Computational and Quantum Chemistry – Telegram
Computational and Quantum Chemistry
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A group dedicated to everything about theoretical and computational/quantum chemistry.
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There is a new release of GAMESS_US available - June 30, 2021 R1 Public Release
The historic and beloved software brings several new features

New Features
* DFTB, TDDFTB, AM1 and PM3 can be used as QM methods in QuanPol QM/MM.
* MD simulation ($QUANPO DIFFUSE=1 COM) of ion mobility and collision cross section (CCS) in neutral buffer gases.
* Force field global optimization method ($QUANPO keyword MDOPT, coded by Rui Lai).
* Pairwise approximation method ($QUANPO IDIMER=3) for larger QM region in QM/MM.

Improvements
* Fixed a few FPE errors.
* Fixed a few bugs in free energy simulation.
* Automatic selection of QM atoms for QM/MM.
* Added/modified a few tests in $GMS_DIR/tests/quanpol
* Added new force field files to $GMS_DIR/auxdata/QUANPOL
* Enable 1e- and 2e- integrals generated by ROHF code in to be written to a file (FCIDUMP) for external use (#407) (J. E. Deustua)

Free Download: https://www.msg.chem.iastate.edu/GAMESS/License_Agreement.html
correl20.pdf
17.8 MB
Topology, Entanglement, and Strong Correlations
AutoDock Vina is arguably one of the fastest and most widely used open-source programs for molecular docking. However, compared to other programs in the AutoDock Suite, it lacks support for modeling specific features such as macrocycles or explicit water molecules. Here, we describe the implementation of this functionality in AutoDock Vina 1.2.0. Additionally, AutoDock Vina 1.2.0 supports the AutoDock4.2 scoring function, simultaneous docking of multiple ligands, and a batch mode for docking a large number of ligands. Furthermore, we implemented Python bindings to facilitate noscripting and the development of docking workflows. This work is an effort toward the unification of the features of the AutoDock4 and AutoDock Vina programs.
http://vina.scripps.edu/download.html
The source code is available at https://github.com/ccsb-scripps/AutoDock-Vina
acs.jcim.1c00203.pdf
2 MB
AutoDock Vina 1.2.0: New Docking Methods, Expanded Force Field, and Python Bindings
Dear ORCA Users,

the ORCA development team is happy to announce the availability
of the first bugfix release in the ORCA 5.0 version series,
namely ORCA 5.0.1!

As we have already been made aware of quite a few bugs in ORCA 5.0.0,
we decided to release this version as quickly as possible.

This is a pure bugfix release, addressing most of the bugs mentioned
in the Known Bugs section of ORCA 5.0.0.
The problems regarding the new %compound block have not yet been
addressed, those will follow shortly afterwards.

If you have encountered problems with ORCA 5.0.0 before,
please give ORCA 5.0.1 a try and hopefully most concerns have been
addressed.


Enjoy this new release of ORCA!

https://orcaforum.kofo.mpg.de/viewtopic.php?f=8&t=7785&sid=3df98e9b291ced282fa3e04cf221b021
Have you published any papers lately? Share with us with a little explanation of your work. 😊
Draw molecules online with 2D to 3D conversion:
https://molview.org/
Albu_et_al_2007_Computational_Chemistry_of_Polyatomic_Reaction_Kinetics.pdf
604.2 KB
Computational Chemistry of Polyatomic Reaction Kinetics and Dynamics: The Quest for an Accurate CH5 Potential Energy Surface
Virtual Lab would like to announce free webinar "Cathode Design Principles
for Alkali-Ion Batteries"
by Dr. Haegyeom Kim (LBNL)

Please registered here

https://www.materialssquare.com/webinar

28 July 2021, 16:00 - 17:00 | LA, PDT
29 July 2021, 01:00 - 02:00 | Paris, CEST
29 July 2021, 04:30 - 05:30 | New Delhi, IST
29 July 2021, 08:00 - 09:00 | Seoul, KST

The development of cathode materials is a key factor in improving the overall battery performance. In this webinar, Dr. Haegyeom Kim(LBNL) will introduce and summarize the critical factors affecting the properties and performance of battery materials, ranging from atomic- to microscopic levels.

- This webinar is a non-commercial event. (no participation fee)
- The video recording and presentation material will be provided for pre-
registrants only.

Thanks!

Minkyu Park
On behalf of the MESMER team, we are delighted to announce that MESMER 6.1 (Master Equation Solver for Multi Energy-well Reactions) is now available for download.

MESMER is designed to analyze and simulate reactions in the gas phase that take place on a potential energy surface that is characterized by having one or more potential wells, and which are typically described by rate coefficients that depend on pressure (or concentration) as well as temperature. MESMER allows you to simulate systems over a wide range of pressures and temperatures, extract rate coefficients, analyze experimental data, fit model parameters and represent rate coefficients in formats that can be used directly in large scale simulations (e.g. Cantera or Chemkin).

The Windows installer and Linux tar file are located at:

https://sourceforge.net/projects/mesmer/

The source can also be viewed and downloaded from this site. There are also bug and feature request tracking facilities which we encourage you to use.

MESMER 6.1 is largely a maintenance release, but includes the following new features:

Biexponential down energy transfer model.
Lennard-Jones parameter calculation for compounds investigated by Jasper.
Extension of definition of diffusive loss in trace fitting. We thank Timo Pekkanen of the University of Helsinki, for suggesting this change.

MESMER Input, bug fixes and Other Changes:

QD libraries used to provided extended precision have been
upgraded to version 2.3.22. Note this update will require a change to build noscripts as the QD library is generated in a sub directory. See manual for details.
Deprecated keywords. Some keywords are to be retired and these are listed in the manual.
An issue with reading the reference temperature used in the ILT method has been addressed.
We thank Timo Pekkanen and Prasenjit Seal of the University of Helsinki for bringing the following issues to our attention:
An issue with extended ILT has been addressed.
An issue with derived Arrhenius parameters has been addressed, e.g., a given pre-exponential factor can now be derived from another pre-exponential factor.
An issue with the weighted trace fitting for an equilibrating system with diffusive loss terms has been addressed.
An issue with reactions with multiple transition states has been addressed.

If you have any comments or suggestions, please do not hesitate to let us know, either through the above site or by email (Mark Blitz(M.Blitz^-^leeds.ac.uk) and Struan Robertson (struanhrobertson^-^gmail.com) would be very happy to receive feedback).

More information is available at the MESMER website:
http://www.chem.leeds.ac.uk/mesmer.html

Also some of the implementation details of MESMER are described in Journal of Physical Chemistry A, 95459560, 116 (2012).

A web based graphical user interface for creating MESMER input files, developed by Dr. Xiaoqing You and colleagues of the University of Tsinghua, in collaboration with the MESMER team, is available for testing and can be found at the following address:

http://www.mesmergui.cn/

Dr. You and the MESMER team would welcome feedback on this interface.
Regards,

Mark Blitz and Struan Robertson