Systematic first principles parameterization of force fields for metal-organic frameworks using a genetic algorithm approach

The Journal of Physical Chemistry. B
Maxim Tafipolsky, Rochus Schmid

Abstract

A systematic strategy is proposed to derive the necessary force field parameters directly from first principles calculations of nonperiodic model systems to reproduce both the structure and curvature of the reference potential energy surface. The parameters are determined using a genetic algorithm combined with a novel fitness criterion based on a representation of structure and curvature in a set of redundant internal coordinates. Due to the efficiency of this approach it is possible to abandon the need for transferability of the parameters. The method is targeted for the application on metal-organic frameworks (MOFs), where parameters for molecular mechanics force fields are often not available, because of the wide range of possible inorganic fragments involved. The scheme is illustrated for Zn4O-based IRMOF materials on the example of MOF-5. In a "building block" approach parameters are derived for the two model systems basic zinc formate (Zn4O(O2CH)6), and dilithium terephthalate with reference data obtained from density functional theory. The resulting potential gives excellent agreement with the structure, vibrational frequencies, thermal behavior and elastic constants of the periodic MOF-5.

References

Sep 15, 1988·Physical Review A: General Physics·A D Becke
Feb 1, 1993·Physical Review. B, Condensed Matter·M J Mehl
Feb 19, 1999·Science·S S ChuiI D Williams
Feb 20, 2002·Chemical Reviews·Pierfranco Demontis, Giuseppe B. Suffritti
Oct 2, 2003·Chemical Society Reviews·Stuart L James
Dec 21, 2004·The Journal of Chemical Physics·Tatsuhiko SagaraEric Ganz
Aug 27, 2005·Science·Jesse L C RowsellOmar M Yaghi
Feb 3, 2006·The Journal of Physical Chemistry. a·Tomica HrenarHans-Joachim Werner
Feb 8, 2006·The Journal of Chemical Physics·Filipp Furche, John P Perdew
Feb 9, 2006·Chemical Communications : Chem Comm·Susumu KitagawaTakayoshi Nakamura
Aug 1, 1988·Proceedings of the National Academy of Sciences of the United States of America·J R MapleA T Hagler
Jun 27, 2006·Proceedings of the National Academy of Sciences of the United States of America·Kyo Sung ParkOmar M Yaghi
Jul 21, 2006·The Journal of Physical Chemistry. B·Qingyuan Yang, Chongli Zhong
Aug 17, 2006·Journal of the American Chemical Society·Jeffery A Greathouse, Mark D Allendorf
Nov 30, 2006·Angewandte Chemie·Saeed AmirjalayerRochus Schmid
Feb 16, 2007·Journal of Computational Chemistry·Maxim TafipolskyRochus Schmid
Apr 14, 2007·Science·Hani M El-KaderiOmar M Yaghi
May 10, 2007·Angewandte Chemie·David DubbeldamRandall Q Snurr
Jun 16, 2007·Journal of the American Chemical Society·Sang Soo Han, Goddard William A
Aug 1, 2007·Angewandte Chemie·Kazuhiro UemuraHidetoshi Kita
Dec 21, 2007·Proceedings of the National Academy of Sciences of the United States of America·A BlomqvistR Ahuja
Feb 22, 2008·Journal of the American Chemical Society·Stephanie L GouldMiguel A Garcia-Garibay
Aug 30, 2008·Journal of the American Chemical Society·Rochus Schmid, Maxim Tafipolsky
Oct 3, 2008·Chemical Communications : Chem Comm·Franck MillangeGérard Férey
Feb 1, 2008·Journal of Chemical Theory and Computation·Víctor M RayónDimas Suárez

❮ Previous
Next ❯

Citations

Jul 5, 2012·The Journal of Chemical Physics·Zhongqiao HuJianwen Jiang
Feb 25, 2014·Journal of Molecular Modeling·Yingxin Sun, Huai Sun
Jul 10, 2014·Biomolecules·Pietro Vidossich, Alessandra Magistrato
Jan 29, 2016·Journal of Chemical Theory and Computation·Maxim Tafipolsky, Kay Ansorg
Dec 5, 2015·Acta Crystallographica Section B, Structural Science, Crystal Engineering and Materials·Scott C McKellar, Stephen A Moggach
Jan 7, 2016·Dalton Transactions : an International Journal of Inorganic Chemistry·Johannes P DürholtRochus Schmid
Dec 9, 2015·Journal of Chemical Theory and Computation·S M J RoggeV Van Speybroeck
Jul 16, 2013·Journal of Computational Chemistry·Henrik R LarssonBernd Hartke
Oct 26, 2010·Advanced Materials·Scott T MeekMark D Allendorf
Mar 17, 2016·Journal of Molecular Modeling·Khalid A H Alzahrani, Robert J Deeth
Dec 10, 2009·Chemistry : a European Journal·Javier Pérez-PelliteroNicolas Bats
Jun 19, 2015·Journal of Computational Chemistry·Mark DittnerBernd Hartke
Feb 5, 2015·The Journal of Physical Chemistry. a·Maxim V IvanovQadir K Timerghazin
Sep 1, 2016·Journal of Chemical Theory and Computation·Damien E CoupryThomas Heine
Feb 11, 2014·Journal of Chemical Theory and Computation·Matthew A AddicoatThomas Heine
Feb 22, 2013·Journal of the American Chemical Society·Liling ZhangJianwen Jiang
Dec 23, 2016·The Journal of Physical Chemistry Letters·Peter G BoydBerend Smit
Feb 9, 2017·Journal of Chemical Information and Modeling·Federico ZaharievMarilu Dick-Perez
Jul 1, 2017·Journal of Chemical Theory and Computation·Jurn HeinenDavid Dubbeldam
Jun 10, 2010·Physical Chemistry Chemical Physics : PCCP·Olexandra ZybayloChristof Wöll
Dec 6, 2019·Chemistry : a European Journal·Elena Kolodzeiski, Saeed Amirjalayer
Jun 5, 2020·Chemical Communications : Chem Comm·Pascal FreundStefan Kaskel
Jul 17, 2018·Wiley Interdisciplinary Reviews. Computational Molecular Science·Jurn Heinen, David Dubbeldam
Oct 13, 2009·Journal of Chemical Theory and Computation·Maxim Tafipolsky, Rochus Schmid
Sep 11, 2012·Journal of Chemical Theory and Computation·L VanduyfhuysV Van Speybroeck
Oct 28, 2019·Journal of Chemical Theory and Computation·Ganna ShchygolToon Verstraelen
Nov 12, 2020·The Journal of Physical Chemistry. B·Elena Kolodzeiski, Saeed Amirjalayer
Mar 6, 2019·The Journal of Physical Chemistry. a·Tingting Weng, J R Schmidt
Aug 12, 2014·Journal of Chemical Theory and Computation·Shihao WangGuillaume Lamoureux
Jan 10, 2012·Journal of Chemical Theory and Computation·Christopher M Handley, Robert J Deeth
Mar 14, 2019·Journal of Chemical Theory and Computation·Johannes P DürholtRochus Schmid
Jul 14, 2016·The Journal of Physical Chemistry. C, Nanomaterials and Interfaces·J WiemeV Van Speybroeck
Jun 14, 2011·Journal of Chemical Theory and Computation·Maxim Tafipolsky, Bernd Engels
May 16, 2019·Journal of Chemical Theory and Computation·Marco Eckhoff, Jörg Behler
Oct 7, 2021·Journal of Chemical Theory and Computation·Elena Kolodzeiski, Saeed Amirjalayer

❮ Previous
Next ❯

Related Concepts

Trending Feeds

COVID-19

Coronaviruses encompass a large family of viruses that cause the common cold as well as more serious diseases, such as the ongoing outbreak of coronavirus disease 2019 (COVID-19; formally known as 2019-nCoV). Coronaviruses can spread from animals to humans; symptoms include fever, cough, shortness of breath, and breathing difficulties; in more severe cases, infection can lead to death. This feed covers recent research on COVID-19.

Blastomycosis

Blastomycosis fungal infections spread through inhaling Blastomyces dermatitidis spores. Discover the latest research on blastomycosis fungal infections here.

Nuclear Pore Complex in ALS/FTD

Alterations in nucleocytoplasmic transport, controlled by the nuclear pore complex, may be involved in the pathomechanism underlying multiple neurodegenerative diseases including Amyotrophic Lateral Sclerosis and Frontotemporal Dementia. Here is the latest research on the nuclear pore complex in ALS and FTD.

Applications of Molecular Barcoding

The concept of molecular barcoding is that each original DNA or RNA molecule is attached to a unique sequence barcode. Sequence reads having different barcodes represent different original molecules, while sequence reads having the same barcode are results of PCR duplication from one original molecule. Discover the latest research on molecular barcoding here.

Chronic Fatigue Syndrome

Chronic fatigue syndrome is a disease characterized by unexplained disabling fatigue; the pathology of which is incompletely understood. Discover the latest research on chronic fatigue syndrome here.

Evolution of Pluripotency

Pluripotency refers to the ability of a cell to develop into three primary germ cell layers of the embryo. This feed focuses on the mechanisms that underlie the evolution of pluripotency. Here is the latest research.

Position Effect Variegation

Position Effect Variagation occurs when a gene is inactivated due to its positioning near heterochromatic regions within a chromosome. Discover the latest research on Position Effect Variagation here.

STING Receptor Agonists

Stimulator of IFN genes (STING) are a group of transmembrane proteins that are involved in the induction of type I interferon that is important in the innate immune response. The stimulation of STING has been an active area of research in the treatment of cancer and infectious diseases. Here is the latest research on STING receptor agonists.

Microbicide

Microbicides are products that can be applied to vaginal or rectal mucosal surfaces with the goal of preventing, or at least significantly reducing, the transmission of sexually transmitted infections. Here is the latest research on microbicides.

Related Papers

Journal of Computational Chemistry
Maxim TafipolskyRochus Schmid
Proceedings of the National Academy of Sciences of the United States of America
J R MapleA T Hagler
The Journal of Physical Chemistry. B
Silvia BordigaKarl Petter Lillerud
© 2021 Meta ULC. All rights reserved