From owner-chemistry@ccl.net Tue Dec 2 07:15:01 2014 From: "Jan H Jensen jhjensen-$-chem.ku.dk" To: CCL Subject: CCL: Computational Chemistry Highlights: November issue Message-Id: <-50787-141202041448-29016-NBTie02xENxy5wgCkryF1w(~)server.ccl.net> X-Original-From: "Jan H Jensen" Date: Tue, 2 Dec 2014 04:14:47 -0500 Sent to CCL by: "Jan H Jensen" [jhjensen-#-chem.ku.dk] The November issue of Computational Chemistry Highlights is out. CCH is an overlay journal that identifies the most important papers in computational and theoretical chemistry published in the last 1-2 years. CCH is not affiliated with any publisher: it is a free resource run by scientists for scientists. You can read more about it here. http://proteinsandwavefunctions.blogspot.com/2012/02/computational-chemistry-highlights- new.html Table of content for this issue features contributions from CCH editors Steven Bachrach, David Bowler, and Jan Jensen: Quantum Chemical Approach to Estimating the Thermodynamics of Metabolic Reactions http://www.compchemhighlights.org/2014/11/quantum-chemical-approach-to-estimating.html Isotope Effects, Dynamic Matching, and Solvent Dynamics in a Wittig Reaction. Betaines as Bypassed Intermediates http://www.compchemhighlights.org/2014/11/isotope-effects-dynamic-matching-and.html Energy-conserving ab initio molecular dynamics http://www.compchemhighlights.org/2014/11/energy-conserving-ab-initio-molecular.html Solution-Phase Dimerization of an Oblong Shape-Persistent Macrocycle http://www.compchemhighlights.org/2014/11/solution-phase-dimerization-of-oblong.html Theoretical Foundation for the Presence of Oxacarbenium Ions in Chemical Glycoside Synthesis http://www.compchemhighlights.org/2014/11/theoretical-foundation-for-presence-of.html Interested in more? There are many ways to subscribe to CCH updates. http://www.compchemhighlights.org/p/get-cch-updates.html From owner-chemistry@ccl.net Tue Dec 2 13:20:00 2014 From: "Steven Bachrach sbachrac~!~trinity.edu" To: CCL Subject: CCL: In Memorium: Paul Schleyer Message-Id: <-50788-141202131733-17131-v6xXTkHzr5CdUy2eDZ1Kiw##server.ccl.net> X-Original-From: Steven Bachrach Content-Type: multipart/alternative; boundary=f46d04428eba2def2305093fbd22 Date: Tue, 2 Dec 2014 10:17:24 -0800 MIME-Version: 1.0 Sent to CCL by: Steven Bachrach [sbachrac-*-trinity.edu] --f46d04428eba2def2305093fbd22 Content-Type: text/plain; charset=UTF-8 In memory of Paul Schleyer, who passed away on November 21 2014, I have posted on my blog a reprint of the interview I had with Paul from my book *Computational Organic Chemistry*. You can find the post at http://comporgchem.com/blog/?p=3403 Steven -- Steven Bachrach Semmes Distinguished Professor and Assistant VP for Special Projects Department of Chemistry Trinity University Phone: 210-999-7379 1 Trinity Place Fax: 210-999-7569 San Antonio, TX 78212 email: sbachrach:trinity.edu --f46d04428eba2def2305093fbd22 Content-Type: text/html; charset=UTF-8 Content-Transfer-Encoding: quoted-printable
In memory of Paul Schleyer, who passed away on Novemb= er 21 2014, I=20 have posted on my blog a reprint of the interview I had with Paul from=20 my book Computational Organic Chemistry. You can find the post at
http://comporgchem.c= om/blog/?p=3D3403

Steven

--
Steven Bachrach
Semmes Distinguished Professor and Assistant VP for Sp= ecial Projects
Department of Chemistry
Trinity University =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 = =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0Phone: 210-999-7379
1 Trinity Place =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2= =A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0Fax: 210-999-7569
San Antonio, TX 78212 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2= =A0 email: sbach= rach:trinity.edu
--f46d04428eba2def2305093fbd22-- From owner-chemistry@ccl.net Tue Dec 2 15:47:01 2014 From: "Elaine Meng meng],[cgl.ucsf.edu" To: CCL Subject: CCL: plotting 3D vectors on molecules (Chimera) Message-Id: <-50789-141202143239-17283-M1SbMY3G9CwDDKHeVhpJ8A:-:server.ccl.net> X-Original-From: "Elaine Meng" Date: Tue, 2 Dec 2014 14:32:38 -0500 Sent to CCL by: "Elaine Meng" [meng[*]cgl.ucsf.edu] Hi Mikael, probably there are similar things in other programs, but in Chimera you can create objects using a simple "bild" file. For example, I created a plain text file named arrows.bild with the following 6 lines: .color yellow .arrow 36.177 29.853 50.124 32 33 48 .color red .arrow 34.968 30.340 48.234 37 26 44 .color green .arrow 39.261 32.018 46.920 35 35 48 Then in Chimera I used commands: open 2gbp delete ~ ligand focus open ~/Desktop/arrows.bild (open pdb 2gbp, delete everything except ligand, focus the view, open object file) The bild object format is described here: http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/bild.html Best, Elaine ---------- Elaine C. Meng, Ph.D. UCSF Computer Graphics Lab (Chimera team) and Babbitt Lab Department of Pharmaceutical Chemistry University of California, San Francisco From owner-chemistry@ccl.net Tue Dec 2 22:39:01 2014 From: "Shawkat Islam sislam/./swin.edu.au" To: CCL Subject: CCL: How can I fix the lattice constants derived from the bulk? Message-Id: <-50790-141202203632-31776-0Sb+Gg2zYe5jj1z2sBK0jg,,server.ccl.net> X-Original-From: "Shawkat Islam" Date: Tue, 2 Dec 2014 20:36:23 -0500 Sent to CCL by: "Shawkat Islam" [sislam_-_swin.edu.au] Hi CCL users, I wanted to study surface interaction. So, I optimized my bulk and prepared surface based on the optimized bulk. Later I relax my surface with ISIF=2. How can I fix the lattice constants derived from the bulk? Thanks Shawkat sislam/./swin.edu.au