From owner-chemistry@ccl.net Mon Jun 11 04:15:01 2018 From: "Ulrike Salzner salzner__fen.bilkent.edu.tr" To: CCL Subject: CCL: How to carry out calculations of an anion with a potential sensor Message-Id: <-53341-180611030832-31675-SgPdDLB5+gpKf6UjK7mM3A:+:server.ccl.net> X-Original-From: Ulrike Salzner Content-Type: multipart/alternative; boundary="00000000000015faf5056e586a44" Date: Mon, 11 Jun 2018 10:07:38 +0300 MIME-Version: 1.0 Sent to CCL by: Ulrike Salzner [salzner,+,fen.bilkent.edu.tr] --00000000000015faf5056e586a44 Content-Type: text/plain; charset="UTF-8" Dear Noorain, As you get different results, it does matter where you put the anion. The structure with the lowest energy is the best and you have try all possibilities to - hopefully - locate the global minimum. For NMR calculations the geometry is important because NMR shifts are very sensitive to the structure. You should also consider solvent effects as gas phase structures involving ions are probably different from those found in solution. Best regards, Ulrike Assoc. Prof. Ulrike Salzner Department of Chemistry Bilkent University 06800 Bilkent, Ankara On Sun, Jun 10, 2018 at 12:09 PM, Noorain Khalifa noorain.k,+, che.christuniversity.in wrote: > > Sent to CCL by: "Noorain Khalifa" [noorain.k _ che.christuniversity.in] > Hello! > This may seem like a really dumb question but I'm just a beginner in this > field. > I have a molecule that could be a sensor for anions and the mechanism that > I > hypothesize it to go through is with the help of hydrogen bonding with a > particular N-H functional group. > The molecule also has another good H-bond donor group - an OH group. > Now to see the interaction using DFT, where I start the calculation with > only > one anion and one receptor, does it matter where I place the anion to do > the > geometry optimization? Because, it gives different results when placed > near > different positions of the receptor. > > Also, to carry out NMR calculations, is a geometry optimized structure > necessary? > > Noorain K> > > --00000000000015faf5056e586a44 Content-Type: text/html; charset="UTF-8" Content-Transfer-Encoding: quoted-printable
Dear Noorain,
As you get different results,= it does matter where you put the anion. The structure with the lowest ener= gy is the best and you have try all possibilities to - hopefully - locate t= he global minimum.
For NMR calculations the geometry is important= because NMR shifts are very sensitive to the structure. You should also co= nsider solvent effects as gas phase structures involving ions are probably = different from those found in solution.
Best regards,
U= lrike

Assoc. Prof. Ulrike Salzner
Department of Che= mistry
Bilkent University
06800 Bilkent, Ankara

On Sun, Jun 10, 2018 at 12:09 PM, Noorain Kh= alifa noorain.k,+,che.christuniv= ersity.in <owner-chemistry],[ccl.net> wrote:

Sent to CCL by: "Noorain=C2=A0 Khalifa" [noorain.k _ che.chr= istuniversity.in]
Hello!
This may seem like a really dumb question but I'm just a beginner in th= is
field.
I have a molecule that could be a sensor for anions and the mechanism that = I
hypothesize it to go through is with the help of hydrogen bonding with a particular N-H functional group.
The molecule also has another good H-bond donor group - an OH group.
Now to see the interaction using DFT, where I start the calculation with on= ly
one anion and one receptor, does it matter where I place the anion to do th= e
geometry optimization? Because, it gives different results when placed near=
different positions of the receptor.

Also, to carry out NMR calculations, is a geometry optimized structure
necessary?

Noorain K



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--00000000000015faf5056e586a44-- From owner-chemistry@ccl.net Mon Jun 11 10:11:00 2018 From: "Meenakshi Dutt meenakshi.dutt{}rutgers.edu" To: CCL Subject: CCL: MRS symposium on Multiscale Modeling Message-Id: <-53342-180611100202-29781-53+o1hVeJM2XQqPXhbeUug^^server.ccl.net> X-Original-From: "Meenakshi Dutt" Date: Mon, 11 Jun 2018 10:02:00 -0400 Sent to CCL by: "Meenakshi Dutt" [meenakshi.dutt||rutgers.edu] Dear Colleagues, We invite you to contribute abstracts to the MRS Fall 2018 Symposium BM03: Multiscale Modeling of Soft Materials and Interfaces. We have a great group of invited speakers, and look forward to a very exciting symposium. We would like to request you to submit abstracts at https://www.mrs.org/fall2018 The abstract submission will be open from May 14 to June 14, 2018. We also would like to ask you to encourage your students, collaborators, and interested colleagues to submit their abstracts as contributed talks for our Symposium. The Call for Papers can be found at: https://www.mrs.org/fall-2018-call-for-papers-detail?code=BM03 We are looking forward to seeing you in Boston! Best regards, Sanket A. Deshmukh (Virginia Tech, USA) Meenakshi Dutt (Rutgers University, USA) Durba Sengupta (National Chemical Laboratory, India) Igor V. Pivkin (University of Lugano, Switzerland) From owner-chemistry@ccl.net Mon Jun 11 22:29:00 2018 From: "Guzman, Francisco fg58()njit.edu" To: CCL Subject: CCL: Complete basis set extrapolation, but with DFT methods Message-Id: <-53343-180611222712-25400-mECEtd1PPRgNec1/1COwSQ[]server.ccl.net> X-Original-From: "Guzman, Francisco" Content-Type: multipart/alternative; boundary="0000000000003a47e5056e689a51" Date: Mon, 11 Jun 2018 22:27:06 -0400 MIME-Version: 1.0 Sent to CCL by: "Guzman, Francisco" [fg58()njit.edu] --0000000000003a47e5056e689a51 Content-Type: text/plain; charset="UTF-8" Hello CCL'ers, Using electron correlation methods, such as CCSD(T), it is a very common approach to extrapolate single point energies to the complete basis set limit (CBS). However, is it also common place to apply the the CBS procedure, but to instead use a DFT method such as wb97x, PBE0, or M06-2X? Best, -- Francisco Guzman PhD Candidate Otto H. York Department of Chemical, Biological and Pharmaceutical Engineering New Jersey Institute of Technology Email: fg58#njit.edu, guzman.research#gmail.com --0000000000003a47e5056e689a51 Content-Type: text/html; charset="UTF-8" Content-Transfer-Encoding: quoted-printable
Hello CCL'ers,

Using electron correl= ation methods, such as CCSD(T), it is a very common approach to extrapolate= single point energies to the complete basis set limit (CBS).=C2=A0
However, is it also common place to apply the the CBS procedure, but to in= stead use a DFT method such as wb97x, PBE0, or M06-2X?

Best,

--
Francisco Gu= zman
= PhD Candidate
Otto H. York Department o= f Chemical, Biological and Pharmaceutical Engineering
New Jersey Institu= te of Technology
--0000000000003a47e5056e689a51--