From owner-chemistry@ccl.net Thu May 18 02:27:01 2023 From: "SUMANGLA ARORA arorasumangla,,gmail.com" To: CCL Subject: CCL: Quantification of non-covalent interactions Message-Id: <-54920-230518022522-4758-nB9Ztf2Cy4995EAfJP38Fw::server.ccl.net> X-Original-From: "SUMANGLA ARORA" Date: Thu, 18 May 2023 02:25:21 -0400 Sent to CCL by: "SUMANGLA ARORA" [arorasumangla[]gmail.com] Dear All, I have generated NCI plots using Multiwfn software and created 3D VMD figures based on these plots. Now, I need to quantify non-covalent interactions at specific points of interest. I would greatly appreciate your guidance in resolving this matter. Thanks & Regards Sumangla From owner-chemistry@ccl.net Thu May 18 05:32:01 2023 From: "Fco. Javier Modrego modrego%x%unizar.es" To: CCL Subject: CCL: Quantification of non-covalent interactions Message-Id: <-54921-230518053003-28460-/3RdXN50nl6wJIBIkvPbqA!=!server.ccl.net> X-Original-From: "Fco. Javier Modrego" Content-Transfer-Encoding: 8bit Content-Type: text/plain; charset=utf-8 Date: Thu, 18 May 2023 11:29:49 +0200 Mime-Version: 1.0 (Mac OS X Mail 16.0 \(3696.120.41.1.3\)) Sent to CCL by: "Fco. Javier Modrego" [modrego]-[unizar.es] Probably you want to have a look to this recent paper: IGMPlot: A program to identify, characterize, and quantify molecular interactions Lefebvre, C., Klein, J., Khartabil, H., Boisson, J.-C., Hénon, E., J. Comput. Chem. 2023, 1. https://doi.org/10.1002/jcc.27123 Regards, F.J Modrego Prof. Dr. F.J. Modrego Departamento de Catálisis y Procesos Catalíticos Instituto de Síntesis Química y Catálisis Homogénea (ISQCH) (Institute of Chemical Synthesis and Homogenous Catalysis) Universidad de Zaragoza-C.S.I.C. E-50009 Zaragoza Spain > El 18 may 2023, a las 8:25, SUMANGLA ARORA arorasumangla,,gmail.com escribió: > > > Sent to CCL by: "SUMANGLA ARORA" [arorasumangla[]gmail.com] > Dear All, > > I have generated NCI plots using Multiwfn software and created 3D VMD figures > based on these plots. Now, I need to quantify non-covalent interactions at > specific points of interest. I would greatly appreciate your guidance in > resolving this matter. > > Thanks & Regards > Sumangla> https://urldefense.com/v3/__http://www.ccl.net/cgi-bin/ccl/send_ccl_message__;!!D9dNQwwGXtA!Wx3Z56R7r92zc0ZLZuLD38yeh4q8vH9np-Dsh6E4r0ZJHdkTQLV-n22Fx1ZFyIQwn9m15CjahXQ3LU5FJ39ijS-G-A$> https://urldefense.com/v3/__http://www.ccl.net/cgi-bin/ccl/send_ccl_message__;!!D9dNQwwGXtA!Wx3Z56R7r92zc0ZLZuLD38yeh4q8vH9np-Dsh6E4r0ZJHdkTQLV-n22Fx1ZFyIQwn9m15CjahXQ3LU5FJ39ijS-G-A$> https://urldefense.com/v3/__http://www.ccl.net/chemistry/sub_unsub.shtml__;!!D9dNQwwGXtA!Wx3Z56R7r92zc0ZLZuLD38yeh4q8vH9np-Dsh6E4r0ZJHdkTQLV-n22Fx1ZFyIQwn9m15CjahXQ3LU5FJ3_7iFF_5w$ > > Before posting, check wait time at: https://urldefense.com/v3/__http://www.ccl.net__;!!D9dNQwwGXtA!Wx3Z56R7r92zc0ZLZuLD38yeh4q8vH9np-Dsh6E4r0ZJHdkTQLV-n22Fx1ZFyIQwn9m15CjahXQ3LU5FJ39thfz_cA$ > > Job: https://urldefense.com/v3/__http://www.ccl.net/jobs__;!!D9dNQwwGXtA!Wx3Z56R7r92zc0ZLZuLD38yeh4q8vH9np-Dsh6E4r0ZJHdkTQLV-n22Fx1ZFyIQwn9m15CjahXQ3LU5FJ384drdNog$ > Conferences: https://urldefense.com/v3/__http://server.ccl.net/chemistry/announcements/conferences/__;!!D9dNQwwGXtA!Wx3Z56R7r92zc0ZLZuLD38yeh4q8vH9np-Dsh6E4r0ZJHdkTQLV-n22Fx1ZFyIQwn9m15CjahXQ3LU5FJ3-T_t6RJQ$ > > Search Messages: https://urldefense.com/v3/__http://www.ccl.net/chemistry/searchccl/index.shtml__;!!D9dNQwwGXtA!Wx3Z56R7r92zc0ZLZuLD38yeh4q8vH9np-Dsh6E4r0ZJHdkTQLV-n22Fx1ZFyIQwn9m15CjahXQ3LU5FJ39aHsb6aA$> https://urldefense.com/v3/__http://www.ccl.net/spammers.txt__;!!D9dNQwwGXtA!Wx3Z56R7r92zc0ZLZuLD38yeh4q8vH9np-Dsh6E4r0ZJHdkTQLV-n22Fx1ZFyIQwn9m15CjahXQ3LU5FJ3-cc0qiiQ$ > > RTFI: https://urldefense.com/v3/__http://www.ccl.net/chemistry/aboutccl/instructions/__;!!D9dNQwwGXtA!Wx3Z56R7r92zc0ZLZuLD38yeh4q8vH9np-Dsh6E4r0ZJHdkTQLV-n22Fx1ZFyIQwn9m15CjahXQ3LU5FJ3_on5_pVA$ > > From owner-chemistry@ccl.net Thu May 18 07:28:00 2023 From: "Jens Spanget-Larsen spanget]=[ruc.dk" To: CCL Subject: CCL: Sv: Quantification of non-covalent interactions Message-Id: <-54922-230518072648-7398-gM0L2BNqrXCEnpDXKkQxHg|-|server.ccl.net> X-Original-From: Jens Spanget-Larsen Content-Language: da-DK Content-Type: multipart/alternative; boundary="_000_8d6073824e8447cba7be191b39c6ca09rucdk_" Date: Thu, 18 May 2023 11:26:36 +0000 MIME-Version: 1.0 Sent to CCL by: Jens Spanget-Larsen [spanget~!~ruc.dk] --_000_8d6073824e8447cba7be191b39c6ca09rucdk_ Content-Type: text/plain; charset="iso-8859-1" Content-Transfer-Encoding: quoted-printable I am not sure if this is of interest, but the Wiberg bond index can be used= to estimate the covalent nature of a 'non-bonded' interaction, such as a h= ydrogen bond, halogen bond, etc. For an application, see for example Molecu= les 2017, 22, 552; https://www.mdpi.com/1420-3049/22/4/552 . Yours, Jens >--< ________________________________ Fra: owner-chemistry+spanget=3D=3Druc.dk _ ccl.net p=E5 vegne af SUMANGLA ARORA arorasumangla,,gmail.com= Sendt: 18. maj 2023 08:25 Til: Jens Spanget-Larsen Emne: CCL: Quantification of non-covalent interactions Sent to CCL by: "SUMANGLA ARORA" [arorasumangla[]gmail.com] Dear All, I have generated NCI plots using Multiwfn software and created 3D VMD figur= es based on these plots. Now, I need to quantify non-covalent interactions at specific points of interest. I would greatly appreciate your guidance in resolving this matter. Thanks & Regards Sumangla -=3D This is automatically added to each message by the mailing script =3D-http://www.ccl.net/cgi-bin/ccl/send_ccl_messagehttp://www.ccl.net/chemistry/sub_unsub.shtmlhttp://www.ccl.net/spammers.txt--_000_8d6073824e8447cba7be191b39c6ca09rucdk_ Content-Type: text/html; charset="iso-8859-1" Content-Transfer-Encoding: quoted-printable


I am not sure if this is of interest, but the Wiberg bond index can be= used to estimate the covalent nature of a 'non-bonded' interaction, such a= s a hydrogen bond, halogen bond, etc. For an application, see for example Molecules 2017, 22, 552; https://www.mdpi.com/1420-3049/22/4/= 552 .
Yours, Jens >--<


Fra: owner-chemistry+= spanget=3D=3Druc.dk _ ccl.net <owner-chemistry+spanget=3D=3Druc.dk _ ccl= .net> p=E5 vegne af SUMANGLA ARORA arorasumangla,,gmail.com <owner-ch= emistry _ ccl.net>
Sendt: 18. maj 2023 08:25
Til: Jens Spanget-Larsen
Emne: CCL: Quantification of non-covalent interactions
 

Sent to CCL by: "SUMANGLA  ARORA" [arorasumangla[]gmail.com]=
Dear All,

I have generated NCI plots using Multiwfn software and created 3D VMD figur= es
based on these plots. Now, I need to quantify non-covalent interactions at =
specific points of interest. I would greatly appreciate your guidance in resolving this matter.

Thanks & Regards
Sumangla



-=3D This is automatically added to each message by the mailing script =3D-=      
     
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--_000_8d6073824e8447cba7be191b39c6ca09rucdk_-- From owner-chemistry@ccl.net Thu May 18 09:42:00 2023 From: "Caio Firme firme.caio-x-gmail.com" To: CCL Subject: CCL: Quantification of non-covalent interactions Message-Id: <-54923-230518093231-13406-+7jhMvvcOLgVhlXMWI01kQ(_)server.ccl.net> X-Original-From: Caio Firme Content-Type: multipart/alternative; boundary="000000000000879be605fbf7d504" Date: Thu, 18 May 2023 10:30:50 -0300 MIME-Version: 1.0 Sent to CCL by: Caio Firme [firme.caio(-)gmail.com] --000000000000879be605fbf7d504 Content-Type: text/plain; charset="UTF-8" Please, read the following paper about LPE (local potential energy): https://www.sciencedirect.com/science/article/abs/pii/S2210271X21000025 All the best Caio Em qui., 18 de mai. de 2023 04:27, SUMANGLA ARORA arorasumangla,,gmail.com < owner-chemistry%x%ccl.net> escreveu: > > Sent to CCL by: "SUMANGLA ARORA" [arorasumangla[]gmail.com] > Dear All, > > I have generated NCI plots using Multiwfn software and created 3D VMD > figures > based on these plots. Now, I need to quantify non-covalent interactions at > specific points of interest. I would greatly appreciate your guidance in > resolving this matter. > > Thanks & Regards > Sumangla> > > --000000000000879be605fbf7d504 Content-Type: text/html; charset="UTF-8" Content-Transfer-Encoding: quoted-printable
Please, read the following paper about LPE (local potenti= al energy):


Em qui., 18 de mai. de 2023= 04:27, SUMANGLA ARORA arorasumangla,,gmail.co= m <owner-chemistry%x%ccl.ne= t> escreveu:

Sent to CCL by: "SUMANGLA=C2=A0 ARORA" [arorasumangla[]gmail.co= m]
Dear All,

I have generated NCI plots using Multiwfn software and created 3D VMD figur= es
based on these plots. Now, I need to quantify non-covalent interactions at =
specific points of interest. I would greatly appreciate your guidance in resolving this matter.

Thanks & Regards
Sumangla



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--000000000000879be605fbf7d504-- From owner-chemistry@ccl.net Thu May 18 15:03:00 2023 From: "Tian Lu sobereva*|*sina.com" To: CCL Subject: CCL: Quantification of non-covalent interactions Message-Id: <-54924-230518145944-29533-Ot4xO7j/+y6+HBSemw34RQ!A!server.ccl.net> X-Original-From: "Tian Lu" Date: Thu, 18 May 2023 14:59:41 -0400 Sent to CCL by: "Tian Lu" [sobereva#sina.com] Dear Sumangla, There are many possible ways for the quantification, an incomplete list is shown below, all the methods can be realized by Multiwfn and you can find corresponding introductions and examples from the manual. (1) QTAIM topology analysis. Properties at bond critical point (BCP) between interacting atoms are known to be closely related to interaction strength and nature, this has been extensively investigated in literatures. For example, H-bond binding energy can be well estimated based on electron density at BCP, see J. Comput. Chem., 40, 28682881 (2019). Application example can be found in section 4.2.1 of manual. (2) Energy decomposition analysis based on force field (EDA-FF). This method is able to decompose interactions to different physical natures between atoms or between fragments, this feature is useful to quantify interaction between local regions, such as pi-pi stacking between two aromatic fragments. See 4.21.1 of manual for example. (3) Integrating real space function within isosurface of reduced density gradient (RDG), this is a way of quantifying interaction defined in the framework of NCI, and can be realized via domain analysis module of Multiwfn. See Section 4.200.14.1 of manual for details and examples. (4) Predicting binding energy using electrostatic potential at nuclear position. This method was proposed in J. Phys. Chem. A, 118, 1697 (2014) and is compatible with wide variety of interaction types, see Section 4.1.2 of manual for example. (5) Core-valence bifurcation (CVB) index. This method was proposed in Theor. Chem. Acc., 104, 13 (2000) based on electron localization function (ELF) and mainly used to distinguish strength of various kind of H-bonds., see Section 3.200.1 of manual for detail. (6) ETS-NOCV. When orbital interaction plays a nonnegligible role in noncovalent interaction, this method will be fairly useful, which is able to quantify the strength and meantime intuitively exhibit characters of orbital interactions. See Section 4.23 of manual for example. (7) There are some indices related to weak interactions defined in the framework of IGM/IGMH, such as delta_G_pair and IBSIW, see Section 3.23.5 of manual for details. See recent review "Visualization Analysis of Weak Interactions in Chemical Systems" Comprehensive Computational Chemistry DOI: 10.1016/B978-0-12-821978- 2.00076-3 for more discussion about quantification of weak interactions. ------------ Sent to CCL by: "SUMANGLA ARORA" [arorasumangla[]gmail.com] Dear All, I have generated NCI plots using Multiwfn software and created 3D VMD figures based on these plots. Now, I need to quantify non-covalent interactions at specific points of interest. I would greatly appreciate your guidance in resolving this matter. Thanks & Regards Sumangla