From owner-chemistry@ccl.net Wed Jun 4 03:32:00 2014 From: "Sergio Manzetti sergio.manzetti[*]outlook.com" To: CCL Subject: CCL: Metallo-organic vc organometallic Message-Id: <-50159-140604033113-11319-pDRl7prFlAdqBc1NhTEeYw{=}server.ccl.net> X-Original-From: Sergio Manzetti Content-Type: multipart/alternative; boundary="_b38c066e-6e4f-4b34-a972-6f35a0677bd0_" Date: Wed, 4 Jun 2014 09:31:06 +0200 MIME-Version: 1.0 Sent to CCL by: Sergio Manzetti [sergio.manzetti/./outlook.com] --_b38c066e-6e4f-4b34-a972-6f35a0677bd0_ Content-Type: text/plain; charset="iso-8859-1" Content-Transfer-Encoding: quoted-printable Dear CCLers=2C is there a difference between the term metallo-organic chemi= stry and organometallic chemistry? There are books on both areas=2C however=2C one wonders why having two name= s for the same thing? Sergio = --_b38c066e-6e4f-4b34-a972-6f35a0677bd0_ Content-Type: text/html; charset="iso-8859-1" Content-Transfer-Encoding: quoted-printable

Dear CCLers=2C is there a differ= ence between the term metallo-organic chemistry and organometallic chemistr= y?

There are books on both areas=2C however=2C one wonders why havin= g two names for the same thing?

Sergio

= --_b38c066e-6e4f-4b34-a972-6f35a0677bd0_-- From owner-chemistry@ccl.net Wed Jun 4 07:51:00 2014 From: "Krisztian Niesz kniesz(~)chemaxon.com" To: CCL Subject: CCL: Metallo-organic vc organometallic Message-Id: <-50160-140604051653-5995-Wq2ydAW3/OJcJb8tgRlkLA]~[server.ccl.net> X-Original-From: Krisztian Niesz Content-Type: multipart/mixed; boundary="------------050005070907020004080309" Date: Wed, 04 Jun 2014 11:16:07 +0200 MIME-Version: 1.0 Sent to CCL by: Krisztian Niesz [kniesz^_^chemaxon.com] This is a multi-part message in MIME format. --------------050005070907020004080309 Content-Type: multipart/alternative; boundary="------------080106090603000304070000" --------------080106090603000304070000 Content-Type: text/plain; charset=ISO-8859-1; format=flowed Content-Transfer-Encoding: quoted-printable Hi Sergio, In organometallic compounds there is a direct carbon-metal bond, while=20 metalorganics refer to organic compounds that contain metal (no direct=20 C-M bond). Alkoxides are good example for the latter. Hope it helps! Krisztian On 6/4/2014 9:31 AM, Sergio Manzetti sergio.manzetti[*]outlook.com wrote: > Dear CCLers, is there a difference between the term metallo-organic=20 > chemistry and organometallic chemistry? > > There are books on both areas, however, one wonders why having two=20 > names for the same thing? > > Sergio --=20 *Krisztian Niesz*,***PhD* Head of Application Science *ChemAxon**Ltd*. Z=E1hony utca 7, Budapest, 1031, Hungary Tel: +361 453 0435 --------------080106090603000304070000 Content-Type: multipart/related; boundary="------------090800090009080705010009" --------------090800090009080705010009 Content-Type: text/html; charset=ISO-8859-1 Content-Transfer-Encoding: 7bit Hi Sergio,

In organometallic compounds there is a direct carbon-metal bond, while metalorganics refer to organic compounds that contain metal (no direct C-M bond). Alkoxides are good example for the latter. Hope it helps!

Krisztian

On 6/4/2014 9:31 AM, Sergio Manzetti sergio.manzetti[*]outlook.com wrote:

Dear CCLers, is there a difference between the term metallo-organic chemistry and organometallic chemistry?

There are books on both areas, however, one wonders why having two names for the same thing?

Sergio

Krisztian Niesz, PhD

Head of Application Science
ChemAxon Ltd.
Záhony utca 7, Budapest, 1031, Hungary
Tel: +361 453 0435

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--------------050005070907020004080309-- From owner-chemistry@ccl.net Wed Jun 4 10:27:00 2014 From: "Matt Challacombe matt.challacombe::gmail.com" To: CCL Subject: CCL: pdb curation, standardization for MM calculations? Message-Id: <-50161-140604102539-12324-OxSFE5naexhOkHXaGVmpGA ~~ server.ccl.net> X-Original-From: Matt Challacombe Content-Transfer-Encoding: 7bit Content-Type: text/plain; charset=ISO-8859-1; format=flowed Date: Wed, 04 Jun 2014 08:25:20 -0600 MIME-Version: 1.0 Sent to CCL by: Matt Challacombe [matt.challacombe,,gmail.com] Hi CCL, I have somewhat unconventional pdb files, eg from neutron calculations, involving D instead of H and etc. Are there simple scripts available to clean up a pbd for these sorts of non-standard differences (ie make recognizable for force field calculations)? Cheers, Matt From owner-chemistry@ccl.net Wed Jun 4 12:16:00 2014 From: "Mezei, Mihaly mihaly.mezei%mssm.edu" To: CCL Subject: CCL: pdb curation, standardization for MM calculations? Message-Id: <-50162-140604112037-3344-uxLo9BYL0a9Amrfiao5mQA{=}server.ccl.net> X-Original-From: "Mezei, Mihaly" Content-Language: en-US Content-Transfer-Encoding: 8bit Content-Type: text/plain; charset="us-ascii" Date: Wed, 4 Jun 2014 15:19:59 +0000 MIME-Version: 1.0 Sent to CCL by: "Mezei, Mihaly" [mihaly.mezei^-^mssm.edu] My program Simulaid (http://inka.mssm.edu/~mezei/simulaid) can convert PDB atom names to more standard ones. It has also the option of adding new names (in case the input PDB has names that are not recognized). Mihaly Mezei Department of Structural and Chemical Biology, Icahn School of Medicine at Mount Sinai Voice: (212) 659-5475 Fax: (212) 849-2456 WWW (MSSM home): http://www.mountsinai.org/Find%20A%20Faculty/profile.do?id=0000072500001497192632 WWW (Lab home - software, publications): http://inka.mssm.edu/~mezei WWW (Department): http://www.mssm.edu/departments-and-institutes/structural-and-chemical-biology ________________________________________ > From: owner-chemistry+mihaly.mezei==mssm.edu[A]ccl.net [owner-chemistry+mihaly.mezei==mssm.edu[A]ccl.net] on behalf of Matt Challacombe matt.challacombe::gmail.com [owner-chemistry[A]ccl.net] Sent: Wednesday, June 04, 2014 10:25 AM To: Mezei, Mihaly Subject: CCL: pdb curation, standardization for MM calculations? Sent to CCL by: Matt Challacombe [matt.challacombe,,gmail.com] Hi CCL, I have somewhat unconventional pdb files, eg from neutron calculations, involving D instead of H and etc. Are there simple scripts available to clean up a pbd for these sorts of non-standard differences (ie make recognizable for force field calculations)? Cheers, Matthttp://www.ccl.net/cgi-bin/ccl/send_ccl_messagehttp://www.ccl.net/chemistry/sub_unsub.shtmlhttp://www.ccl.net/spammers.txt From owner-chemistry@ccl.net Wed Jun 4 12:51:01 2014 From: "Jason Swails jason.swails^-^gmail.com" To: CCL Subject: CCL: pdb curation, standardization for MM calculations? Message-Id: <-50163-140604121853-18214-FJWn9HttILgkWwuv9rFtXg---server.ccl.net> X-Original-From: Jason Swails Content-Transfer-Encoding: 7bit Content-Type: text/plain; charset="UTF-8" Date: Wed, 04 Jun 2014 12:21:00 -0400 Mime-Version: 1.0 Sent to CCL by: Jason Swails [jason.swails.:.gmail.com] On Wed, 2014-06-04 at 08:25 -0600, Matt Challacombe matt.challacombe::gmail.com wrote: > Sent to CCL by: Matt Challacombe [matt.challacombe,,gmail.com] > Hi CCL, > > I have somewhat unconventional pdb files, eg from neutron calculations, > involving D instead of H and etc. Are there simple scripts available to > clean up a pbd for these sorts of non-standard differences (ie make > recognizable for force field calculations)? You can try pdbfixer to see if it does what you need it to. Available on Github: https://github.com/SimTk/pdbfixer The project is still quite young (<1 year old), and is still under fairly active development as far as I know. You can always start discussions on the issue tracker if it doesn't handle your PDB files and see if maybe its functionality can be expanded to your use cases as well. (Of course, it may just work out of the box). Hope this helps, Jason -- Jason M. Swails BioMaPS, Rutgers University Postdoctoral Researcher From owner-chemistry@ccl.net Wed Jun 4 14:30:00 2014 From: "haya Kornweitz hayak-,-ariel.ac.il" To: CCL Subject: CCL: rotein and Solvent Effects Message-Id: <-50164-140604142827-14355-554A4mNhGfU5d+v3ygu7tA|,|server.ccl.net> X-Original-From: "haya Kornweitz" Date: Wed, 4 Jun 2014 14:28:26 -0400 Sent to CCL by: "haya Kornweitz" [hayak^_^ariel.ac.il] Dear CCLs I didn't get any answer to my previous answer, so I believe that I didn't express myself well. I am interested in G of reaction in which an active site of an enzyme is involved. Usually I perform optimization in gas phase and then using PCM (e.g. SMD) I am calculating the solvation energy. Now I cut out the active site of the enzyme (about 50 atoms), and treat it as a molecule. This molecule is of course not in gas phase, but it is not really solvated in water, it is a part of a protein. How do you suggest treating this molecule? Is it possible the get a reasonable value of G in this case? I am anxious to get your opinion. Gratefully Haya From owner-chemistry@ccl.net Wed Jun 4 15:36:00 2014 From: "Abrash, Samuel sabrash{:}richmond.edu" To: CCL Subject: CCL: Molpro Input for Ions Message-Id: <-50165-140604153516-12613-2AC2lpEXU8eTy63ARAceGw+*+server.ccl.net> X-Original-From: "Abrash, Samuel" Content-Language: en-US Content-Type: multipart/alternative; boundary="_000_A7C78D2AEE62DB40B9CB1ADE9D5990A2D80EFD0Arinzlerrichmond_" Date: Wed, 4 Jun 2014 19:35:09 +0000 MIME-Version: 1.0 Sent to CCL by: "Abrash, Samuel" [sabrash[]richmond.edu] --_000_A7C78D2AEE62DB40B9CB1ADE9D5990A2D80EFD0Arinzlerrichmond_ Content-Type: text/plain; charset="us-ascii" Content-Transfer-Encoding: quoted-printable Hi Folks, I'm new to Molpro and am trying to decipher the users manual. I need to kn= ow how to specify charge and multiplicity. It looks as if I use the WF card to do this, with the format WF, nelec=3D#ofelectrons, spin=3Dmultiplicity, charge=3Dcharge Ie. For a 15 electron molecule with a charge of +1 in a doublet state it wo= uld be WF, nelec=3D15, spin=3D2, charge=3D1 Is this correct? Thanks, Sam --_000_A7C78D2AEE62DB40B9CB1ADE9D5990A2D80EFD0Arinzlerrichmond_ Content-Type: text/html; charset="us-ascii" Content-Transfer-Encoding: quoted-printable

Hi Folks,

I’m new to Molpro and am trying to decipher th= e users manual. I need to know how to specify charge and multiplicity= .

It looks as if I use the WF card to do this, with th= e format

WF, nelec=3D#ofelectrons, spin=3Dmultiplicity, charg= e=3Dcharge

Ie. For a 15 electron molecule with a charge of += ;1 in a doublet state it would be

WF, nelec=3D15, spin=3D2, charge=3D1

Is this correct?

Thanks,

Sam

--_000_A7C78D2AEE62DB40B9CB1ADE9D5990A2D80EFD0Arinzlerrichmond_-- From owner-chemistry@ccl.net Wed Jun 4 16:11:01 2014 From: "Hopmann Kathrin Helen kathrin.hopmann()uit.no" To: CCL Subject: CCL: SV: Protein and Solvent Effects Message-Id: <-50166-140604154437-18938-8mRsMP6oYXw0SzvGhUECgA::server.ccl.net> X-Original-From: Hopmann Kathrin Helen Content-Language: nb-NO Content-Transfer-Encoding: 8bit Content-Type: text/plain; charset="us-ascii" Date: Wed, 4 Jun 2014 19:44:29 +0000 MIME-Version: 1.0 Sent to CCL by: Hopmann Kathrin Helen [kathrin.hopmann^uit.no] Dear Haya, To model the solvation effect of a protein on a QM active site model, you would typically use PCM(water), but set the dielectric constant to a much smaller value than eps = 80. Eps=4 seems to be some sort of consensus (supposedly representing a protein interior with some water molecules), but it is really a bit of an arbitrary choice. You could equally well choose eps=5 or 6 or 7. Some choose eps=20. This choice will affect the computed energies, but how much the variation will be depends on the model. In general, it is a good idea to keep some additional residues around the reacting fragments in order to provide explicit solvation effects including hydrogen bonds. In particular charged groups (e.g. an aspartate side chain, or an emerging charge on the substrate) should not be kept at the edge of a QM model, but be solvated explicitly. 50 atoms sounds small for an enzyme active site model; depending on the computational resources available to you, you might consider enlarging your model. When it comes to the reaction energies/barriers - you can do electronic energies, and also enthalpies will be reasonable, but I do not think you can compute Gibbs free energies with this type of model. In order to keep the integrity of the active site, you will probably have to freeze each residue at the atom where you truncated it. This freezing scheme will result in small imaginary frequencies. Calculations of Gibbs free energies will not be meaningful in this case and could give completely wrong values. There are many literature studies with QM calculations on active site models of enzymes. You could have a look at work by e.g. Per Siegbahn or Fahmi Himo to get some more ideas on how to set up your system. best regards Kathrin ------ Kathrin H. Hopmann CTCC, Dept. of Chemistry, University of Tromsoe, Norway http://www.ctcc.no/people/researchers/hopmann ________________________________________ Fra: owner-chemistry+kathrin.hopmann==uit.no _ ccl.net [owner-chemistry+kathrin.hopmann==uit.no _ ccl.net] på vegne av haya Kornweitz hayak-,-ariel.ac.il [owner-chemistry _ ccl.net] Sendt: 4. juni 2014 20:28 Til: Hopmann Kathrin Helen Emne: CCL: rotein and Solvent Effects Sent to CCL by: "haya Kornweitz" [hayak^_^ariel.ac.il] Dear CCLs I didn't get any answer to my previous answer, so I believe that I didn't express myself well. I am interested in G of reaction in which an active site of an enzyme is involved. Usually I perform optimization in gas phase and then using PCM (e.g. SMD) I am calculating the solvation energy. Now I cut out the active site of the enzyme (about 50 atoms), and treat it as a molecule. This molecule is of course not in gas phase, but it is not really solvated in water, it is a part of a protein. How do you suggest treating this molecule? Is it possible the get a reasonable value of G in this case? I am anxious to get your opinion. Gratefully Hayahttp://www.ccl.net/cgi-bin/ccl/send_ccl_messagehttp://www.ccl.net/chemistry/sub_unsub.shtmlhttp://www.ccl.net/spammers.txt From owner-chemistry@ccl.net Wed Jun 4 16:46:01 2014 From: "Peterson, Kirk kipeters a wsu.edu" To: CCL Subject: CCL: Molpro Input for Ions Message-Id: <-50167-140604160640-30590-DxIN5vXroNNfWZXCVuYnXw * server.ccl.net> X-Original-From: "Peterson, Kirk" Content-Language: en-US Content-Type: multipart/alternative; boundary="_000_9D52A72BB75F4E91930DC97B0DB41B07wsuedu_" Date: Wed, 4 Jun 2014 20:06:20 +0000 MIME-Version: 1.0 Sent to CCL by: "Peterson, Kirk" [kipeters\a/wsu.edu] --_000_9D52A72BB75F4E91930DC97B0DB41B07wsuedu_ Content-Type: text/plain; charset="Windows-1252" Content-Transfer-Encoding: quoted-printable Sam, the wavefunction command does not contain the charge - this is implicit in = the # of electrons, right? What it does generally contain is the irrep number for the spatial symmetry of t= he wavefunction. Btw, you'll have better luck with these types of questions by addressing th= em to the Molpro user list, molpro-user at molpro.net regards, -Kirk On Jun 4, 2014, at 12:35 PM, Abrash, Samuel sabrash{:}richmond.edu

> wrot= e: Hi Folks, I=92m new to Molpro and am trying to decipher the users manual. I need to = know how to specify charge and multiplicity. It looks as if I use the WF card to do this, with the format WF, nelec=3D#ofelectrons, spin=3Dmultiplicity, charge=3Dcharge Ie. For a 15 electron molecule with a charge of +1 in a doublet state it wo= uld be WF, nelec=3D15, spin=3D2, charge=3D1 Is this correct? Thanks, Sam --_000_9D52A72BB75F4E91930DC97B0DB41B07wsuedu_ Content-Type: text/html; charset="Windows-1252" Content-ID: <940545B3379D2349BF6A140922816A97\a/ad.wsu.edu> Content-Transfer-Encoding: quoted-printable Sam,

the wavefunction command does not contain the charge - this is implici= t in the # of electrons, right? What

it does generally contain is the irrep number for the spatial symmetry= of the wavefunction.

Btw, you'll have better luck with these types of questions by addressi= ng them to the Molpro user list, molpro-user at molpro.net

regards,

-Kirk

On Jun 4, 2014, at 12:35 PM, Abrash, Samuel sabrash{:}richmond.edu <owner-chemistry\a/ccl.net> wrote:

Hi Folks,

I=92m new to Molpro and am trying to decipher the us= ers manual. I need to know how to specify charge and multiplicity.&nb= sp;

It looks as if I use the WF card to do this, with th= e format

WF, nelec=3D#ofelectrons, spin=3Dmultiplicity, charg= e=3Dcharge

Ie. For a 15 electron molecule with a charge of += ;1 in a doublet state it would be

WF, nelec=3D15, spin=3D2, charge=3D1

Is this correct?

Thanks,

Sam

--_000_9D52A72BB75F4E91930DC97B0DB41B07wsuedu_-- From owner-chemistry@ccl.net Wed Jun 4 21:47:00 2014 From: "John Keller jwkeller###alaska.edu" To: CCL Subject: CCL: rotein and Solvent Effects Message-Id: <-50168-140604161727-5221-nhYJd1l2EpN5Js+tJNEnzw{=}server.ccl.net> X-Original-From: John Keller Content-Type: text/plain; charset=UTF-8 Date: Wed, 4 Jun 2014 12:17:18 -0800 Mime-Version: 1.0 (1.0) Sent to CCL by: John Keller [jwkeller!A!alaska.edu] Hello Haya, A lot of theoretical work has been carried out on SODs. I found one (JACS, 128, 7466(2006)) by googling. Check the earlier refs, and use SCI to find later ones. John Keller Univ of Alaska > On Jun 4, 2014, at 11:44 AM, "haya Kornweitz hayak-,-ariel.ac.il" wrote: > > > Sent to CCL by: "haya Kornweitz" [hayak^_^ariel.ac.il] > Dear CCLs > I didn't get any answer to my previous answer, so I believe that I didn't > express myself well. > I am interested in G of reaction in which an active site of an enzyme is > involved. > Usually I perform optimization in gas phase and then using PCM (e.g. SMD) I am > calculating the solvation energy. > Now I cut out the active site of the enzyme (about 50 atoms), and treat it as a > molecule. > This molecule is of course not in gas phase, but it is not really solvated in > water, it is a part of a protein. > How do you suggest treating this molecule? Is it possible the get a reasonable > value of G in this case? > I am anxious to get your opinion. > Gratefully > Haya> >