Literature DB >> 14531050

Inclusion of the ligand field contribution in a polarizable molecular mechanics: SIBFA-LF.

Jean-Philip Piquemal1, Ben Williams-Hubbard, Natalie Fey, Robert J Deeth, Nohad Gresh, Claude Giessner-Prettre.   

Abstract

To account for the distortion of the coordination sphere that takes place in complexes containing open-shell metal cations such as Cu(II), we implemented, in sum of interactions between fragments ab initio computed (SIBFA) molecular mechanics, an additional contribution to take into account the ligand field splitting of the metal d orbitals. This term, based on the angular overlap model, has been parameterized for Cu(II) coordinated to oxygen and nitrogen ligands. The comparison of the results obtained from density functional theory computations on the one hand and SIBFA or SIBFA-LF on the other shows that SIBFA-LF gives geometric arrangements similar to those obtained from quantum mechanical computations. Moreover, the geometric improvement takes place without downgrading the energetic agreement obtained from SIBFA. The systems considered are Cu(II) interacting with six water molecules, four ammonia or four imidazoles, and four water plus two formate anions. Copyright 2003 Wiley Periodicals, Inc. J Comput Chem 24: 1963-1970, 2003

Entities:  

Year:  2003        PMID: 14531050     DOI: 10.1002/jcc.10354

Source DB:  PubMed          Journal:  J Comput Chem        ISSN: 0192-8651            Impact factor:   3.376


  18 in total

1.  Copper Oxidation/Reduction in Water and Protein: Studies with DFTB3/MM and VALBOND Molecular Dynamics Simulations.

Authors:  Haiyun Jin; Puja Goyal; Akshaya Kumar Das; Michael Gaus; Markus Meuwly; Qiang Cui
Journal:  J Phys Chem B       Date:  2015-12-17       Impact factor: 2.991

2.  A combination of docking, QM/MM methods, and MD simulation for binding affinity estimation of metalloprotein ligands.

Authors:  Akash Khandelwal; Viera Lukacova; Dogan Comez; Daniel M Kroll; Soumyendu Raha; Stefan Balaz
Journal:  J Med Chem       Date:  2005-08-25       Impact factor: 7.446

Review 3.  Classical electrostatics for biomolecular simulations.

Authors:  G Andrés Cisneros; Mikko Karttunen; Pengyu Ren; Celeste Sagui
Journal:  Chem Rev       Date:  2013-08-27       Impact factor: 60.622

Review 4.  Metal Ion Modeling Using Classical Mechanics.

Authors:  Pengfei Li; Kenneth M Merz
Journal:  Chem Rev       Date:  2017-01-03       Impact factor: 60.622

5.  Exploring the applicability of density functional tight binding to transition metal ions. Parameterization for nickel with the spin-polarized DFTB3 model.

Authors:  Milena Vujović; Mioy Huynh; Sebastian Steiner; Pablo Garcia-Fernandez; Marcus Elstner; Qiang Cui; Maja Gruden
Journal:  J Comput Chem       Date:  2018-10-09       Impact factor: 3.376

Review 6.  Biomolecular electrostatics and solvation: a computational perspective.

Authors:  Pengyu Ren; Jaehun Chun; Dennis G Thomas; Michael J Schnieders; Marcelo Marucho; Jiajing Zhang; Nathan A Baker
Journal:  Q Rev Biophys       Date:  2012-11       Impact factor: 5.318

7.  Study of interactions between metal ions and protein model compounds by energy decomposition analyses and the AMOEBA force field.

Authors:  Zhifeng Jing; Rui Qi; Chengwen Liu; Pengyu Ren
Journal:  J Chem Phys       Date:  2017-10-28       Impact factor: 3.488

8.  Study of the docking of competitive inhibitors at a model of tyrosinase active site: insights from joint broken-symmetry/Spin-Flip DFT computations and ELF topological analysis.

Authors:  A de la Lande; J Maddaluno; O Parisel; T A Darden; J-P Piquemal
Journal:  Interdiscip Sci       Date:  2010-03       Impact factor: 2.233

9.  Numerical study on the partitioning of the molecular polarizability into fluctuating charge and induced atomic dipole contributions.

Authors:  Ye Mei; Andrew C Simmonett; Frank C Pickard; Robert A DiStasio; Bernard R Brooks; Yihan Shao
Journal:  J Phys Chem A       Date:  2015-05-18       Impact factor: 2.781

10.  The metal bonding domain of the antitumor drug Fe(II)-bleomycin: a DFT investigation.

Authors:  Anna Karawajczyk; Francesco Buda
Journal:  J Biol Inorg Chem       Date:  2004-12-01       Impact factor: 3.358

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