From owner-chemistry@ccl.net Wed Oct 29 00:10:00 2008 From: "Mr shabbir shabbir{:}nenu.edu.cn" To: CCL Subject: CCL: Absolute shielding values of B2H6 or BF3:OEt2 at GIAO-Mp2/6-31+G* Message-Id: <-37988-081029000846-14140-kpuxACbBAwFSloVFhEhSwQ:server.ccl.net> X-Original-From: "Mr shabbir" Date: Wed, 29 Oct 2008 00:08:42 -0400 Sent to CCL by: "Mr shabbir" [shabbir(-)nenu.edu.cn] Hello CCL user, I am in a bit little confusion. I have calculated the 11B NMR spectra of a compound at GIAO-Mp2/6-31+G*. Now I want to correlate it with experimental.For this purpose I have to take reference compound as B2H6 or BF3:OEt2. I have tried my best to find their absolute shielding value and can get following important references as under The B NMR chemical shifts were first computed with B2H6 [calculated absolute shift, (sigma B) = 96.7] as a reference. The 11B NMR chemical shifts were finally referenced to BF3:OEt2 [deta (B2H6) 16.6 vs. BF3:OEt2]. The 11B and 13C chemical shifts (6 values) are reported relative to the experimental standards, BF3OEt2 and tetramethylsilane (TMS), respectively. For 11B, where it is inconvenient to compute the experimental NMR standard, B2H6 (which has delta 16.6 vs BF3eOEt2) is used instead. The sigma values for B2H6 are as follows: GIAO-MP2/DZP =102.8 ppm and GIAO-MP2/TZP =100.7 ppm My question 1- On the basis of above lines, Can I take, 102.8 absolute shielding value of BF3OEt2 at GIAO-MP2/6-31+G*or (96.7+16.6)=113.3 .....? 2- Any one who knows any reference about the Absolute shielding values of B2H6 or BF3:OEt2 at GIAO-Mp2/6-31+G* or higher? 3- Is there any scaling factor that can we use for NMR calctions? 4- Two signs are used in NMR shieldings, sigma or deta (lower cases of greek) difference b/w these two? thanks in advance Mr.Shabbir From owner-chemistry@ccl.net Wed Oct 29 11:23:00 2008 From: "Maxim Kholin maxim.kholin],[q-pharm.com" To: CCL Subject: CCL: Download a new release of ADMET software (Volume of distribution, Fraction absorbed, half-life, Caco-2, LD50, MRDD etc) from Quantum Pharmaceuticals. Message-Id: <-37989-081029112216-31059-t9c+wMkFtzPS/dQisBe5vw ~~ server.ccl.net> X-Original-From: "Maxim Kholin" Content-Type: multipart/alternative; boundary="----=_Part_14561_21840889.1225293722927" Date: Wed, 29 Oct 2008 18:22:02 +0300 MIME-Version: 1.0 Sent to CCL by: "Maxim Kholin" [maxim.kholin(_)q-pharm.com] ------=_Part_14561_21840889.1225293722927 Content-Type: text/plain; charset=ISO-8859-1 Content-Transfer-Encoding: 7bit Content-Disposition: inline Dear Colleagues, Please download a free trial of new release of q-ADME software from http://www.q-lead.com/adme_pk (Volume of distribution, Fraction absorbed, half-life, Caco-2, LogP prediction). Based on entirely different paradigm than QSPR. Other trials available for immediate download: 1. Toxicity prediction http://www.q-lead.com/toxicity (maximum recommended daily dose, LD50 (rodent, dog, rabbit; oral, intravenous, intraperitoneal, subcutaneous) 2. hERG binding prediction http://www.q-lead.com/HERG_cardio_toxicity 3. Human Serum Albumin Binding Prediction http://www.q-lead.com/albumin_plasma_protein_binding 4. Physical properties prediction http://www.q-lead.com/qmol ( Solubility in H2O and DMSO, LogP, water/octanol etc 12 parameters total). Publications are available at http://drugdiscoverywizzards.blogspot.com/search/label/publications Maxim Kholin Quantum Pharmaceuticals Tel. +7(499) 150 8332 maxim.kholin*q-pharm.com www.q-pharm.com www.q-lead.com ------=_Part_14561_21840889.1225293722927 Content-Type: text/html; charset=UTF-8 Content-Transfer-Encoding: base64 Content-Disposition: inline PG1ldGEgaHR0cC1lcXVpdj0iQ29udGVudC1UeXBlIiBjb250ZW50PSJ0ZXh0L2h0bWw7IGNoYXJz ZXQ9dXRmLTgiPjxtZXRhIG5hbWU9IlByb2dJZCIgY29udGVudD0iV29yZC5Eb2N1bWVudCI+PG1l dGEgbmFtZT0iR2VuZXJhdG9yIiBjb250ZW50PSJNaWNyb3NvZnQgV29yZCA5Ij48bWV0YSBuYW1l PSJPcmlnaW5hdG9yIiBjb250ZW50PSJNaWNyb3NvZnQgV29yZCA5Ij48bGluayByZWw9IkZpbGUt TGlzdCIgaHJlZj0iZmlsZTovLy9DOi9ET0NVTUUlN0UxL01heGltL0xPQ0FMUyU3RTEvVGVtcC9t c29jbGlwMS8wMi9jbGlwX2ZpbGVsaXN0LnhtbCI+PHN0eWxlPgombHQ7IS0tCiAvKiBGb250IERl ZmluaXRpb25zICovCkBmb250LWZhY2UKCXtmb250LWZhbWlseTpXaW5nZGluZ3M7CglwYW5vc2Ut MTo1IDAgMCAwIDAgMCAwIDAgMCAwOwoJbXNvLWZvbnQtY2hhcnNldDoyOwoJbXNvLWdlbmVyaWMt 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text/plain Date: Wed, 29 Oct 2008 16:49:18 +0100 Mime-Version: 1.0 Sent to CCL by: Jan Sielk [sielk-#-phc.uni-kiel.de] Hello CCL users! I have the following problem: I want to perform a quantum dynamics calculation with a molecule in internal coordinates (Z-matrix). Also, I obtain normal mode coordinates (let's call them normal_modes_xyz) with respect to the molecule in standard oriented cart. coordinates (call them Ref_xyz) by running a frequency calculation (using e.g. molpro). What I need now (for some reason) is as follows: As I change the geometry of the molecule in internal coordinates (e.g. scaning an angle), I want to express this new geometry (named aim_geo_zmat) as normal mode deflection. In other words, I want to know how much I need to stretch the different normal modes to obtain my aimed (internal coordinates) geometry. This means determine the vector "n" in the following equation: Ref_xyz + n * normal_modes_xyz = new_geo_xyz where new_geo_xyz should be equal (after conversion to a defined Z-matrix) to aim_geo_zmat. Does anybody know how to get the right deflection vector "n"? Thanks in advance! Jan --------------------------------------------------- Jan Sielk, Dipl. Chem., PhD candidate Kiel University Institute for Physical Chemistry Theoretical Chemistry email: sielk]*[phc.uni-kiel.de homepage: http://ravel.phc.uni-kiel.de phone: +49 431 880-1759 fax: +49 431 880-1758 mailing address: Olshausenstr. 40 D-24098 Kiel, Germany --------------------------------------------------- From owner-chemistry@ccl.net Wed Oct 29 17:32:00 2008 From: "Emilio =?ISO-8859-1?Q?Jos=E9_Ju=E1rez_P=E9rez?= ejjuarez_+_icmab.es" To: CCL Subject: CCL: Absolute shielding values of B2H6 or BF3:OEt2 at GIAO-Mp2/6-31+G* Message-Id: <-37991-081029045755-24163-WnMZl29ko7ahHL1/zaZzKw---server.ccl.net> X-Original-From: Emilio =?ISO-8859-1?Q?Jos=E9_Ju=E1rez_P=E9rez?= Content-Transfer-Encoding: 8bit Content-Type: text/plain; charset=UTF-8 Date: Wed, 29 Oct 2008 09:01:36 +0100 Mime-Version: 1.0 Sent to CCL by: Emilio =?ISO-8859-1?Q?Jos=E9_Ju=E1rez_P=E9rez?= [ejjuarez_._icmab.es] Hello Mr Shabbir, I hope help to you, > My question > 1- On the basis of above lines, Can I take, 102.8 absolute > shielding value of BF3OEt2 at GIAO-MP2/6-31+G*or (96.7 > +16.6)=113.3 .....? I followed this formulae in my paper: ( E. J. Juárez-Pérez, C. Viñas, A. González-Campo, F. Teixidor, R. Sillanpää, R. Kivekäs, R. Núñez, Chem. Eur. J. 2008, 14, 4924-4938. ) A + B - C = D A: Computed Absolute shielding of the B2H6 at level X of theory. B: Experimental chemical shift of the B2H6 if the nmr reference is BF3·OEt2 == 16.6 ppm (as you quoted ) C: Computed Absolute shielding of the case study borons at level X of theory. D: Computed Chemical shift at level X of theory of the case study borons with BF3·OEt2 as nmr reference . A few data (sorry I did not MP2) B 106.7 "B2H6 HF/6-31G(d) GIAO" B 83.6 "B2H6 B3LYP/6-311+G(2d,p) GIAO" B 93.5055 "B2H6 B3LYP/6-31G(d) GIAO" B 84.08645 "B2H6 B3LYP/6-311+G(d,p) GIAO" B 107.9845 "B2H6 B3LYP/sto-3G GIAO d:acetone" B 89.1058 "B2H6 B3LYP/6-311G GIAO d:acetone" B 93.0753 "B2H6 B3LYP/6-31+G(d) GIAO d:acetone" B 98.3005 "B2H6 B3LYP/sto-3G SINGLE GAUGE ORIGIN d:acetone" B 62.6983 "B2H6 B3LYP/sto-3G IGAIM d:acetone" B 62.6976 "B2H6 B3LYP/sto-3G CGST d:acetone" B 100.7578 "BF3OEt2 B3LYP/6-311+G(d,p) GIAO B 83.931 "B2H6 BP86/TZ2P GIAO" > > 3- Is there any scaling factor that can we use for NMR calctions? I dont know. But it is very fast to calculate absolute shielding in boron atoms of the B2H6 at the same level that you optimized molecule. The calculation over BF3·OEt2 obviously is more complicated. My starting B2H6 structure (from Cambridge Database ) was it: 1 B -0.212824556797 0.815972688028 0.277083624792 2 H -1.178708708530 0.956389357742 0.961317434319 3 H 0.475157611526 1.732217182820 -0.051321081303 4 H 0.549202398820 -0.127486734845 0.801036573432 5 H -0.549201706108 0.127486656264 -0.801037123218 6 B 0.212824556978 -0.815972733325 -0.277083646957 7 H 1.178709056940 -0.956389500060 -0.961316770576 8 H -0.475158654622 -1.732216467110 0.051321209476 > > 4- Two signs are used in NMR shieldings, sigma or deta (lower cases of greek) difference b/w these two? I am not sure that means exactly sigma (or tau?) and I dont know the factor conversion between delta and sigma(tau?). You can see it in old papers (70th) and now I think that all people use delta (and BF3·OEt2 as reference) Regards, Emilio José Juárez Pérez PhD Student ICMAB-CSIC Campus UAB 08193 Bellaterra (Barcelona). Spain ejjuarez _ icmab.es www.emiliojuarez.es Tel. + 34 93 580 1853 (ext. 255) Fax + 34 93 580 5729 From owner-chemistry@ccl.net Wed Oct 29 21:05:00 2008 From: "Richard L. Wood woodx278*umn.edu" To: CCL Subject: CCL: A couple of ChemCraft questions Message-Id: <-37992-081029210225-18613-CE/tPBtwoDgvFNSwERF6Pw : server.ccl.net> X-Original-From: "Richard L. Wood" Date: Wed, 29 Oct 2008 21:02:21 -0400 Sent to CCL by: "Richard L. Wood" [woodx278]|[umn.edu] Hi all, I've sent one of these questions to the people that develop ChemCraft, but I have yet to get a response, so I haven't sent the second one. The first one is fairly simple. Does anyone out there have any experience installing ChemCraft under SuSe Linux, and if so would you be willing to share any tips? Second, we just upgraded to version 1.6 from version 1.5 under Windows NT (Windows XP Professional, actually), and when we try to close the program we get an error message telling us "cannot create "c:\Program Files\Chemcraft\~last.tmp". I assume this is because we don't have permission to write to the c:\drive since we're "networked". Does anyone know of a work around for this problem? Thanks in advance, Richard