Dear Rocky,

= You are right! Generally, trans alkenes are more stable than their cis coun= terparts but in case of 1,2 dihaloalkenes the relative stability is reverse= ! Cis isomers of 1,2 difluoro, 1,2 dichloro even 1-halo, 2-methyl alkenes a= re more stable compared to their trans isomers. If you look at stereochemis= try text books or journals you will find different examples of such compoun= ds and many explanations for this unexpected stability. This effect even ha= s a name in stereochemistry; it is called cis effect.

Good luck,
= Cina
-------------------------------------------------------------------= ---------------------------------------------------------------------------= ------------
Cina Foroutan-Nejad, PhD
http://muni.academia.edu/CinaFo= routanNejad

From: Ulrike Salzner salzner[-]g= mail.com <owner-chemistry]-[ccl.net>
To: "Foroutan-Nejad, Cina " <canyslopus]-[yahoo= .co.uk>
Sent: Frid= ay, 8 February 2013, 9:14
Subject= : CCL: Reg: computation of Delta H

Dear Rocky,

hea= ts of formation can be positive or negative. The molecule is the more stabl= e with respect to its elements, the lower, the more negative the heat of fo= rmation. If greater means a larger positive value, the cis form shoul= d have the 'greater' heat of formation. It is possible that the level of theory, you = are using is getting it wrong.
=0A

Regards,

Ulrike

On Thu, Feb 7, 2013 at 4:57 PM, rocky walden rocky.walden19[]<= a rel=3D"nofollow" target=3D"_blank" href=3D"http://gmail.com/">gmail.com <= owner-chemistry*o*ccl.net> wrote:
=0A

=0ASent to CCL by: rocky walden [rocky.walden19[= a]gmail.co= m]
=0AHi,
=0A
=0AI have computed heat of formation for few com= pounds, ( cis butene &
=0Atrans butene) and ( cis 1,2 dichloro ethen= e, & trans ( 1,2
=0Adichloroethene).
=0AI see the Delta H formati= on for trans is greater than cis, but as far
=0Aas I, know Heat of forma= tion is inversely proportional to stability.
=0AAm I doing some thing wr= ong ? Or the application is behaving /
=0Athrowing some value?
=0AYou= r suggestions much appreciated.
=0A
=0ARocky M. Walden
=0A
=0A<= br>=0A
=0A-=3D This is automatically added to each message by the mailin= g script =3D-
=0A
=0AE-mail to subscribers: CHEMISTRY*o*ccl.net or use:
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=0A http://www.ccl.net/chemistry/sub_unsub.shtml
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=0A
=0AJob: http://www.ccl.net= /jobs
=0AConferences: http://server.c= cl.net/chemistry/announcements/conferences/
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=0ASearch Message= s: http://www.ccl.net/chemistry/searchccl/index.shtm= l
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=0ARTFI: http://www.ccl.net/chemistr= y/aboutccl/instructions/
=0A
=0A
=0A

--
Assoc. Prof. Ulrike Salzner
Department of Chem= istry
Bilkent University
06800 Bilkent, Ankara=0A

=0A

<= br>

---1712059246-541556474-1360317239=:76066-- From owner-chemistry@ccl.net Fri Feb 8 07:13:00 2013 From: "Eldar Mamin yeldar443++mail.ru" To: CCL Subject: CCL: Error in trnsition state search in MOLPRO Message-Id: <-48196-130208071143-7762-5lR8Znf6oTa9cSTQnEv9ZA()server.ccl.net> X-Original-From: "Eldar Mamin" Date: Fri, 8 Feb 2013 07:11:42 -0500 Sent to CCL by: "Eldar Mamin" [yeldar443%x%mail.ru] Dear Molpro users, i have a question, how to eliminate error in CASSCF transition state search. Calculation stops when optimization started with the message: ".........Geometry optimization using default procedure for command MULTI Geometry written to block 1 of record 700 GETMEM ERROR IN GETMEM HerR Free GLOBAL ERROR fehler on processor 0 " What does it mean? Isufficient memory? My script: #!/bin/bash -l #SBATCH -p parallel #SBATCH -N 2 # Number of nodes #SBATCH -n 12 # total nuber of cores #SBATCH -t 1:30:00 # time as hh:mm:ss #SBATCH -J molpro-parallel #SBATCH -e jobfile.err%J #SBATCH -o jobfile.out%J #SBATCH --mem-per-cpu=2000 # requested memory per process in MB #SBATCH --tmp=500000 # requested scratch disk in total on /tmp in MB # # the maximum value is 800000 SDIR=`pwd` echo "Submission directory is: $SDIR" echo "The job ID assigned by the Batch system is: $SLURM_JOBID" echo "Number of requested processes $SLURM_NPROCS" export MOLPRO_RUN=/tmp/$USER/$SLURM_JOB_ID export MOLPRO_INTS=/tmp/$USER/$SLURM_JOB_ID export HOSTS_FILE=$SDIR/molpro.machines rm -f $HOSTS_FILE srun hostname > $HOSTS_FILE module load molpro/2010.1_pl25 /usr/bin/time -p $MOLPROP -d$MOLPRO_RUN -I$MOLPRO_INTS -W$PWD ts1_numhess.com rm -rf $MOLPRO_RUN rm -rf $MOLPRO_INTS My INPUT: ***for molpro memory,120,M geomtyp=xyz geometry={ 9 commentarii C,-1.285931204,-0.679845705,0.0384570 C,-1.290781036,0.703050546,0.00609033 H,-1.598552675,1.192930366,-0.8940176 H,-1.343206131,1.268340424,0.98632563 H,-1.237244334,-1.177851631,0.9916567 H,-1.627936272,-1.235763131,-0.818137 O,0.792292436,-1.081638240,-0.3296444 O,0.750752436,1.068477397,-0.08057969 O,1.272191642,-0.067146013,0.36858585 } basis={O=AVDZ,C=AVDZ,H=AVDZ} {hf;wf,40,1,0,0} {multi,MAXIT=512;cpmcscf,hess,accu=1.d-4;occ,24;closed,15;wf,40,1,0,0} {optg,root=2,gradient=1.d-4} --- Best regards, Eldar. Yeldar443__mail.ru From owner-chemistry@ccl.net Fri Feb 8 08:36:00 2013 From: "Giuseppe Mallia g.mallia|imperial.ac.uk" To: CCL Subject: CCL: MSSC2013 - Ab initio Modelling in Solid State Chemistry - FIRST CALL Message-Id: <-48197-130208070012-7280-0U7eBhMF/f0MVjeHCo4eRw,server.ccl.net> X-Original-From: "Giuseppe Mallia" Date: Fri, 8 Feb 2013 07:00:06 -0500 Sent to CCL by: "Giuseppe Mallia" [g.mallia[*]imperial.ac.uk] ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ WORKSHOP ANNOUNCEMENTS MSSC2013 - Ab initio Modelling in Solid State Chemistry ==> Turin Edition (Experienced Users): Featuring CRYSTAL13 and CRYSCOR13 Torino, Italy, September 1-5, 2013 ==> London Edition (New Users): Discovering quantum-mechanical simulations with CRYSTAL London (UK), September 16-20, 2013 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ MSSC2013 - Ab initio Modelling in Solid State Chemistry Turin Edition (Experienced Users): Featuring CRYSTAL13 and CRYSCOR13 Torino, Italy, September 1-5, 2013 Director: R. Dovesi Its aim is to illustrate the features of the CRYSTAL13 and CRYSCOR13 programs. The school is addressed to all CRYSTAL's users, senior researchers and scientists with a good background in solid state chemistry and physics, who can take advantage of the two codes for their applications *** Workshop in memory of Cesare Pisani *** Torino, Italy, September 6-7, 2013 On September 6-7th, 2013, a two-day workshop in memory of Cesare Pisani will follow the MSSC2013 School. The workshop celebrates the life and accomplishments of Cesare Pisani, during his more than fourty-year academic career, and provides an occasion to remember his contributions to computational solid state chemistry and physics. The program features talks by several eminent scientists on the recent development of theoretical and computational chemistry of crystalline systems. Website is under construction. ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ MSSC2013 - Ab initio Modelling in Solid State Chemistry London Edition (New Users): Discovering quantum-mechanical simulations with CRYSTAL London (UK), September 16-20, 2013 Directors: N.M. Harrison - G. Mallia The week long school is designed for CRYSTAL users, PhD students, Post-Docs and researchers with interests in solid state chemistry, physics, materials science, surface science, catalysis, magnetism and nano-science. It will provide both an introduction to the capabilities of quantum mechanical simulation and to the practical use of CRYSTAL and CRYSCOR. Website is under construction. ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ From owner-chemistry@ccl.net Fri Feb 8 11:27:01 2013 From: "Emilio Gallicchio emilio],[biomaps.rutgers.edu" To: CCL Subject: CCL: Unbinned-WHAM R package release Message-Id: <-48198-130208111545-9395-VxV0YL/sSDo0RGSNXfnwGg=-=server.ccl.net> X-Original-From: Emilio Gallicchio Content-Type: text/plain; charset=ISO-8859-1 Date: Fri, 8 Feb 2013 11:15:37 -0500 MIME-Version: 1.0 Sent to CCL by: Emilio Gallicchio [emilio%x%biomaps.rutgers.edu] Dear Colleagues, "UWHAM", a R package for multi-state free energy estimation and thermodynamic reweighting has been released to the R network (CRAN). To install it enter: > install.packages("UWHAM") within a R session. Documentation is available within R by entering > library("UWHAM") > help(uwham) or in pdf format from http://cran.r-project.org/web/packages/UWHAM/index.html The package has been developed jointly with Zhiqiang Tan at the Department of Statistics at Rutgers University. The method implemented can be understood as an extension of WHAM not requiring binning of input data; hence the name "unbinned"-WHAM, or UWHAM for short. The main UWHAM publication is: Tan Z, Gallicchio E, Lapelosa M, Levy RM. Theory of binless multi-state free energy estimation with applications to protein-ligand binding. J Chem Phys, 136, 144102 (2012). http://hpcp.rutgers.edu/~emilio/Tan-et-al2012.html http://dx.doi.org/10.1063/1.3701175 The UWHAM package provides to R users functionality similar to the MBAR python package by Michael Shirts & John Chodera. MBAR and UWHAM return identical point estimates of free energies and expectations using different numerical routes. Variance estimation is based on the Fisher or Sandwich formulas, or, for correlated data, by block bootstrap. Processes corresponding to multiple independent simulations, serial tempering or serial Hamiltonian hopping simulations, and parallel replica exchange simulations of both the synchronous and asynchronous varieties are supported. The UWHAM package is particularly robust in terms of scalability; we have been able to process within minutes large 2D replica exchange datasets with ~300,000 snapshots from ~200 thermodynamic states. UWHAM is freely released in the hope that it will benefit the computational chemistry community. Feedback, comments, and bug reports are greatly appreciated. Emilio Gallicchio -- Prof. Emilio Gallicchio Dept. of Chemistry & Chemical Biology and BioMaPS Institute Rutgers University, New Jersey (USA) Email: emilio:_:biomaps.rutgers.edu WWW: http://hpcp.rutgers.edu/~emilio From owner-chemistry@ccl.net Fri Feb 8 12:02:01 2013 From: "Errol Lewars elewars]~[trentu.ca" To: CCL Subject: CCL: Reg: computation of Delta H Message-Id: <-48199-130208112614-10149-GXd3g6YL4eMYhySJiD8v4Q|server.ccl.net> X-Original-From: Errol Lewars Content-Transfer-Encoding: 7bit Content-Type: text/plain; charset=ISO-8859-1; format=flowed Date: Fri, 08 Feb 2013 11:26:23 -0500 MIME-Version: 1.0 Sent to CCL by: Errol Lewars [elewars(_)trentu.ca] 2013 Feb 08 I don't know what computational level you used. G4MP2 enthalpies are good; as one of *many* examples, they agree closely with very high-level values for furan, 2-methylfuran and 2,5-dimethylfuran (D. Feller, J. M. Simmie, J Phys Chem A, 2012, 116(47), 11768), being within 3 kJ mol-1 of those benchmark enthalpies of formation. G4MP2 puts the 298 K enthalpy of cis-2-butene 5.1 kJ mol-1 above that of trans-2-butene (and the free energy 3.9 above). The NIST website puts it 3.1 kJ mol-1 above. So these values agree that the cis is of higher energy than the trans. The results for the 1,2-dichloroethene stereoisomers are ambiguous. G4MP2 puts the cis lower, but by only 2.7 kJ mol-1 (free energy 2.4 kJ mol-1 lower), while experiment (NIST) puts it 2-3 kJ mol-1 lower or higher, depending on the experiment. E. Lewars == rocky walden rocky.walden19[]gmail.com wrote: > Sent to CCL by: rocky walden [rocky.walden19[a]gmail.com] > Hi, > > I have computed heat of formation for few compounds, ( cis butene & > trans butene) and ( cis 1,2 dichloro ethene, & trans ( 1,2 > dichloroethene). > I see the Delta H formation for trans is greater than cis, but as far > as I, know Heat of formation is inversely proportional to stability. > Am I doing some thing wrong ? Or the application is behaving / > throwing some value? > Your suggestions much appreciated. > > Rocky M. Walden> >