From owner-chemistry@ccl.net Mon Jun 17 01:09:01 2013 From: "Andreas Klamt klamt++cosmologic.de" To: CCL Subject: CCL: Hydrogen bond of sulfur containing molecules Message-Id: <-48834-130617010331-8978-+Py7MxAF1EMDx/g+3f8dnQ*|*server.ccl.net> X-Original-From: Andreas Klamt Content-Transfer-Encoding: 8bit Content-Type: text/plain; charset=ISO-8859-15; format=flowed Date: Mon, 17 Jun 2013 07:03:21 +0200 MIME-Version: 1.0 Sent to CCL by: Andreas Klamt [klamt^cosmologic.de] Adel, we have recently published two papers on the estimation of hydrogen bond strength using the COSMO polarization charge density as descriptor. In one paper we consider the quantum chemically calculated hb-enthapies of a broad range of donors and acceptors, including sulfur acceptor atoms and SH donor groups. In the other paper we analyzed experimental hb enthalpies and hb-free energies measured experimentally by a group in Nantes (the pKBHx) data. This paper also covers sulfur as acceptor. Andreas Polarization charge densities provide a predictive quantification of hydrogen bond energies Phys. Chem. Chem. Phys., 2012,14, 955-963; DOI: 10.1039/C1CP22640A http://pubs.rsc.org/en/content/articlelanding/2012/cp/c1cp22640a Interpretation of experimental hydrogen-bond enthalpies and entropies > from COSMO polarisation charge densities Phys. Chem. Chem. Phys., 2013,15, 7147-7154; DOI: 10.1039/C3CP44611E http://pubs.rsc.org/en/content/articlelanding/2013/cp/c3cp44611e Am 16.06.2013 12:38, schrieb Adel El-Azhary azhary*ksu.edu.sa: > Sent to CCL by: "Adel El-Azhary" [azhary^ksu.edu.sa] > Dear all, > Does anyone know a study of the estimate of the hydrogen bond in sulfur containing molecules? I made an intensive search but could not get any solid conclusion. > > Best regards, > > Adel El-Azhary > Chemistry Department, > Faculty of Science > King Saud University > P.O. Box 2455 > Riyadh, 11451 > Saudi Arabia> > > -- Prof. Dr. Andreas Klamt CEO / Geschäftsführer COSMOlogic GmbH & Co. KG Imbacher Weg 46 D-51379 Leverkusen, Germany phone +49-2171-731681 fax +49-2171-731689 e-mail klamt|*|cosmologic.de web www.cosmologic.de [University address: Inst. of Physical and Theoretical Chemistry, University of Regensburg] HRA 20653 Amtsgericht Koeln, GF: Prof. Dr. Andreas Klamt Komplementaer: COSMOlogic Verwaltungs GmbH HRB 49501 Amtsgericht Koeln, GF: Prof. Dr. Andreas Klamt From owner-chemistry@ccl.net Mon Jun 17 08:34:00 2013 From: "azin azarkamand azin.azarkamand]-[gmail.com" To: CCL Subject: CCL: Abinit Message-Id: <-48835-130617052215-31455-JS9b6Y1Q5T3Q76NulgrzjQ|a|server.ccl.net> X-Original-From: "azin azarkamand" Date: Mon, 17 Jun 2013 05:22:14 -0400 Sent to CCL by: "azin azarkamand" [azin.azarkamand-*-gmail.com] Dear all I am recent user of Abinit and I am interested to work on different DFT functional such as LDA and PBE and ( phonon calculation ). I would be grateful if you could supply me with some input example in these two subjects. all usefull notes will be appreciated. Thanks in advance Azin Azarkamand. From owner-chemistry@ccl.net Mon Jun 17 15:56:00 2013 From: "Thomas Vent-Schmidt thomas.vent-schmidt+/-ac.uni-freiburg.de" To: CCL Subject: CCL: Problem with EDA in gamess Message-Id: <-48836-130617145745-25045-bARjbiva4s67q5T1eBU1EA[A]server.ccl.net> X-Original-From: "Thomas Vent-Schmidt" Date: Mon, 17 Jun 2013 14:57:44 -0400 Sent to CCL by: "Thomas Vent-Schmidt" [thomas.vent-schmidt[]ac.uni-freiburg.de] Hello I have some problems with an EDA analysis using the Gamess-US program. The job is killed without any special error message in the first orbital localisation part (see output below). I also included the input. I use the aug-cc-pVTZ basis sets for fluorine and hydrogen and the Stuttgart RSc 1997 ECP basis for uranium but I also tried a all-electron basis set which results in the same error. Input: $CONTRL SCFTYP=UHF DFTTYP=B3LYP MULT=5 PP=Read RunTYP=EDA Coord=ZMT $END $CONTRL MAXIT=200 QMTTOL=3.0E-07 $END $CONTRL LOCAL=BOYS $END $INTGRL NINTMX=2000 $END $TRANS MPTRAN=2 CUTTRF=1E-07 $END $SCF Shift=.t. DIIS=.t. $End ! $DFT Method=Grid SWOFF=1.0E03 SWITCH=1.00E01 $END $system MWords=1000 $end $guess guess=hcore $end $basis EXTFIL=.true. GBASIS=avtzbasi $End $lmoeda supbas=.f. matom(1)=2,1 mcharg(1)=0,0 mmult(1)=4,2 $end $data HUF C1 U H 1 uh F 1 uf 2 huf uh= 2.0557 uf= 2.0637 huf= 101.4622 $end $ecp U-ECP GEN 60 4 1 ----- g-ul potential ----- -60.129989580 2 12.804088440 2 ----- s-ul potential ----- 536.516627780 2 16.414038690 60.129989580 2 12.804088440 2 ----- p-ul potential ----- 169.544924650 2 9.060556060 60.129989580 2 12.804088440 2 ----- d-ul potential ----- 142.615598370 2 8.831831980 60.129989580 2 12.804088440 2 ----- f-ul potential ----- 60.393076020 2 7.018516290 60.129989580 2 12.804088440 H:none F:none $END Output:(Error part) ...... END OF UHF CALCULATION ...... STEP CPU TIME = 99.92 TOTAL CPU TIME = 110.4 ( 1.8 MIN) TOTAL WALL CLOCK TIME= 116.2 SECONDS, CPU UTILIZATION IS 95.00% --------------------------------------- EDMISTON-RUEDENBERG ENERGY LOCALIZATION --------------------------------------- C.EDMISTON AND K.RUEDENBERG, REV.MOD.PHYS. 35, 457-465 (1963) ***** ALPHA ORBITAL LOCALIZATION ***** -------------------------------------------- PARTIAL TWO ELECTRON INTEGRAL TRANSFORMATION -------------------------------------------- NUMBER OF CORE MOLECULAR ORBITALS = 0 NUMBER OF OCCUPIED MOLECULAR ORBITALS = 18 TOTAL NUMBER OF MOLECULAR ORBITALS = 18 TOTAL NUMBER OF ATOMIC ORBITALS = 130 THRESHOLD FOR KEEPING TRANSFORMED 2E- INTEGRALS = 1.000E-07 AO INTEGRALS WILL BE READ IN FROM DISK... # OF WORDS AVAILABLE = 995113683 # OF WORDS NEEDED = 20017862 FOR IN MEMORY TRANSFORMATION FOR THE SEGMENTED TRANSFORMATION: MINIMUM= 1199712 WORDS FOR 1 MOLECULAR ORBITAL PER PASS MAXIMUM= 20017862 WORDS FOR ALL MOLECULAR ORBITALS IN 1 PASS ( 1106950 EXTRA WORDS WOULD INCLUDE AN EXTRA ORBITAL/PASS) SEGMENTED PARTIAL TRANSFORMATION WILL USE 20017862 WORDS, DISTRIBUTING 1 PASSES EACH CONTAINING 18 ORBITALS OVER 1 PROCESSORS. CHOOSING OUT-OF-MEMORY BIN-SORT TRANSFORMATION... # PASSES = 1 # WORDS USED = 20020049 OPENING FILE DASORT WITH 2187 LOGICAL RECORDS OF 8515 WORDS WITH A MAXIMUM OF 10935 PHYSICAL RECORDS OF 2048 WORDS ddikick.x: application process 0 quit unexpectedly. ddikick.x: Sending kill signal to DDI processes. ddikick.x: Execution terminated due to error(s). ----- accounting info ----- Files used on the master node seb12 were: -rw------- 1 tgaisser users 1,2K 3. Nov 00:19 /var/tmp/gamess/huf.F05 -rw------- 1 tgaisser users 141M 3. Nov 00:19 /var/tmp/gamess/huf.F08 -rw------- 1 tgaisser users 1,4K 3. Nov 00:21 /var/tmp/gamess/huf.F09 -rw------- 1 tgaisser users 7,4M 3. Nov 00:21 /var/tmp/gamess/huf.F10 -rw------- 1 tgaisser users 14M 3. Nov 00:21 /var/tmp/gamess/huf.F20 Di 3. Nov 00:21:33 CET 2009 0.118u 0.092s 2:05.03 0.1% 0+0k 1000+104io 6pf+0w Has anyone an idea what`s wrong? Thanks a lot M.Sc. Thomas Vent-Schmidt AK Riedel Universitt Freiburg Institut fr Anorganische und Analytische Chemie Albertstr. 21 D-79104 Freiburg Tel. ++49(0)761/203-6125