From owner-chemistry@ccl.net Tue May 10 08:22:01 2016 From: "Yury Minenkov yury.minenkov++gmail.com" To: CCL Subject: CCL: conformational search for the realistic-size transition metal species Message-Id: <-52188-160510075157-6945-Zs/aepM/SUo5bBveJDO+Dw _ server.ccl.net> X-Original-From: Yury Minenkov Content-Type: multipart/alternative; boundary=f46d042c609b0a999c05327b8d6f Date: Tue, 10 May 2016 14:51:52 +0300 MIME-Version: 1.0 Sent to CCL by: Yury Minenkov [yury.minenkov]_[gmail.com] --f46d042c609b0a999c05327b8d6f Content-Type: text/plain; charset=UTF-8 Content-Transfer-Encoding: quoted-printable Dear Computational Chemistry List Members, Many of you study the reaction mechanisms involving quite large (100-200 atoms) transition metal complexes (or organometallic species) with high degree of conformational freedom. Undoubtedly, the realistic Gibbs free energy profiles require knowledge of the most stable conformers for all the species involved (or to be even more strict =E2=80=93 one would need to kno= w the Boltzmann distribution of the conformers). Could you share your experience/expertise in the conformational search of the realistic-size transition metal complexes with large number (10-20) of rotatable bonds? What software do you use? Is it free/commercial? Are you satisfied with it? Do you trust the results? Another similar question =E2= =80=93 do you find it useful to carry out the conformational search on the transition states? My two cents: Usually, when possible I use the X-Ray structures of the species I am interested in. Even though the most stable gas phase conformation might be different from the one in the solid state, still I believe the conformation > from the X-Ray is more reliable than the one from the quick conformational search, especially when the large number of rotatable bonds is the case. When the X-Ray structure is not accessible, and the number of reasonable conformers is not that large (5-10) =E2=80=93 I try to optimize them at DFT= level (since with the Density fitting algorithms it is often affordable). I have tried to use HyperChem, OpenBabel, Tinker, PCModel for the systematic conformational search at molecular mechanics level, but I do not know how reliable the results of such searches are for the transition metal species. Wrt to the conformational search on the transition state =E2=80=93 I try to= avoid it because if the conformation of the transition state is different from the conformation of the reactant, then another transition state associated with conformational change has to be found, and sometimes the transition state associated with the conformational change might be higher in energy than the original TS we were looking at. Any comments, suggestions, constructive discussions are appreciated and deeply encouraged. With kind regards, Yury --f46d042c609b0a999c05327b8d6f Content-Type: text/html; charset=UTF-8 Content-Transfer-Encoding: quoted-printable
=09 =09 =09 =09

Dear Computational Chemistry List Members,


Many of you study the reaction mechanisms involving quite large (100-200 atoms) transition metal complexes (or organometallic species) with high degree of conformational freedom. Undoubtedly, the realistic Gibbs free energy profiles require knowledge of the most stable conformers for all the species involved (or to be even more strict =E2=80= =93 one would need to know the Boltzmann distribution of the conformers).

Could you share your experience/expertise in the conformational search of the realistic-size transition metal complexes with large number (10-20) of rotatable bonds? What software do you use? Is it free/commercial? Are you satisfied with it? Do you trust the results? Another similar question =E2=80=93 do you find it useful to carry out the conformational search on the transition states?

My two cents:

Usually, when possible I use the X-Ray structures of the species I am interested in. Even though the most stable gas phase conformation might be different from the one in the solid state, still I believe the conformation from the X-Ray is more reliable than the one from the quick conformational search, especially when the large number of rotatable bonds is the case.

When the X-Ray structure is not accessible, and the number of reasonable conformers is not that large (5-10) =E2=80=93 I try to optimize them at DFT level (since with the Density fitting algorithms it is often affordable).

I have tried to use HyperChem, OpenBabel, Tinker, PCModel for the systematic conformational search at molecular mechanics level, but I do not know how reliable the results of such searches are for the transition metal species.=20

Wrt to the conformational search on the transition state =E2=80=93 I try to avoid it because if the conformation of the transition state is different from the conformation of the reactant, then another transition state associated with conformational change has to be found, and sometimes the transition state associated with the conformational change might be higher in energy than the original TS we were looking at.

Any comments, suggestions, constructive discussions are appreciated and deeply encouraged.=20

With kind regards,

Yury




--f46d042c609b0a999c05327b8d6f-- From owner-chemistry@ccl.net Tue May 10 10:43:01 2016 From: "Norrby, Per-Ola Per-Ola.Norrby()astrazeneca.com" To: CCL Subject: CCL: conformational search for the realistic-size transition metal species Message-Id: <-52189-160510102638-28151-d+ZdTwaTG3lMTXB8NZdTZg*server.ccl.net> X-Original-From: "Norrby, Per-Ola" Content-Language: en-US Content-Type: multipart/alternative; boundary="_000_HE1PR04MB20923C5AF60D9C61D010948DCA710HE1PR04MB2092eurp_" Date: Tue, 10 May 2016 14:26:28 +0000 MIME-Version: 1.0 Sent to CCL by: "Norrby, Per-Ola" [Per-Ola.Norrby]|[astrazeneca.com] --_000_HE1PR04MB20923C5AF60D9C61D010948DCA710HE1PR04MB2092eurp_ Content-Type: text/plain; charset="utf-8" Content-Transfer-Encoding: base64 RGVhciBZdXJ5LA0KDQpPdXIgYXBwcm9hY2ggdG8gdGhpcyBpcyB0byBERVZFTE9QIGEgbW9sZWN1 bGFyIG1lY2hhbmljcyBmb3JjZSBmaWVsZCBmb3IgZWFjaCBpbnRlcmVzdGluZyB0cmFuc2l0aW9u IG1ldGFsIGNvbXBsZXggb3IgdHJhbnNpdGlvbiBzdGF0ZSwgYW5kIHVzZSB0aGF0IGZvciBjb25m 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T05ULVNJWkU6IDhwdCI+PC9wPg0KPHAgY2xhc3M9IntJbXByaW50LlVuaXF1ZUlEfSIgc3R5bGU9 IkZPTlQtU0laRTogOHB0Ij48L3A+DQo8L2JvZHk+DQo8L2h0bWw+DQo= --_000_HE1PR04MB20923C5AF60D9C61D010948DCA710HE1PR04MB2092eurp_-- From owner-chemistry@ccl.net Tue May 10 11:18:01 2016 From: "Sofia Vasilakaki svasilak||chem.uoa.gr" To: CCL Subject: CCL: DataBases Message-Id: <-52190-160510110100-4141-zLrP9BhtLs7d5nt59tzycA.:.server.ccl.net> X-Original-From: "Sofia Vasilakaki" Content-Transfer-Encoding: 8bit Content-Type: text/plain;charset=utf-8 Date: Tue, 10 May 2016 18:00:54 +0300 MIME-Version: 1.0 Sent to CCL by: "Sofia Vasilakaki" [svasilak]-[chem.uoa.gr] Dear all, I would like to use a database of natural compounds from medicinal herbs and plans in order to perform substructure search or virtual screening. I have found some (super natural, gnps.ucsd.edu, nubbe.iq.unesp.br) but not enough info about each compound and no mol2 files available for download. I would appreciate it if you could share any links for similar databases. Also, could you suggest software tools like these in OpenEye and Maestro packages, for performing calculations of structures properties (pKa, rule of 5, ADME...)? Thank you! Kind Regards, Sofia V. From owner-chemistry@ccl.net Tue May 10 18:20:01 2016 From: "Peter Kraus p.kraus12/a\imperial.ac.uk" To: CCL Subject: CCL:G: About phosphorus-carbon double bond vibrational-frequency(ies) Message-Id: <-52191-160510152301-8396-oG9eVktNwhCV4hKQD8qQ+w- -server.ccl.net> X-Original-From: Peter Kraus Content-Type: multipart/alternative; boundary=94eb2c048db81bd2e9053281dac4 Date: Tue, 10 May 2016 20:22:54 +0100 MIME-Version: 1.0 Sent to CCL by: Peter Kraus [p.kraus12~~imperial.ac.uk] --94eb2c048db81bd2e9053281dac4 Content-Type: text/plain; charset=UTF-8 Dear Daniel, Provided that you have the chk file, you can "pick" vibrational modes that involve selected atoms using the freqchk utility. http://www.gaussian.com/g_tech/g_ur/u_freqchk.htm That might help reduce the noise, if there are many modes in the same frequency range. Regards, Peter On 9 May 2016 03:37, "David Shobe avidshobe|a|yahoo.com" < owner-chemistry a ccl.net> wrote: > Daniel, > It may indeed be easier to look at the Gaussian text output. I'm assuming > you have some idea of the frequency value for the C=P stretch. (if not, a > quick calculation of CH2=PH or CH2=P-CH3 might help). Gaussian prints the > vibrational data in frequency order, so note those vibrational modes that > are near the expected frequency, and animate those vibrational nodes > individually (as opposed to plotting the entire IR spectrum, which it > sounds like you are doing). If you're lucky, there won't be too many > vibrational nodes with frequencies in your range, and you can pick out the > C=P stretch from watching the animation. > If you are unlucky, there will be several other vibrational nodes with > similar frequencies, and every one of those modes will be a mixed mode that > has only some C=P stretching character. > I write about C=P stretching, but the same is true for the C=P twist only > my guess is that you will be less likely to be "lucky" with the twist. > --David > > > > On Saturday, May 7, 2016 5:34 PM, Daniel Salazar > danielmoralessalazar91:+:gmail.com wrote: > > > > Sent to CCL by: "Daniel Salazar" [danielmoralessalazar91]=[gmail.com] > Hello, > > I am using B3LYP on Gaussian 09. I used it to obtain the vibrational > frequencies of a molecule (C39H41PS2) containing one phosphorus carbon > double bond by using the keyword "freq". I used Molden to visualize the > calculated IR Spectrum. Since there are a lot of frequencies and the > phosphorus carbon double bond may have a low intensity, I am having a hard > time finding its frequency on the "Molden Frequency Select" panel. I wonder > if there is any way to obtain this information in other ways, such as from > the text output file, and if there is, how can I do it? Thank you very > much. > Sincerely, > Daniel Morales Salazar> ------=art_668200_166460360.1462755339092 > Content-Type: text/html; charset=F-8 > Content-Transfer-Encoding: quoted-printable > >
id="yui_3_16_0_ym19_1_1462744162038_44235">Daniel,
id="yui_3_16_0_ym19_1_1462744162038_44235">
id="yui_3_16_0_ym19_1_1462744162038_44235">It may indeed be easier to look > at the Gaussian text output.  I'm assuming you have some idea of the > frequency value for the C=P stretch.  (if not, a quick calculation of > CH2=PH or CH2=P-CH3 might help).  Gaussian prints the vibrational data > in frequency order, so note those vibrational modes that are near the > expected frequency, and animate those vibrational nodes individually (as > opposed to plotting the entire IR spectrum, which it sounds like you are > doing).  If you're lucky, there won't be too many vibrational nodes > with frequencies in your range, and you can pick out the C=P stretch from > watching the animation.
id="yui_3_16_0_ym19_1_1462744162038_44235">
id="yui_3_16_0_ym19_1_1462744162038_44235">If you are unlucky, there will > be several other vibrational nodes with similar frequencies, and every one > of those modes will be a mixed mode that has only some C=P stretching > character.
id="yui_3_16_0_ym19_1_1462744162038_44235">
id="yui_3_16_0_ym19_1_1462744162038_44235">I write about C=P stretching, > but the same is true for the C=P twist only my guess is that you will be > less likely to be "lucky" with the twist.
id="yui_3_16_0_ym19_1_1462744162038_44235">
id="yui_3_16_0_ym19_1_1462744162038_44235">--David
id="yui_3_16_0_ym19_1_1462744162038_44235">
id="yui_3_16_0_ym19_1_1462744162038_44235">
class="qtdSeparateBR">

style="display: block;">
style="font-family: HelveticaNeue, Helvetica Neue, Helvetica, Arial, Lucida > Grande, sans-serif; font-size: 16px;">
face="Arial"> On Saturday, May 7, 2016 5:34 PM, Daniel Salazar > danielmoralessalazar91:+:gmail.com <owner-chemistry_-_ccl.net> > wrote:



Sent to > CCL by: "Daniel  Salazar" [danielmoralessalazar91]=[gmail.com]
Hello,

I > am using B3LYP on Gaussian 09. I used it to obtain the vibrational >
frequencies of a molecule (C39H41PS2) containing one phosphorus carbon >
double bond by using the keyword "freq". I used Molden to visualize the >
calculated IR Spectrum. Since there are a lot of frequencies and the >
phosphorus carbon double bond may have a low intensity, I am having a > hard
time finding its frequency on the "Molden Frequency Select" panel. > I wonder
if there is any way to obtain this information in other ways, > such as > from
the text output file, and if there is, how can I do it? > Thank you very
much.
Sincerely,
Daniel Morales > Salazar



-= This is automatically added to each message by > the mailing script =-
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--94eb2c048db81bd2e9053281dac4 Content-Type: text/html; charset=UTF-8 Content-Transfer-Encoding: quoted-printable

Dear Daniel,
Provided that you have the chk file, you can "pick" vibrational m= odes that involve selected atoms using the freqchk utility.

http://www.gaussian.com/g_tech/g_ur/u_freqchk.htm

That might help reduce the noise, if there are many modes in= the same frequency range.

Regards,
Peter

On 9 May 2016 03:37, "David Shobe avidshobe= |a|yahoo.com" <owner-chemistry a ccl.net> wrote:
Daniel,
It may indeed be easier to look at the Gaussian text output.=C2=A0 I'm = assuming you have some idea of the frequency value for the C=3DP stretch. = =C2=A0(if not, a quick calculation of CH2=3DPH or CH2=3DP-CH3 might help).= =C2=A0 Gaussian prints the vibrational data in frequency order, so note tho= se vibrational modes that are near the expected frequency, and animate thos= e vibrational nodes individually (as opposed to plotting the entire IR spec= trum, which it sounds like you are doing).=C2=A0 If you're lucky, there= won't be too many vibrational nodes with frequencies in your range, an= d you can pick out the C=3DP stretch from watching the animation.
If you are unlucky, there will be several other vibrational nodes with simi= lar frequencies, and every one of those modes will be a mixed mode that has= only some C=3DP stretching character.
I write about C=3DP stretching, but the same is true for the C=3DP twist on= ly my guess is that you will be less likely to be "lucky" with th= e twist.
--David



=C2=A0 =C2=A0 On Saturday, May 7, 2016 5:34 PM, Daniel Salazar danielmorale= ssalazar91:+:gmail.com <owner-chemistry_-_ccl.net> wrote:



Sent to CCL by: "Daniel=C2=A0 Salazar" [danielmoralessalazar91]= =3D[gmail= .com]
Hello,

I am using B3LYP on Gaussian 09. I used it to obtain the vibrational
frequencies of a molecule (C39H41PS2) containing one phosphorus carbon
double bond by using the keyword "freq". I used Molden to visuali= ze the
calculated IR Spectrum. Since there are a lot of frequencies and the
phosphorus carbon double bond may have a low intensity, I am having a hard<= br> time finding its frequency on the "Molden Frequency Select" panel= . I wonder
if there is any way to obtain this information in other ways, such as from<= br> the text output file, and if there is, how can I do it? Thank you very
much.
Sincerely,
Daniel Morales Salazar



-=3D This is automatically added to each message by the mailing script =3D-= =C2=A0 =C2=A0 =C2=A0=C2=A0 =C2=A0 =C2=A0Subscribe/Unsubscribe:
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<html><head></head><body><div style=3D"colo= r:#000; background-color:#fff; font-family:HelveticaNeue, Helvetica Neue, H= elvetica, Arial, Lucida Grande, sans-serif;font-size:13px"><div = dir=3D"ltr" id=3D"yui_3_16_0_ym19_1_1462744162038_44235"= ;>Daniel,</div><div dir=3D"ltr" id=3D"yui_3_16_0= _ym19_1_1462744162038_44235"><br></div><div dir=3D&q= uot;ltr" id=3D"yui_3_16_0_ym19_1_1462744162038_44235">It = may indeed be easier to look at the Gaussian text output. &nbsp;I'm= assuming you have some idea of the frequency value for the C=3DP stretch. = &nbsp;(if not, a quick calculation of CH2=3DPH or CH2=3DP-CH3 might hel= p). &nbsp;Gaussian prints the vibrational data in frequency order, so n= ote those vibrational modes that are near the expected frequency, and anima= te those vibrational nodes individually (as opposed to plotting the entire = IR spectrum, which it sounds like you are doing). &nbsp;If you're l= ucky, there won't be too many vibrational nodes with frequencies in you= r range, and you can pick out the C=3DP stretch from watching the animation= .</div><div dir=3D"ltr" id=3D"yui_3_16_0_ym19_1_146= 2744162038_44235"><br></div><div dir=3D"ltr&quo= t; id=3D"yui_3_16_0_ym19_1_1462744162038_44235">If you are unl= ucky, there will be several other vibrational nodes with similar frequencie= s, and every one of those modes will be a mixed mode that has only some C= =3DP stretching character.</div><div dir=3D"ltr" id=3D&q= uot;yui_3_16_0_ym19_1_1462744162038_44235"><br></div>&l= t;div dir=3D"ltr" id=3D"yui_3_16_0_ym19_1_1462744162038_4423= 5">I write about C=3DP stretching, but the same is true for the C= =3DP twist only my guess is that you will be less likely to be "lucky&= quot; with the twist.</div><div dir=3D"ltr" id=3D"y= ui_3_16_0_ym19_1_1462744162038_44235"><br></div><div= dir=3D"ltr" id=3D"yui_3_16_0_ym19_1_1462744162038_44235&quo= t;>--David</div><div dir=3D"ltr" id=3D"yui_3_16_= 0_ym19_1_1462744162038_44235"><br></div><div dir=3D&= quot;ltr" id=3D"yui_3_16_0_ym19_1_1462744162038_44235">&l= t;br></div><div class=3D"qtdSeparateBR"><br>= <br></div><div class=3D"yahoo_quoted" style=3D&quo= t;display: block;"> <div style=3D"font-family: HelveticaNeu= e, Helvetica Neue, Helvetica, Arial, Lucida Grande, sans-serif; font-size: = 13px;"> <div style=3D"font-family: HelveticaNeue, Helvetica= Neue, Helvetica, Arial, Lucida Grande, sans-serif; font-size: 16px;"&= gt; <div dir=3D"ltr"><font size=3D"2" face=3D&= quot;Arial"> On Saturday, May 7, 2016 5:34 PM, Daniel Salazar danie= lmoralessalazar91:+:gmail.com &lt;owner-chemistry_-_ccl.net&= gt; wrote:<br></font></div>=C2=A0 <br><br> &l= t;div class=3D"y_msg_container"><br>Sent to CCL by: &quo= t;Daniel&nbsp; Salazar" [danielmoralessalazar91]=3D[gmail.com]<br>= ;Hello,<br><br>I am using B3LYP on Gaussian 09. I used it to ob= tain the vibrational <br>frequencies of a molecule (C39H41PS2) contai= ning one phosphorus carbon <br>double bond by using the keyword "= ;freq". I used Molden to visualize the <br>calculated IR Spectru= m. Since there are a lot of frequencies and the <br>phosphorus carbon= double bond may have a low intensity, I am having a hard <br>time fi= nding its frequency on the "Molden Frequency Select" panel. I won= der <br>if there is any way to obtain this information in other ways,= such as > from <br>the text output file, and if there is, how can= I do it? Thank you very <br>much.<br>Sincerely,<br>Danie= l Morales Salazar<br><br><br><br>-=3D This is autom= atically added to each message by the mailing script =3D-<br>To recov= er the email address of the author of the message, please change<br>= =3Dr><br><= br>E-mail to subscribers: <a ymailto=3D"mailto:CHEMISTRY_-_ccl.net" href=3D"mailto:CHEMISTRY_-_ccl.net">CHEMIS= TRY_-_ccl.net</a> or use:<br>&nbsp; &nbsp; &nbsp; &= lt;a href=3D"http://www.ccl.net/cgi-bin/ccl/send= _ccl_message" target=3D"_blank">http://www.ccl.net/cgi-bin/ccl/send_ccl_message</a><br><= ;br>E-mail to administrators: <a ymailto=3D"mailto:CHEMISTRY-REQUEST_-_ccl.net" hre= f=3D"mailto:CHEMISTRY-R= EQUEST_-_ccl.net">CHEMISTRY-REQUEST_-_ccl.net</a> or use&= lt;br>&nbsp; &nbsp; &nbsp; <a href=3D"http://www.ccl.net/cgi-bin/ccl/send_ccl_message" target=3D= "_blank">http://www.ccl.net/cgi-bin/ccl/= send_ccl_message</a><br><br>&l= t;br>&nbsp; &nbsp; &nbsp; <a href=3D"http://www.ccl.net/chemistry/sub_unsub.shtml" target=3D"_= blank">http://www.ccl.net/chemistry/sub_unsub.sh= tml</a><br><br>Before posting, check wait time at: &l= t;a href=3D"http://www.ccl.net/" target=3D"_blank">http://ww= w.ccl.net</a><br><br>Job: <a href=3D"http://ww= w.ccl.net/jobs" target=3D"_blank">http://www.ccl.net/jo= bs </a><br>Conferences: <a href=3D"http://server.ccl.net/chemistry/announcements/conferences/= " target=3D"_blank">= http://server.ccl.net/chemistry/announcements/conferences/</a><= ;br><br>Search Messages: <a href=3D"http://www.ccl.net/chemistry/searchccl/index.shtml" target=3D&q= uot;_blank">http://www.ccl.net/chemistry/s= earchccl/index.shtml</a><br><br>If your mail bounces = > from CCL with 5.7.1 error, check:<br>&nbsp; &nbsp; &nbsp;= <a href=3D"http://www.ccl.net/spammers.txt" target= =3D"_blank">http://www.ccl.net/spammers.txt</a>= ;<br><br>RTFI: <a href=3D"htt= p://www.ccl.net/chemistry/aboutccl/instructions/" target=3D"_= blank">http://www.ccl.net/chemistry/about= ccl/instructions/</a><br><br><br><br><= br></div>=C2=A0 </div> </div>=C2=A0 </div></d= iv></body></html>
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