From owner-chemistry@ccl.net Mon Jan 21 01:24:01 2019
From: "David Beratan david.beratan * duke.edu" <owner-chemistry**server.ccl.net>
To: CCL
Subject: CCL: 2019 Summer Undergraduate Research Program at Duke University
Message-Id: <-53589-190120110222-11610-n7GvuWHlafkbL+ZVFjvEpw**server.ccl.net>
X-Original-From: "David Beratan" <david.beratan],[duke.edu>
Date: Sun, 20 Jan 2019 11:02:20 -0500
Sent to CCL by: "David Beratan" [david.beratan-#-duke.edu]
A new summer undergraduate research program at Duke University is aimed at rising seniors
> from North America (US, Mexico, Canada) with a strong interest in theoretical chemistry. Ten
faculty from across Duke's campus will run this seven week program in 2019, which will include
a mentored research project and frequent seminars, discussions, and tutorials covering topics
in modern theoretical chemistry. The program will provide a stipend, on-campus housing, and
a travel allowance.
Our web site with program details is here: https://chem.duke.edu/research/summer-
undergraduate-research-theoretical-chemistry-duke
The application deadline is February 1.
Faculty mentors will include: Hashim Al-Hashimi, David Beratan, Volker Blum, Patrick
Charbonneau, Stephen Craig, Bruce Donald, Jianfeng Lu, Michael Rubinstein, Warren Warren
and Weitao Yang.
From owner-chemistry@ccl.net Mon Jan 21 07:45:00 2019
From: "Mo Fateh mo.fateh+/-yahoo.com" <owner-chemistry . server.ccl.net>
To: CCL
Subject: CCL:G: All electron basis set for H2Te
Message-Id: <-53590-190121072738-8041-ZVPwqScAmXlHoZYl9Mq1eg . server.ccl.net>
X-Original-From: "Mo Fateh" <mo.fateh[*]yahoo.com>
Date: Mon, 21 Jan 2019 07:27:36 -0500
Sent to CCL by: "Mo Fateh" [mo.fateh]_[yahoo.com]
Dear CCL Subscribers,
I am going to do geometry optimization for H2O, H2S, H2Se, and H2Te using
Gaussian 09. What is the suitable All electron basis set for optimization
with B3LYP?
I have checked the Gaussian website and found that the following bais sets
are suitable:
1- DGDZVP basis set
2- QZVPand Def2
3- UGBS basis set
Which is one you recommended? and Why? Please suggest any other suitable
basis set
Mo Fateh
From owner-chemistry@ccl.net Mon Jan 21 12:13:00 2019
From: "Stefano Alcaro alcaro^unicz.it" <owner-chemistry%server.ccl.net>
To: CCL
Subject: CCL: Computationally Driven Drug Discovery Meeting - Rome 28-29 March 2019
Message-Id: <-53591-190121050059-16986-XUDNBfg6apDXHfCGv+8T4w%server.ccl.net>
X-Original-From: "Stefano Alcaro" <alcaro+*+unicz.it>
Date: Mon, 21 Jan 2019 05:00:56 -0500
Sent to CCL by: "Stefano Alcaro" [alcaro++unicz.it]
On March 28-29 2019, under the auspices of the Division of Medicinal Chemistry of the SCI the Centro Congressi Europa Sala Italia of the Universit Cattolica del Sacro Cuore at Largo Francesco Vito 1, Rome will host the Computationally Driven Drug Discovery Meeting (CDDD 6th Meeting)
Following the previous editions held in LAquila in 2011, in Genova 2013, in Verona 2014, in Pomezia 2016 and in Milan 2017, the convention aims to gather together researchers who make use of techniques such as computational chemistry, chemoinformatics, QSAR, property prediction to direct their effort towards integrated drug discovery program.
Researchers from both academia and industry are cordially invited to attend and to contribute to set up the state of the art of the discipline in Italy.
Expected outcomes of the convention are:
- to promote a deep scientific discussion in the multifaceted field of computational drug discovery;
- to promote the mutual acquaintance of research groups and to devise potential areas of collaboration;
- to promote the integration between industrial needs and academic expertise towards more effective drug discovery programs.
The sessions will be focused on topical issues among which Kinetics and residence time in drug discovery, Cryptic and allosteric pocket identification and related computational methods, and Big data and machine Learning.
The participation to the convention is free, but the number of participants is limited to 80. The selection will be made by the scientific committee on the basis of first come, first serve.
All those who are interested in participating must send an email to cddd2019%x%gmail.com
Info at the web site http://users.unimi.it/cddd/
Best regards
The scientific committee
- Stefano Alcaro (Universit di Catanzaro)
- Andrea Cavalli (Universit di Bologna e IIT, Genova)
- Maria Cristina De Rosa (local organizer, CNR, Rome)
- Rosella Ombrato (Angelini, Pomezia)
- Luca Sartori (S-IN, Soluzioni Informatiche, Vicenza)
- Francesca Spyrakis (Universit di Torino)
- Giulio Vistoli (Universit di Milano)
From owner-chemistry@ccl.net Mon Jan 21 13:16:00 2019
From: "Susi Lehtola susi.lehtola|a|alumni.helsinki.fi" <owner-chemistry*|*server.ccl.net>
To: CCL
Subject: CCL:G: All electron basis set for H2Te
Message-Id: <-53592-190121125727-9840-nvsGz15FNA/ho9APjf5sUw*|*server.ccl.net>
X-Original-From: Susi Lehtola <susi.lehtola-x-alumni.helsinki.fi>
Content-Language: en-US
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Date: Mon, 21 Jan 2019 19:57:18 +0200
MIME-Version: 1.0
Sent to CCL by: Susi Lehtola [susi.lehtola%x%alumni.helsinki.fi]
On 1/21/19 2:27 PM, Mo Fateh mo.fateh+/-yahoo.com wrote:
>
> Sent to CCL by: "Mo Fateh" [mo.fateh]_[yahoo.com] Dear CCL
> Subscribers,
>
> I am going to do geometry optimization for H2O, H2S, H2Se, and H2Te
> using Gaussian 09. What is the suitable All electron basis set for
> optimization with B3LYP?
>
> I have checked the Gaussian website and found that the following bais
> sets are suitable:
>
> 1- DGDZVP basis set 2- QZVPand Def2 3- UGBS basis set
>
> Which is one you recommended? and Why? Please suggest any other
> suitable basis set
First, do you really need an all-electron treatment? Using an effective
core potential (ECP) typically gives you good results with a low cost.
The def2 sets are not all-electron, but use relativistic core potentials
starting from the 5th period.
In addition to def2, you can also use the correlation consistent series,
cc-pVXZ-PP, for the heavy atoms, which employs ECPs. These are probably
not in the code you are using, but you can download the sets from the
Basis Set Exchange (BSE) at https://bse.pnl.gov/bse/portal.
If you want to do all-electron calculations, then you have to include
relativistic effects to get any kind of reasonable accuracy. It looks
like Gaussian can do second-order Douglas-Kroll-Hess (DKH2)
calculations, and that the program uses a finite nuclear model in such a
case. But, when you do a relativistic calculation, you have to make sure
that the basis set has actually been designed for the method you are using.
Unfortunately, there aren't many relativistic basis sets available on
BSE. IIRC, the ANO-RCC set by Almlöf, Roos, and coworkers available on
BSE has been parametrized with DKH2, so that would be an okay choice.
Then, there are the x2c-SV(P)all, x2c-SVPall, x2c-TZVPall and
x2c-TZVPPall basis sets by Pollak and Weigend, which are all-electron
versions of the def2 basis sets; however, these basis sets have been
formed with the eponymous X2C approach which differs from DKH2, and so
the contractions may not be right for DKH2.
If you want to play on the safe side, you could decontract these sets;
like I implied before, the main problem with different relativistic
models is that the core orbitals may be dissimilar. Using a fully
uncontracted basis set takes away this problem; of course, then your
basis set becomes larger.
Personally, I would recommend either using ECP sets like def2, or if you
really need all electrons, then I'd go with the x2c series. These are
both commonly used, so I'd expect fewer problems.
UGBS is a fine basis set for mean-field calculations on atoms. The
problem is just that it is pretty huge (71, 84, 163, and 179 for O, S,
Se, and Te, respectively), while it lacks polarization and correlation
functions altogether. This means that calculations in molecules and/or
at a post-HF level of theory will be unbalanced; you could trade off a
small decrease in accuracy for atoms for a large improvement for
molecules with the same number of basis functions by using a different
kind of basis set.
There are variants of UGBS with polarization functions, but
1) these are much larger than even the plain UGBS basis set; several
hundred functions per atom,
2) I haven't been able to find any description on how the polarized
basis sets have been formed, and
3) I am not aware of any accuracy benchmarks with these sets.
--
------------------------------------------------------------------
Mr. Susi Lehtola, PhD Junior Fellow, Adjunct Professor
susi.lehtola-*-alumni.helsinki.fi University of Helsinki
http://susilehtola.github.io/ Finland
------------------------------------------------------------------
Susi Lehtola, dosentti, FT tutkijatohtori
susi.lehtola-*-alumni.helsinki.fi Helsingin yliopisto
http://susilehtola.github.io/
------------------------------------------------------------------
From owner-chemistry@ccl.net Mon Jan 21 16:48:00 2019
From: "Salter-Duke, Brian James - brian.james.duke||gmail.com" <owner-chemistry##server.ccl.net>
To: CCL
Subject: CCL:G: All electron basis set for H2Te
Message-Id: <-53593-190121164429-16041-jESpMT0ZB3KDTh5oF+Kefw##server.ccl.net>
X-Original-From: "Salter-Duke, Brian James -" <brian.james.duke~!~gmail.com>
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Date: Tue, 22 Jan 2019 08:44:17 +1100
MIME-Version: 1.0
Sent to CCL by: "Salter-Duke, Brian James -" [brian.james.duke]=[gmail.com]
My advice to Mo Fateh, although I want to make it for everyone, is to
NOT use B3LYP. I am fed up with reading on CCL of people proposing to
use B3LYP. B3LYP is an old method and has been superceded my many
better methods that are no more computer intensive. Do some research
to find a better method. I would also point out that you can get, if
you do make a special effort, different B3LYP results using different
programs. For example, there are I think 5 different B3LYP methods,
and Gaussian and GAMESS(US) chose different ones by default.
Just my 5c worht, Brian.
On Mon, Jan 21, 2019 at 07:27:36AM -0500, Mo Fateh mo.fateh+/-yahoo.com wrote:
>
> Sent to CCL by: "Mo Fateh" [mo.fateh]_[yahoo.com]
> Dear CCL Subscribers,
>
> I am going to do geometry optimization for H2O, H2S, H2Se, and H2Te using
> Gaussian 09. What is the suitable All electron basis set for optimization
> with B3LYP?
>
> I have checked the Gaussian website and found that the following bais sets
> are suitable:
>
> 1- DGDZVP basis set
> 2- QZVPand Def2
> 3- UGBS basis set
>
> Which is one you recommended? and Why? Please suggest any other suitable
> basis set
>
> Mo Fateh>
--
Brian Salter-Duke (Brian Duke) Brian.Salter-Duke-$-monash.edu
Adjunct Associate Professor
Monash Institute of Pharmaceutical Sciences
Monash University Parkville Campus, VIC 3052, Australia