From owner-chemistry@ccl.net Thu Sep 18 04:46:01 2014 From: "Sergio Manzetti sergio.manzetti a outlook.com" To: CCL Subject: CCL: Metal-Carbene sigma type bond Message-Id: <-50503-140918044457-23613-CB9+/DfIXsd2Xp7TIVFGDw(0)server.ccl.net> X-Original-From: "Sergio Manzetti" Date: Thu, 18 Sep 2014 04:44:55 -0400 Sent to CCL by: "Sergio Manzetti" [sergio.manzetti!=!outlook.com] Dear all, I have a question regarding the formation of a sigma-type bond between Tantalum and the carbene ion. The sigma type bond is apparently a sp2 hybridized bond. Accounting for the configuration of carbon, it donates its two 2px electrons which interact with one of the tantalum 6s? The pi type bond is more clear, it is formed by an empty 2py of the carbon interacting with one of the 5d electrons. However, if the sigma type bond is formed by two 2px electrons, where does the second 6s electron go? Alternatively, this was wrong assumption. Orginally, I was looking for the energy diagram of the sigma type bond of the Ta=CH2, but could not find it. Thanks From owner-chemistry@ccl.net Thu Sep 18 05:21:01 2014 From: "Adel Reisi areisi{=}kashanu.ac.ir" To: CCL Subject: CCL: Question abaut NBO analysis calculation in GENNBO 5.0 Message-Id: <-50504-140918044912-24855-u/SviVEq4LXYSem0EN+Gaw!A!server.ccl.net> X-Original-From: "Adel Reisi" Date: Thu, 18 Sep 2014 04:49:09 -0400 Sent to CCL by: "Adel Reisi" [areisi]~[kashanu.ac.ir] Dear... I want to do an NBO calculation in GENNBO 5.0 and I need to ***.47 file but I can not create it in windows. Please help to me, if it is possible to you. From owner-chemistry@ccl.net Thu Sep 18 06:24:00 2014 From: "Russell Driver rwdriver]|[kaist.ac.kr" To: CCL Subject: CCL: implicit solvation of a peptide with TINKER Message-Id: <-50505-140918062253-28355-fCiHbvz5e6DiYC1IRTpWYQ],[server.ccl.net> X-Original-From: "Russell Driver" Date: Thu, 18 Sep 2014 06:22:52 -0400 Sent to CCL by: "Russell Driver" [rwdriver*_*kaist.ac.kr] Hello computational chemists, I would like to minimize the geometry of an uncharged polypeptide in implicit organic solvent (such as MeOH or CDCl3, not water) using TINKER. When I use the solvate keyword and a modifier in the keyfile, ( "solvate ace" for instance) the calculation finishes almost immediately. Am I missing something basic? Energy minimization works fine in a vacuum. Also, does anyone have an idea which algorithm might be best (ASP/SASA/ONION/STILL/HCT/ACE/GBSA) for this type of calculation? Any info is appreciated, thanks, Russell From owner-chemistry@ccl.net Thu Sep 18 08:26:00 2014 From: "Fedor Goumans goumans .. scm.com" To: CCL Subject: CCL: Metal-Carbene sigma type bond Message-Id: <-50506-140918074715-7536-LRet/VjwGFt1GfBKf4aSxw||server.ccl.net> X-Original-From: Fedor Goumans Content-Transfer-Encoding: 7bit Content-Type: text/plain; charset=ISO-8859-1; format=flowed Date: Thu, 18 Sep 2014 13:46:58 +0200 MIME-Version: 1.0 Sent to CCL by: Fedor Goumans [goumans^-^scm.com] Hi Sergio, You may consider using any of the chemical bonding analysis tools out there to dig in to the bonding situation (aside from the phenomenological Dewar-Chatt-Duncanson model). Or if anything, just look at the Mulliken population analysis. My guess is that for tantalum carbene complexes the 6s orbitals will not be occupied at all. I suggest the thorough paper by Frenking et al. (Chemical bonding in transition metal carbene complexes, J. Organomet. Chem. 690, p. 6178-6204 (2005)) as a starting point. Most of it is on Cr carbenes, but you can exctend the analysis to group-5 transition metals as well ('early TMs'). Best wishes, Fedor On 9/18/2014 10:44 AM, Sergio Manzetti sergio.manzetti a outlook.com wrote: > Sent to CCL by: "Sergio Manzetti" [sergio.manzetti!=!outlook.com] > Dear all, I have a question regarding the formation of a sigma-type bond between Tantalum and the carbene ion. The sigma type bond is apparently a sp2 hybridized bond. Accounting for the configuration of carbon, it donates its two 2px electrons which interact with one of the tantalum 6s? The pi type bond is more clear, it is formed by an empty 2py of the carbon interacting with one of the 5d electrons. However, if the sigma type bond is formed by two 2px electrons, where does the second 6s electron go? > > Alternatively, this was wrong assumption. > > Orginally, I was looking for the energy diagram of the sigma type bond of the Ta=CH2, but could not find it. > > Thanks> > -- Dr. T. P. M. (Fedor) Goumans Business Developer Scientific Computing & Modelling NV (SCM) Vrije Universiteit, FEW, Theoretical Chemistry De Boelelaan 1083 1081 HV Amsterdam, The Netherlands T +31 20 598 7625 F +31 20 598 7629 E-mail: goumans\a/scm.com http://www.scm.com From owner-chemistry@ccl.net Thu Sep 18 12:20:00 2014 From: "Sergio Manzetti sergio.manzetti%%outlook.com" To: CCL Subject: CCL: Metal-Carbene sigma type bond Message-Id: <-50507-140918104154-31091-SD6n+YI/WZ0C5ccRzXd83A^_^server.ccl.net> X-Original-From: "Sergio Manzetti" Date: Thu, 18 Sep 2014 10:41:53 -0400 Sent to CCL by: "Sergio Manzetti" [sergio.manzetti-.-outlook.com] Dear Fedor, thanks. I have looked further in the book, and it seems there are two mechanisms at hand: one Fischer mechanism and one other the Schrock mechanism. The difference between the two, is that one considers the Metal bonding d-electrons as a singlet, while the other as a triplet. The singlet gives apparently a "regular" double bond by 4 electrons, pairing with the carbons 2p2. While the other, has one electron in the dxy and the other in the dxz, each of these unpaired electrons form a pair with the unpaired electrons of equally considered carbene in its triplet state. Eventually, it says that the latter (The Schrock mechanism) is more for likely for the heavier transition metals, while the Fischer more likely for light metals, such as Cr and V. Your guess on the non-participating 6s2 was right. I take its because the 6s really has a slightly lower energy than the 5d, at the end of the day (aufbau). Thanks for your tip. I May use software to check it out. Sergio > From: owner-chemistry%ccl.net > To: sergio.manzetti%gmx.com > Subject: CCL: Metal-Carbene sigma type bond > Date: Thu, 18 Sep 2014 13:46:58 +0200 > > > Sent to CCL by: Fedor Goumans [goumans^-^scm.com] > Hi Sergio, > > You may consider using any of the chemical bonding analysis tools out > there to dig in to the bonding situation (aside from the > phenomenological Dewar-Chatt-Duncanson model). Or if anything, just look > at the Mulliken population analysis. > My guess is that for tantalum carbene complexes the 6s orbitals will not > be occupied at all. > > I suggest the thorough paper by Frenking et al. (Chemical bonding in > transition metal carbene complexes, J. Organomet. Chem. 690, p. > 6178-6204 (2005)) as a starting point. Most of it is on Cr carbenes, but > you can exctend the analysis to group-5 transition metals as well > ('early TMs'). > > Best wishes, > Fedor > > On 9/18/2014 10:44 AM, Sergio Manzetti sergio.manzetti a outlook.com wrote: > > Sent to CCL by: "Sergio Manzetti" [sergio.manzetti!=!outlook.com] > > Dear all, I have a question regarding the formation of a sigma-type bond between Tantalum and the carbene ion. The sigma type bond is apparently a sp2 hybridized bond. Accounting for the configuration of carbon, it donates its two 2px electrons which interact with one of the tantalum 6s? The pi type bond is more clear, it is formed by an empty 2py of the carbon interacting with one of the 5d electrons. However, if the sigma type bond is formed by two 2px electrons, where does the second 6s electron go? > > > > Alternatively, this was wrong assumption. > > > > Orginally, I was looking for the energy diagram of the sigma type bond of the Ta=CH2, but could not find it. > > > > Thanks> > > > > > -- > Dr. T. P. M. (Fedor) Goumans > Business Developer > Scientific Computing & Modelling NV (SCM) > Vrije Universiteit, FEW, Theoretical Chemistry > De Boelelaan 1083 > 1081 HV Amsterdam, The Netherlands > T +31 20 598 7625 > F +31 20 598 7629 > E-mail: goumans**scm.com > http://www.scm.com> From owner-chemistry@ccl.net Thu Sep 18 15:06:00 2014 From: "Gary Breton gbreton%a%berry.edu" To: CCL Subject: CCL: Modeling extent of electron density transfer Message-Id: <-50508-140918150521-17284-FRy10eX8okL0JrfiTU3gAw]-[server.ccl.net> X-Original-From: "Gary Breton" Date: Thu, 18 Sep 2014 15:05:19 -0400 Sent to CCL by: "Gary Breton" [gbreton-.-berry.edu] Hi all, I'm seeking some advice on how best to measure/model the extent of electron transfer from a nucleophile (i.e., Nu:) to an electrophile (e.g., the carbon of a C=O bond). I would like to be able to visualize and/or calculate the electron density transfer from the nucleophile to the electrophile (prior to bond formation). Ideally I could do this by minimizing the Nu---C=O complex, calculate the electron density along the Nu---C=O bond, and then subtract the electron density for the same system where the interaction is "turned off". Is there a recommended way, or several ways, in which to approach a problem such as this? Recommended method/basis set? Thank you in advance for your help! Gary Gary Breton Berry College gbreton : berry.edu From owner-chemistry@ccl.net Thu Sep 18 15:45:00 2014 From: "Mariusz Radon mariusz.radon]![gmail.com" To: CCL Subject: CCL: Modeling extent of electron density transfer Message-Id: <-50509-140918154259-13061-ywNsWi38gWhfYzfdBAXTvA.@.server.ccl.net> X-Original-From: Mariusz Radon Content-Transfer-Encoding: 7bit Content-Type: text/plain; charset=ISO-8859-1 Date: Thu, 18 Sep 2014 21:42:48 +0200 MIME-Version: 1.0 Sent to CCL by: Mariusz Radon [mariusz.radon*_*gmail.com] On 09/18/2014 09:05 PM, Gary Breton gbreton%a%berry.edu wrote: > Sent to CCL by: "Gary Breton" [gbreton-.-berry.edu] > Hi all, > > I'm seeking some advice on how best to measure/model the extent of electron transfer from a nucleophile (i.e., Nu:) to an electrophile (e.g., the carbon of a C=O bond). I would like to be able to visualize and/or calculate the electron density transfer from the nucleophile to the electrophile (prior to bond formation). Ideally I could do this by minimizing the Nu---C=O complex, calculate the electron density along the Nu---C=O bond, and then subtract the electron density for the same system where the interaction is "turned off". > > Is there a recommended way, or several ways, in which to approach a problem such as this? Recommended method/basis set? > I would consider to use Natural Orbitals for Chemical Valence (NOCV) approach or its combination with energy decomposition analysis (ETS-NOCV). These methods are based on analysis of the differential density, i.e., precisely what you are interested in. As to the choice of method, I think that any DFT functional would give you a reasonable starting point, although the quantiative results may be somewhat functional-dependent. Note that treatment of correlation can be potentially important for the extent of charge donation, so I would probably not use HF or low-order post-HF methods (like MP2) for this problem; however, DFT should be fine. All the best, Mariusz -- Dr Mariusz Radon, Ph.D. Coordination Chemistry Group Faculty of Chemistry Jagiellonian University ul. Ingardena 3, 30-060 Krakow, Poland http://www2.chemia.uj.edu.pl/~mradon From owner-chemistry@ccl.net Thu Sep 18 16:23:00 2014 From: "Emilio Xavier Esposito emilio.esposito^-^gmail.com" To: CCL Subject: CCL: NVIDIA GPU Award for Best GPU Poster (COMP; Denver, spring 2015) Message-Id: <-50510-140918142016-15420-TdA+LrDU596r+QK4aypBYA..server.ccl.net> X-Original-From: Emilio Xavier Esposito Content-Type: text/plain; charset=UTF-8 Date: Thu, 18 Sep 2014 14:19:41 -0400 MIME-Version: 1.0 Sent to CCL by: Emilio Xavier Esposito [emilio.esposito . gmail.com] Hi Have GPUs drastically improved your ability to do research? Are you writing GPU code that will help you and other scientists do more, faster? If so, submit an abstract to the NVIDIA GPU Award for Best GPU Poster competition at the ACS national meeting in Denver, Colorado (March 22-26, 2015). The COMP division hosts the NVIDIA GPU Award for Best GPU Poster. More information regarding this competition can be found here: http://www.acscomp.org/awards/nvidia-gpu-award Information on submitting your abstract using MAPS ( maps.acs.org ) can be found here: http://www.acscomp.org/meetings/presenter-information#TOC-Abstract-Submissions Abstract submission via MAPS closes for COMP division submissions at 11pm Eastern Time on Tuesday, October 28, 2014. Good luck! Emilio -- Emilio Xavier Esposito, PhD COMP Programming Chair