From owner-chemistry@ccl.net Tue Jun 13 02:33:00 2017 From: "Simmie, John john.simmie-#-nuigalway.ie" To: CCL Subject: CCL:G: Torsion profiles Message-Id: <-52838-170613023126-13238-qDuag5A6UJPG0xB/iFt0aA ~ server.ccl.net> X-Original-From: "Simmie, John" Content-Language: en-US Content-Type: multipart/alternative; boundary="_000_DB6PR0102MB2840945DD8AEC685F6B21CA994C20DB6PR0102MB2840_" Date: Tue, 13 Jun 2017 06:31:17 +0000 MIME-Version: 1.0 Sent to CCL by: "Simmie, John" [john.simmie.]-[.nuigalway.ie] --_000_DB6PR0102MB2840945DD8AEC685F6B21CA994C20DB6PR0102MB2840_ Content-Type: text/plain; charset="us-ascii" Content-Transfer-Encoding: quoted-printable It is a common procedure nowadays, "relaxed potential energy scan" and avai= lable for example in Gaussian via the keyword OPT=3DModRedundant Where the chosen dihedral angle comprising atoms 1--2--3--4 is varied 36 ti= mes in 10 degree intervals is further specified as D 1 2 3 4 S 36 10.0 In addition all other dihedrals about 2-3 are allowed to optimise D * 2 3 * R >Sent to CCL by: Joseph Leonard [jleonard42_._gmail.com] Folks, I would app= reciate learning of any literature citations that discuss torsion >profiles= (constrained minimization used to carry out rotatable bond scan). I am fa= miliar with rapid, rigid-rotor scans, but they can lead to >arbitrarily lar= ge energy barriers as the rest of the molecule cannot relax. >This seems like an older idea, but I do not recall reading about it over t= he years nor hearing about it at conferences. The increased >availability = of computer power means that calculations can be done with QM codes as well= but the results and I assume the various >arguments for/against these calc= ulations are the same. >Thanks in advance! >Joe Professor Emeritus John M. Simmie School of Chemistry & Combustion Chemistry Centre National University of Ireland, Galway --_000_DB6PR0102MB2840945DD8AEC685F6B21CA994C20DB6PR0102MB2840_ Content-Type: text/html; charset="us-ascii" Content-Transfer-Encoding: quoted-printable

It is a common procedure nowadays, “relaxed po= tential energy scan” and available for example in Gaussian via the ke= yword

OPT=3DModRedundant

Where the chosen dihedral angle comprising atoms 1--= 2--3--4 is varied 36 times in 10 degree intervals is further specified as

D 1 2 3 4 S 36 10.0

In addition all other dihedrals about 2—3 are = allowed to optimise

D * 2 3 * R=

>Sent to CCL by: Joseph Leonard [jleonard42_._= gmail.com] Folks, I would appreciate learning of any literature citations t= hat discuss torsion >profiles (constrained minimization used to carry ou= t rotatable bond scan). I am familiar with rapid, rigid-rotor scans, but they can lead to >arbitrarily large energ= y barriers as the rest of the molecule cannot relax.

>This seems like an older idea, but I do not r= ecall reading about it over the years nor hearing about it at conferences.&= nbsp; The increased >availability of computer power means that calculati= ons can be done with QM codes as well but the results and I assume the various >arguments for/against these calculati= ons are the same.

>Thanks in advance!

>Joe

&= nbsp; Professor Emeritus John M. Simmie

School of Chemistry & Combu= stion Chemistry Centre

Nation= al University of Ireland, Galway

--_000_DB6PR0102MB2840945DD8AEC685F6B21CA994C20DB6PR0102MB2840_-- From owner-chemistry@ccl.net Tue Jun 13 06:15:01 2017 From: "Mina Haghdadi mhaghdadi2 ~~ yahoo.co.uk" To: CCL Subject: CCL:G: ELF analysis Message-Id: <-52839-170613044618-1819-uYbbINyfkHbuVuB4TN8kjg#%#server.ccl.net> X-Original-From: Mina Haghdadi Content-Type: multipart/alternative; boundary="----=_Part_14292569_517135543.1497343572181" Date: Tue, 13 Jun 2017 08:46:12 +0000 (UTC) MIME-Version: 1.0 Sent to CCL by: Mina Haghdadi [mhaghdadi2~~yahoo.co.uk] ------=_Part_14292569_517135543.1497343572181 Content-Type: text/plain; charset=UTF-8 Content-Transfer-Encoding: quoted-printable Dear all I have two question : 1) I would like to know about ELF analysis. Recently I have seen in some of= =C2=A0 articles that ELF analysis=C2=A0 could explain the regioselectivity.. I would like to know what parameter does calculate and how can analysis them.=C2=A0=C2=A0 there wasn't any explain about keywords need to calculations in Gaussian.2) Does any body know how we can plot a ma= p of atomic spin density for a radical anion or radical cation. what does s= oftware can we use to visualize the output of gaussian for this plot?=20 Could you help me? ------=_Part_14292569_517135543.1497343572181 Content-Type: text/html; charset=UTF-8 Content-Transfer-Encoding: 7bit

Dear all

I have two question :

1) I would like to know about ELF analysis.

Recently I have seen in some of articles that ELF
analysis could explain the regioselectivity.. I
would like to know what parameter does calculate and how can analysis
them. there wasn't any explain about keywords
need to calculations in Gaussian.

2) Does any body know how we can plot a map of atomic spin density for a radical anion or radical cation. what does software can we use to visualize the output of gaussian for this plot?

Could you help me?

------=_Part_14292569_517135543.1497343572181-- From owner-chemistry@ccl.net Tue Jun 13 07:26:01 2017 From: "Mikael Johansson mikael.johansson{}iki.fi" To: CCL Subject: CCL: symmetry breaking Message-Id: <-52840-170613072516-14129-V66vVtIFFugP70yKsCAxwQ:server.ccl.net> X-Original-From: Mikael Johansson Content-Language: en-US Content-Transfer-Encoding: 7bit Content-Type: text/plain; charset=utf-8; format=flowed Date: Tue, 13 Jun 2017 14:25:07 +0300 MIME-Version: 1.0 Sent to CCL by: Mikael Johansson [mikael.johansson,iki.fi] Hello Ulrike, On 9.6.2017 15:59, Ulrike Salzner salzner*_*fen.bilkent.edu.tr wrote: > I am comparing three large conjugated pi-systems with density > functional theory (global and range-separated hybrids). The difference > between them is that one contains phenyl rings, one thiophene, and the > last one selenophene. > [...] > Is there any way other way to find the broken the symmetry ground > state? Or - is the lack of a broken symmetry solution after 50:50 > HOMO-LUMO mixing sufficient to prove that the ground state is > closed-shell? Some thoughts on how I would go about trying to obtain a BS solution, they might or might not work, and implementing them is code-specific of course. 1) Start out by doing a calculation on the cation. Then the alpha and beta orbitals could already be different enough to drive the system towards the BS solution, if you use the orbitals as an input for the calculation of the neutral BS state (assuming it is neutral) 2) Take you closed shell solution. Flip the spin of two orbitals at opposite ends of the molecule, or rather, where you suspect the excess spin to reside. So in one region, change one alpha orbital to a beta orbital, and in another, flip a beta to an alpha. Choose orbitals close to the HOMO, that are local to the region. 3) If 1 or 2 doesn't work, you could retry them, initially using a higher amount of HF exchange, in order to exaggerate spin polarisation. This might drive the solution to the BS state. Then go back to the desired amount of HF exchange, and use the previous orbitals as a starting guess. Increased level-shifting can help keep the SCF procedure within the BS solution region, if the starting guess corresponds to it, even if the closed-shell solution would be lower in energy. Hope it works, Mikael -- Dr. Mikael Johansson Academy Researcher Department of Chemistry University of Helsinki http://www.iki.fi/~mpjohans From owner-chemistry@ccl.net Tue Jun 13 09:15:00 2017 From: "Norrby, Per-Ola Per-Ola.Norrby*astrazeneca.com" To: CCL Subject: CCL: Torsion profiles (forcefield or QM) Message-Id: <-52841-170613010100-4586-rB9+XqN85PWl0pFcJ/iElQ^_^server.ccl.net> X-Original-From: "Norrby, Per-Ola" Content-Language: en-US Content-Transfer-Encoding: 8bit Content-Type: text/plain; charset="utf-8" Date: Tue, 13 Jun 2017 05:00:51 +0000 MIME-Version: 1.0 Sent to CCL by: "Norrby, Per-Ola" [Per-Ola.Norrby() astrazeneca.com] Hi Joe, I published on the reason for rigid-rotor scans in force field parameterization, and how to do it properly. Yes, you must avoid the arbitrarily high energies, but that can be done. The advantage (or, if you wish, disadvantage) of rigid rotor is that small errors in other parameters will not be compensated by torsions in a non-physical way, so you can get the right parameters for the right reason. "Unusual Conformational Determining Interactions in Oxymethylpyridines. An Ab Initio Study and an Improved Method for Refining Molecular Mechanics Parameters", http://dx.doi.org/10.1002/jcc.540160510 Per-Ola Norrby, Kenneth Wärnmark, Björn Åkermark, and Christina Moberg, J. Comput. Chem. 1995, 16, 620-627. We also, a bit later, published a general method for parameterizing a force field from QM data, alone or in combination with experimental data. "Automated Molecular Mechanics Parameterization with Simultaneous Utilization of Experimental and Quantum Chemical Data", http://dx.doi.org/10.1002/(SICI)1096-987X(19980730)19:10%3C1146::AID-JCC4%3E3.0.CO;2-M Per-Ola Norrby and Tommy Liljefors, J. Comput. Chem. 1998, 19, 1146-1166. The successor of the methods used above were recently made available by Eric Hansen on GitHub as part of the Q2MM method, http://www.github.com/Q2MM/ For a review of the method, see: "Prediction of Stereochemistry using Q2MM", http://dx.doi.org/10.1021/acs.accounts.6b00037 Eric Hansen, Anthony Rosales, Brandon Tutkowski, Per-Ola Norrby, and Olaf Wiest, Acc. Chem. Res. 2016, 49, 996-1005. Cheers, Per-Ola -----Original Message----- > From: owner-chemistry+per-ola.norrby==astrazeneca.com#ccl.net [mailto:owner-chemistry+per-ola.norrby==astrazeneca.com#ccl.net] On Behalf Of Joseph Leonard jleonard42]~[gmail.com Sent: den 13 juni 2017 04:28 To: Norrby, Per-Ola Subject: CCL: Torsion profiles (forcefield or QM) Sent to CCL by: Joseph Leonard [jleonard42_._gmail.com] Folks, I would appreciate learning of any literature citations that discuss torsion profiles (constrained minimization used to carry out rotatable bond scan). I am familiar with rapid, rigid-rotor scans, but they can lead to arbitrarily large energy barriers as the rest of the molecule cannot relax. This seems like an older idea, but I do not recall reading about it over the years nor hearing about it at conferences. The increased availability of computer power means that calculations can be done with QM codes as well but the results and I assume the various arguments for/against these calculations are the same. Thanks in advance! Joe -- “The problem with today’s world is that everyone believes they have the right to express their opinion AND have others listen to it. The correct statement of individual rights is that everyone has the right to an opinion, but crucially, that opinion can be roundly ignored and even made fun of, particularly if it is demonstrably nonsense!” — Brian 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If you have received this message in error, please notify us and remove it from your system and note that you must not copy, distribute or take any action in reliance on it. Any unauthorized use or disclosure of the contents of this message is not permitted and may be unlawful. From owner-chemistry@ccl.net Tue Jun 13 09:50:00 2017 From: "Tian Lu sobereva{=}sina.com" To: CCL Subject: CCL:G: ELF analysis Message-Id: <-52842-170613075817-651-Iyi+cgOogcQXzvFwC4Ip5Q*_*server.ccl.net> X-Original-From: "Tian Lu" Date: Tue, 13 Jun 2017 07:58:15 -0400 Sent to CCL by: "Tian Lu" [sobereva---sina.com] Hi, (1) Gaussian is not able to directly calculate ELF, you need addition analysis programs to do that. For example, Multiwfn (http://sobereva.com/multiwfn) can be used, it supports almost all kinds of ELF analyses (e.g. plotting ELF as curve/plane/isosurface map, integrating a real space function in ELF basin or domain, locating ELF critical points and generating topology paths, etc.). The .wfn, .wfx or .fch produced by Gaussian can be used as input file (other kinds of input files are also supported, see Section 2.5 of the manual). You can find many ELF analysis examples in Chapter 4 of Multiwfn manual. There are many possible ways to use ELF to interpret/predict regioselectivity. For example, when you studying ELF isosurface map, if you find an evident void of ELF around an atom, then corresponding site may be easily attacked by nucleophilic species (you may consult Fig. 9 of RSC Adv., 2015, 5, 6224862259). (2) Main function 3, 4 and 5 of Multiwfn can plot spin density as curve, plane and isosurface maps based on above mentioned input files, respectively. GaussView can also plot it. -------------------------------- Best wishes, Dr. Tian Lu Beijing Kein Research Center for Natural Sciences, Beijing, P. R. China ----- Original Message ----- > From: "Mina Haghdadi mhaghdadi2 ~~ yahoo.co.uk" Subject: CCL:G: ELF analysis Date: 2017-06-13 18:49 Dear all I have two question : 1) I would like to know about ELF analysis. Recently I have seen in some of articles that ELF analysis could explain the regioselectivity.. I would like to know what parameter does calculate and how can analysis them. there wasn't any explain about keywords need to calculations in Gaussian. 2) Does any body know how we can plot a map of atomic spin density for a radical anion or radical cation. what does software can we use to visualize the output of gaussian for this plot? Could you help me? From owner-chemistry@ccl.net Tue Jun 13 10:28:01 2017 From: "Wadud Miah wadud.miah{}nag.co.uk" To: CCL Subject: CCL: Fully funded software performance improvement service Message-Id: <-52843-170613090402-18486-HRt02wi6rU1oYmJTjOJirw|*|server.ccl.net> X-Original-From: "Wadud Miah" Date: Tue, 13 Jun 2017 09:04:00 -0400 Sent to CCL by: "Wadud Miah" [wadud.miah|-|nag.co.uk] I am working on a European Commission (EC) funded project which analyses parallel computer applications and makes recommendations on how to improve their speed and performance, as demonstrated by our success stories: https://pop-coe.eu/target-customers/success-stories As the project is funded by the EC, there is no charge for use by organisations based in the EU. Further information on the application analysis service can be found at: https://pop-coe.eu/services If there are intellectual property issues involved, we are happy to sign any reasonable NDAs. Please contact either myself at wadud.miah|,|nag.co.uk or pop|,|bsc.es if you would like further information. If you know of anyone who might be interested in this service, please feel free to forward it to them. Best regards, Wadud. From owner-chemistry@ccl.net Tue Jun 13 11:03:01 2017 From: "youyno(0)gmail.com" To: CCL Subject: CCL:G: =?UTF-8?Q?=E7=AD=94=E5=A4=8D:_G:_ELF_analysis?= Message-Id: <-52844-170613092345-26626-DDGKrZwksgNOQaCjLQ6O6w+/-server.ccl.net> X-Original-From: Content-Language: zh-cn Content-Type: multipart/alternative; boundary="----=_NextPart_000_002E_01D2E48B.0B578D80" Date: Tue, 13 Jun 2017 21:21:35 +0800 MIME-Version: 1.0 Sent to CCL by: [youyno : gmail.com] This is a multipart message in MIME format. ------=_NextPart_000_002E_01D2E48B.0B578D80 Content-Type: text/plain; charset="UTF-8" Content-Transfer-Encoding: quoted-printable Multiwfn should be the best choice for you to solve all your questions,=20 http://sobereva.com/multiwfn/ There is detailed manual at = http://sobereva.com/multiwfn/misc/Manual_3.4.pdf =20 =20 Dr. David Chen Wuhan Institute of Physics and Mathematics, CAS.=20 West No.30 Xiao Hong Shan,Wuhan 430071 China=20 =20 =20 =20 =E5=8F=91=E4=BB=B6=E4=BA=BA: = owner-chemistry+youyno=3D=3Dgmail.com]~[ccl.net = [mailto:owner-chemistry+youyno=3D=3Dgmail.com]~[ccl.net] = =E4=BB=A3=E8=A1=A8 Mina Haghdadi mhaghdadi2 ~~ yahoo.co.uk =E5=8F=91=E9=80=81=E6=97=B6=E9=97=B4: 2017=E5=B9=B46=E6=9C=8813=E6=97=A5 = 16:46 =E6=94=B6=E4=BB=B6=E4=BA=BA: Wei, Chen =E4=B8=BB=E9=A2=98: CCL:G: ELF analysis =20 Dear all I have two question : 1) I would like to know about ELF analysis. Recently I have seen in some of articles that ELF analysis could explain the regioselectivity.. I would like to know what parameter does calculate and how can analysis them. there wasn't any explain about keywords need to calculations in Gaussian. 2) Does any body know how we can plot a map of atomic spin density for a = radical anion or radical cation. what does software can we use to = visualize the output of gaussian for this plot?=20 Could you help me? ------=_NextPart_000_002E_01D2E48B.0B578D80 Content-Type: text/html; charset="UTF-8" Content-Transfer-Encoding: quoted-printable

Multiwfn = should be the best choice for you to solve all your questions, =

http://sobereva.com/multiwfn/<= o:p>

There is = detailed manual at http://sobereva= .com/multiwfn/misc/Manual_3.4.pdf

Dr. David = Chen

Wuhan = Institute of Physics and Mathematics, CAS.

West No.30 = Xiao Hong Shan,Wuhan 430071 China

=E5=8F=91=E4=BB= =B6=E4=BA=BA: = owner-chemistry+youyno=3D=3Dgmail.com]~[ccl.net = [mailto:owner-chemistry+youyno=3D=3Dgmail.com]~[ccl.net] =E4=BB=A3=E8=A1= =A8 Mina Haghdadi = mhaghdadi2 ~~ yahoo.co.uk
=E5=8F=91=E9=80= =81=E6=97=B6=E9=97=B4: = 2017=E5=B9=B46=E6=9C=8813=E6=97=A5 16:46
=E6=94=B6=E4=BB=B6=E4=BA=BA: Wei, Chen = <youyno]~[gmail.com>
=E4=B8=BB=E9=A2=98: CCL:G: ELF = analysis

= Dear all

= I have two question :

= 1) I would like to know about ELF = analysis.

= Recently I have seen in some of articles that ELF
analysis could explain the = regioselectivity.. I
would = like to know what parameter does calculate and how can analysis
them. there wasn't = any explain about keywords
need to calculations in = Gaussian.

= 2) Does any body know how we can plot a map of atomic spin density for a = radical anion or radical cation. what does software can we use to = visualize the output of gaussian for this plot? =

= Could you help me?

------=_NextPart_000_002E_01D2E48B.0B578D80-- From owner-chemistry@ccl.net Tue Jun 13 12:11:00 2017 From: "Carlos Simmerling carlos.simmerling|a|gmail.com" To: CCL Subject: CCL: Torsion profiles (forcefield or QM) Message-Id: <-52845-170613120759-16042-9ByEhgSJzx+m+je1QgFFbQ-,-server.ccl.net> X-Original-From: Carlos Simmerling Content-Type: multipart/alternative; boundary="001a114bc35a05747e0551d9a3b0" Date: Tue, 13 Jun 2017 12:07:17 -0400 MIME-Version: 1.0 Sent to CCL by: Carlos Simmerling [carlos.simmerling|*|gmail.com] --001a114bc35a05747e0551d9a3b0 Content-Type: text/plain; charset="UTF-8" Content-Transfer-Encoding: quoted-printable we did large numbers of multidimensional dihedral scans in both QM and MM to train the ff14SB protein force field... the article has some discussion of relaxed scans and some of the issues we encountered and how we tested the sensitivity to various options. ff14SB: Improving the accuracy of protein side chain and backbone parameters from ff99SB Maier, J., Martinez, C., Kasavajhala, K., Wickstrom, L., Hauser, K., Simmerling, C., Journal of Chemical Theory and Computation, 2015, 11 (8), 3696-3713 DOI: 10.1021/acs.jctc.5b00255 PMCID: PMC4821407 On Mon, Jun 12, 2017 at 10:28 PM, Joseph Leonard jleonard42]~[gmail.com < owner-chemistry(-)ccl.net> wrote: > > Sent to CCL by: Joseph Leonard [jleonard42_._gmail.com] > Folks, I would appreciate learning of any literature citations that > discuss torsion profiles (constrained minimization used to carry out > rotatable bond scan). I am familiar with rapid, rigid-rotor scans, > but they can lead to arbitrarily large energy barriers as the rest of > the molecule cannot relax. > > This seems like an older idea, but I do not recall reading about it > over the years nor hearing about it at conferences. The increased > availability of computer power means that calculations can be done > with QM codes as well but the results and I assume the various > arguments for/against these calculations are the same. > > Thanks in advance! > > Joe > > -- > =E2=80=9CThe problem with today=E2=80=99s world is that everyone believes= they have > the right to express their opinion AND have others listen to it. The > correct statement of individual rights is that everyone has the right > to an opinion, but crucially, that opinion can be roundly ignored and > even made fun of, particularly if it is demonstrably nonsense!=E2=80=9D > =E2=80=94 Brian Cox > > > > -=3D This is automatically added to each message by the mailing script = =3D-> > > --001a114bc35a05747e0551d9a3b0 Content-Type: text/html; charset="UTF-8" Content-Transfer-Encoding: quoted-printable

we did large numbers of multidimensional dihedral scans in= both QM and MM to train the ff14SB protein force field... the article has = some discussion of relaxed scans and some of the issues we encountered and = how we tested the sensitivity to various options.

ff14SB= : Improving the accuracy of protein side chain and backbone parameters from= ff99SB

Maier, J., Martinez, C., Kasavajhala, K., Wickstrom, L., Hauser= , K., Simmerling, C., Journal of Chemical Theory and Computation, 2015, 11 = (8), 3696-3713

DOI: 10.1021/acs.jctc.5b00255

PMCID: PMC= 4821407

On Mon, Jun 12, 2017 at 10:28 PM, Jos= eph Leonard jleonard42]~[gmail.com <owner-chemistry(-)ccl.net> wrote:

Sent to CCL by: Joseph Leonard [jleonard42_._gmail.com]
Folks, I would appreciate learning of any literature citations that
discuss torsion profiles (constrained minimization used to carry out
rotatable bond scan).=C2=A0 I am familiar with rapid, rigid-rotor scans, but they can lead to arbitrarily large energy barriers as the rest of
the molecule cannot relax.

This seems like an older idea, but I do not recall reading about it
over the years nor hearing about it at conferences.=C2=A0 The increased
availability of computer power means that calculations can be done
with QM codes as well but the results and I assume the various
arguments for/against these calculations are the same.

Thanks in advance!

Joe

--
=E2=80=9CThe problem with today=E2=80=99s world is that everyone believes t= hey have
the right to express their opinion AND have others listen to it.=C2=A0 The<= br> correct statement of individual rights is that everyone has the right
to an opinion, but crucially, that opinion can be roundly ignored and
even made fun of, particularly if it is demonstrably nonsense!=E2=80=9D
=C2=A0 =E2=80=94 Brian Cox

-=3D This is automatically added to each message by the mailing script =3D-=
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