        3PZ        -0.14942   0.00001  -0.14256  -0.10704  -0.00008

170        4S          0.00002  -0.25348   0.00023  -0.00037   0.09649

171        4PX        -0.00010   0.07780   0.00005   0.00005  -0.05391
172        4PY         0.00002  -0.07692   0.00024  -0.00010   0.00907
173        4PZ        -0.16396  -0.00005  -0.17391  -0.16705  -0.00011
174        5S          0.00008  -0.31318   0.00020  -0.00140   0.89693
175        5PX        -0.00024  -0.09505   0.00045  -0.00043  -0.21030

176        5PY        -0.00024  -0.15548   0.00046   0.00029  -0.33094

177        5PZ        -0.05292   0.00003  -0.05002  -0.17772  -0.00018
178        6D 0        0.00000  -0.00185   0.00000   0.00002  -0.00149
179        6D+1        0.00364   0.00000   0.00520  -0.02009  -0.00003
180        6D-1       -0.00039   0.00000  -0.00057   0.01129   0.00001
181        6D+2        0.00000   0.00150   0.00000  -0.00001   0.00611
182        6D-2        0.00000  -0.00183   0.00000   0.00000   0.00022
183 12  S  1S          0.00000   0.00290   0.00000  -0.00001   0.00163
184        2S          0.00000   0.00837   0.00000  -0.00003   0.00464
185        3S          0.00000  -0.01879  -0.00001   0.00006  -0.00998
186        4S          0.00000  -0.03107  -0.00001   0.00011  -0.01976
187        5S          0.00000   0.06171   0.00001  -0.00029   0.05265

188        6S         -0.00006   0.14997   0.00031   0.00004  -0.02952
189        7S         -0.00086  -0.63601   0.00275   0.00698  -2.70572

190        7PX         0.00011   0.08675  -0.00009   0.00205  -0.38791
191        7PY         0.00022   0.16721  -0.00061  -0.00068   0.46445

192        7PZ        -0.02854  -0.00013   0.04463  -0.19770  -0.00015
193        8PX         0.00000   0.01606   0.00000  -0.00004   0.01283
194        8PY        -0.00003   0.01951   0.00002  -0.00003   0.00473
195        8PZ        -0.04816   0.00002   0.04326   0.02805   0.00002
196        9PX         0.00000   0.03105   0.00000  -0.00008   0.02428
197        9PY        -0.00006   0.03729   0.00004  -0.00006   0.00882
198        9PZ        -0.09209   0.00003   0.08258   0.05304   0.00004
199       10PX         0.00000  -0.04744  -0.00001   0.00011  -0.03405
200       10PY         0.00008  -0.05379  -0.00005   0.00009  -0.01131
201       10PZ         0.13230  -0.00004  -0.11935  -0.07694  -0.00007
202       11PX         0.00001  -0.08915  -0.00001   0.00029  -0.09302

203       11PY         0.00018  -0.12713  -0.00019   0.00022  -0.04127

204       11PZ         0.28539  -0.00008  -0.26406  -0.19142  -0.00016
205       12PX         0.00005  -0.03524   0.00007   0.00081  -0.22530
206       12PY         0.00014  -0.09592  -0.00016   0.00003   0.02799
207       12PZ         0.15826  -0.00003  -0.19006  -0.20245  -0.00022
208       13D 0        0.00001   0.00601  -0.00001   0.00005  -0.00229
209       13D+1       -0.00454  -0.00001   0.00983  -0.02539  -0.00003
210       13D-1       -0.00987  -0.00001   0.00459  -0.04352  -0.00003
211       13D+2        0.00000  -0.01900  -0.00002  -0.00003   0.01677
212       13D-2        0.00000   0.00397   0.00000   0.00003  -0.01970
213 13  C  1S          0.00000  -0.00054   0.00001  -0.00007   0.00707
214        2S          0.00000  -0.00087   0.00001  -0.00011   0.01133
215        2PX         0.00000   0.00412   0.00000   0.00002  -0.01209
216        2PY         0.00000   0.00413   0.00000   0.00006  -0.01879
217        2PZ         0.00044   0.00001   0.00137   0.19642   0.0002
218        3S          0.00000  -0.00105  -0.00002   0.00032  -0.02794
219        3PX         0.00000   0.00728   0.00001   0.00004  -0.02614
220        3PY         0.00000   0.01138   0.00001   0.00009  -0.03399
221        3PZ         0.00049   0.00002   0.00146   0.30948   0.00035

222        4S         -0.00002   0.11622  -0.00015   0.00089  -0.17612
223        4PX         0.00009   0.10208  -0.00035   0.00019  -0.04885
224        4PY         0.00008  -0.15266  -0.00010   0.00015  -0.00317

225        4PZ         0.02778   0.00000   0.02512   0.47540   0.00056
226        5S         -0.00002   0.24610  -0.00057  -0.00686   2.55118

227        5PX         0.00063   0.06008  -0.00196  -0.00210   0.82602
228        5PY         0.00056   0.32064  -0.00117   0.00218  -0.06420

229        5PZ         0.00365  -0.00003   0.00989   0.49364  -0.00012
230        6D 0        0.00000   0.00053   0.00000   0.00002  -0.00347
231        6D+1       -0.00533  -0.00001  -0.03539   0.00094   0.00000
232        6D-1        0.01987   0.00000  -0.00369   0.00682   0.00000
233        6D+2        0.00000  -0.01008   0.00002   0.00001  -0.00922
234        6D-2        0.00001   0.04164   0.00000   0.00000   0.00012
235 14  S  1S          0.00000  -0.00023   0.00000  -0.00001   0.00057
236        2S          0.00000  -0.00066   0.00000  -0.00002   0.00160
237        3S          0.00000   0.00144   0.00000   0.00004  -0.00315
238        4S          0.00000   0.00259   0.00000   0.00008  -0.00798
239        5S          0.00000  -0.00662   0.00001  -0.00018   0.02430
240        6S          0.00011   0.01941  -0.00027   0.00004  -0.03475

241        7S          0.00088   0.10246  -0.00234   0.00077   0.12869

242        7PX         0.00021   0.01705  -0.00053   0.00011   0.07181
243        7PY         0.00000   0.04548  -0.00001  -0.00031   0.05435
244        7PZ         0.00797   0.00000  -0.04975  -0.23449  -0.00012
245        8PX         0.00000  -0.01267   0.00005   0.00001   0.00038
246        8PY         0.00002   0.09670  -0.00002   0.00000   0.00285
247        8PZ        -0.00531  -0.00001  -0.07103   0.04261   0.00005
248        9PX         0.00001  -0.02407   0.00009   0.00003   0.00077

249        9PY         0.00003   0.18538  -0.00003   0.00000   0.00564

250        9PZ        -0.01020  -0.00003  -0.13601   0.08045   0.00009
251       10PX        -0.00001   0.03338  -0.00012  -0.00004  -0.00168

252       10PY        -0.00004  -0.26602   0.00004   0.00001  -0.00954

253       10PZ         0.01444   0.00004   0.19208  -0.11091  -0.00012
254       11PX         0.00002   0.07699  -0.00034  -0.00006   0.00332

255       11PY        -0.00009  -0.53528   0.00009   0.00002  -0.01279

256       11PZ         0.02904   0.00009   0.41149  -0.29074  -0.00033
257       12PX         0.00003   0.06051  -0.00024   0.00035  -0.11187

258       12PY        -0.00008  -0.36514   0.00009  -0.00007  -0.02518

259       12PZ         0.00517   0.00006   0.25799  -0.27088  -0.00028
260       13D 0        0.00000   0.00005   0.00002   0.00006  -0.00304
261       13D+1        0.00124   0.00001   0.01518   0.05558   0.00007
262       13D-1        0.00295  -0.00001   0.00167   0.00834   0.00001
263       13D+2        0.00000   0.00432  -0.00001  -0.00002   0.00215
264       13D-2       -0.00001  -0.02106   0.00000   0.00000  -0.00360
265 15  H  1S          0.00000   0.00080   0.00001   0.00002  -0.00804
266        2S         -0.00002   0.01162   0.00008   0.00001  -0.00684
267        3S         -0.00015  -0.02440   0.00023   0.00024  -0.29261

268        4S          0.00000   0.10929   0.00001   0.00126  -0.61549

269        5PX         0.00000  -0.00083   0.00000   0.00000  -0.00002
270        5PY         0.00000   0.00011   0.00001  -0.00002   0.01104
271        5PZ        -0.00915   0.00000  -0.00861  -0.00943   0.00000

Any type of help is highly appreciated.
regards
utpal



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-- 
Ar cieņu,
Igors Mihailovs
Organisko materiālu laboratorija
LU CFI
--------------45FB059704A67A6E497FEE81-- From owner-chemistry@ccl.net Thu Jan 5 18:09:01 2017 From: "Susi Lehtola susi.lehtola*alumni.helsinki.fi" To: CCL Subject: CCL: Understading the nature of molecular orbital (non bonding or sigma) Message-Id: <-52588-170105140759-8717-iw+vGTBpAG4Pu/VOCZVnfg|a|server.ccl.net> X-Original-From: Susi Lehtola Content-Transfer-Encoding: 7bit Content-Type: text/plain; charset=windows-1252; format=flowed Date: Thu, 5 Jan 2017 11:07:45 -0800 MIME-Version: 1.0 Sent to CCL by: Susi Lehtola [susi.lehtola[]alumni.helsinki.fi] On 01/05/2017 01:32 AM, Neus Aguilera neusaguilera,+,yahoo.com wrote: > Dear Utpal, > > I would consider relaunching the calculations with some extra keywords > to be able to use a molecular orbital visualizer, as MOLDEN > > *#P gfinput gfprint IOP(6/7=1)* > (source:http://www.cmbi.ru.nl/molden/gauss.html) > > Then you will be able to open the .out with MOLDEN. While MOLDEN indeed is a possibility, I'd like to point out that there's also an even better possibility - the checkpoint file - that stores the data with full machine precision compared to the fixed point format used in the MOLDEN files that often loses a lot of precision. http://www.ccl.net/cca/documents/dyoung/topics-orig/checkpoint.html Although this is probably unimportant for visualization, it is often significant for properties, since e.g. tight functions may have small coefficients (that are zero in fixed point format) but their matrix elements can still yield significant contributions to the overall property. So, just use the %Chk directive to get a checkpoint file and then convert it to formatted checkpoint with the formchk utility. Formatted checkpoint files can be read by a number of different programs, such as JMol and IQmol. -- ----------------------------------------------------------------------- Mr. Susi Lehtola, PhD Chemist Postdoctoral Fellow susi.lehtola===alumni.helsinki.fi Lawrence Berkeley National Laboratory http://www.helsinki.fi/~jzlehtol USA -----------------------------------------------------------------------