From owner-chemistry@ccl.net Mon Jun 11 04:15:01 2018
From: "Ulrike Salzner salzner__fen.bilkent.edu.tr" <owner-chemistry:+:server.ccl.net>
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 <salzner- -fen.bilkent.edu.tr>
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Date: Mon, 11 Jun 2018 10:07:38 +0300
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Sent to CCL by: Ulrike Salzner [salzner,+,fen.bilkent.edu.tr]
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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 <owner-chemistry],[ccl.net> 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>
>
>
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<div dir=3D"ltr"><div>Dear Noorain,</div><div>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.</div><div>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.</div><div>Best regards,</div><div>U=
lrike<br></div></div><div class=3D"gmail_extra"><br clear=3D"all"><div><div=
class=3D"gmail_signature">Assoc. Prof. Ulrike Salzner<br>Department of Che=
mistry<br>Bilkent University<br>06800 Bilkent, Ankara</div></div>
<br><div class=3D"gmail_quote">On Sun, Jun 10, 2018 at 12:09 PM, Noorain Kh=
alifa noorain.k,+,<a href=3D"http://che.christuniversity.in">che.christuniv=
ersity.in</a> <span dir=3D"ltr"><<a href=3D"mailto:owner-chemistry],[ccl.n=
et" target=3D"_blank">owner-chemistry],[ccl.net</a>></span> wrote:<br><blo=
ckquote class=3D"gmail_quote" style=3D"margin:0px 0px 0px 0.8ex;border-left=
:1px solid rgb(204,204,204);padding-left:1ex"><br>
Sent to CCL by: "Noorain=C2=A0 Khalifa" [noorain.k _ <a href=3D"h=
ttp://che.christuniversity.in" rel=3D"noreferrer" target=3D"_blank">che.chr=
istuniversity.in</a>]<br>
Hello! <br>
This may seem like a really dumb question but I'm just a beginner in th=
is <br>
field. <br>
I have a molecule that could be a sensor for anions and the mechanism that =
I <br>
hypothesize it to go through is with the help of hydrogen bonding with a <b=
r>
particular N-H functional group. <br>
The molecule also has another good H-bond donor group - an OH group. <br>
Now to see the interaction using DFT, where I start the calculation with on=
ly <br>
one anion and one receptor, does it matter where I place the anion to do th=
e <br>
geometry optimization? Because, it gives different results when placed near=
<br>
different positions of the receptor. <br>
<br>
Also, to carry out NMR calculations, is a geometry optimized structure <br>
necessary? <br>
<br>
Noorain K<br>
<br>
<br>
<br>
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</blockquote></div><br></div>
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From owner-chemistry@ccl.net Mon Jun 11 10:11:00 2018
From: "Meenakshi Dutt meenakshi.dutt{}rutgers.edu" <owner-chemistry^^server.ccl.net>
To: CCL
Subject: CCL: MRS symposium on Multiscale Modeling
Message-Id: <-53342-180611100202-29781-53+o1hVeJM2XQqPXhbeUug^^server.ccl.net>
X-Original-From: "Meenakshi Dutt" <meenakshi.dutt a rutgers.edu>
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" <owner-chemistry[]server.ccl.net>
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" <fg58^_^njit.edu>
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]
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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
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Content-Transfer-Encoding: quoted-printable
<div dir=3D"ltr"><div>Hello CCL'ers,<br><br></div>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 <br><br=
>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? <br clear=3D"all"><d=
iv><div><div><br></div><div>Best,<br></div><div><br>-- <br><div class=3D"gm=
ail_signature" data-smartmail=3D"gmail_signature"><div dir=3D"ltr"><div><di=
v dir=3D"ltr"><div><div dir=3D"ltr"><span style=3D"color:rgb(34,34,34);font=
-family:arial;font-size:small;font-style:normal;font-variant:normal;font-we=
ight:normal;letter-spacing:normal;line-height:normal;text-align:start;text-=
indent:0px;text-transform:none;white-space:normal;word-spacing:0px;backgrou=
nd-color:rgb(255,255,255);display:inline!important;float:none">Francisco Gu=
zman</span><br style=3D"color:rgb(34,34,34);font-family:arial;font-size:sma=
ll;font-style:normal;font-variant:normal;font-weight:normal;letter-spacing:=
normal;line-height:normal;text-align:start;text-indent:0px;text-transform:n=
one;white-space:normal;word-spacing:0px;background-color:rgb(255,255,255)">=
<span style=3D"color:rgb(34,34,34);font-family:arial;font-size:small;font-s=
tyle:normal;font-variant:normal;font-weight:normal;letter-spacing:normal;li=
ne-height:normal;text-align:start;text-indent:0px;text-transform:none;white=
-space:normal;word-spacing:0px;background-color:rgb(255,255,255);display:in=
line!important;float:none">PhD Candidate</span><div style=3D"color:rgb(34,3=
4,34);font-family:arial;font-size:small;font-style:normal;font-variant:norm=
al;font-weight:normal;letter-spacing:normal;line-height:normal;text-align:s=
tart;text-indent:0px;text-transform:none;white-space:normal;word-spacing:0p=
x;background-color:rgb(255,255,255)"><span style=3D"background-color:rgb(25=
5,255,255)"><font color=3D"#000000"></font></span>Otto H. York Department o=
f Chemical, Biological and Pharmaceutical Engineering<br>New Jersey Institu=
te of Technology</div><div style=3D"color:rgb(34,34,34);font-family:arial;f=
ont-size:small;font-style:normal;font-variant:normal;font-weight:normal;let=
ter-spacing:normal;line-height:normal;text-align:start;text-indent:0px;text=
-transform:none;white-space:normal;word-spacing:0px;background-color:rgb(25=
5,255,255)">Email:=C2=A0<font color=3D"#0000ff"><a href=3D"mailto:fg58#njit=
.edu" style=3D"color:rgb(17,85,204)" target=3D"_blank">fg58#njit.edu</a>,<s=
pan>=C2=A0</span><a href=3D"mailto:guzman.research#gmail.com" style=3D"colo=
r:rgb(17,85,204)" target=3D"_blank">guzman.research#gmail.com</a></font></d=
iv></div></div></div></div></div></div>
</div></div></div></div>
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