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A valence bond model for aqueous Cu(II) and Zn(II) ions in the AMOEBA polarizable force field

Jin Yu Xiang, Jay W. Ponder
2012 Journal of Computational Chemistry  
A general molecular mechanics (MM) model for treating aqueous Cu 2+ and Zn 2+ ions was developed based on valence bond (VB) theory and incorporated into the AMOEBA polarizable force field.  ...  Analyses of the MD trajectories revealed a 6-coordination first solvation shell for both Cu 2+ and Zn 2+ ions in aqueous solution, with ligation geometries falling in the range reported by previous studies  ...  Additional support for the work was provided by the United States National Science Foundation (NSF) under Awards 0535675 and CHE 1152823 to JWP.  ... 
doi:10.1002/jcc.23190 pmid:23212979 pmcid:PMC3584243 fatcat:w5cqsndo2fdqdbykndobymi5pq

An Angular Overlap Model for Cu(II) Ion in the AMOEBA Polarizable Force Field

Jin Yu Xiang, Jay W. Ponder
2013 Journal of Chemical Theory and Computation  
An extensible polarizable force field for transition-metal ions was developed based on AMOEBA and the angular overlap model (AOM) with consistent treatment of electrostatics for all atoms.  ...  Analyses of MD trajectories resulted in a six-coordination first solvation shell for aqueous copper(II) ion and a 1.8 ns average residence time of water molecules.  ...  ■ ACKNOWLEDGMENTS We would like to thank the National Science Foundation (Award CHE1152823) and National Institutes of Health (R01 GM106137) for their generous support of this research via grants to  ... 
doi:10.1021/ct400778h pmid:25045338 pmcid:PMC4102146 fatcat:mfhg6eolj5f2nirvj4doq2q6fy

Metal Ion Modeling Using Classical Mechanics

Pengfei Li, Kenneth M. Merz
2017 Chemical Reviews  
, Drude oscillator, and the induced dipole models), the angular overlap model, and valence bond-based models.  ...  With computational tools increasingly becoming important in chemical research, methods have emerged to effectively face the challenge of modeling metal ions in the gas, aqueous, and solid phases.  ...  Xiang and Ponder incorporated the VB model into the AMOEBA force field for the Zn 2+ and Cu 2+ ions in aqueous solution. 1017 he following representation was used: 2+ complex to be more stable than  ... 
doi:10.1021/acs.chemrev.6b00440 pmid:28045509 pmcid:PMC5312828 fatcat:vrfsaiek6bhlbc7rcvsaxteuga

Polarizable Force Fields for Biomolecular Modeling [chapter]

Yue Shi, Pengyu Ren, Michael Schnieders, Jean-Philip Piquemal
2015 Reviews in computational chemistry  
343 interesting Gaussian charge polarizable force field for ions and in polyethylene oxide 344 (PEO). 145-147 A polarizable force field for ionic liquids was also reported to provide 345 accurate thermodynamics  ...  Only in the past decade or so has there been a systematic effort to develop general 57 polarizable force fields for molecular modeling.  ...  Reinhardt, and P.Y. Ren, Polarizable Molecular 881 Dynamics Simulation of Zn(II) in Water Using the AMOEBA Force Field.  ... 
doi:10.1002/9781118889886.ch2 fatcat:mlpsbxtjmbgdxfvzhtwffqvumi

Design, Parameterization, and Implementation of Atomic Force Fields for Adsorption in Nanoporous Materials

David Dubbeldam, Krista S. Walton, Thijs J. H. Vlugt, Sofia Calero
2019 Advanced Theory and Simulations  
Much of the reliability of the modeling predictions depends on the accuracy and transferability of the force field.  ...  Recent developments in design, parameterization, and implementation of force fields for MOFs and zeolites are reviewed. contain silicon and oxygen.  ...  Vlugt would like to thank NWO-CW (Chemical Sciences) for a VICI grant and S. Calero would like to thank the Spanish Ministerio de Economia y Competitividad (CTQ2016-80206-P).  ... 
doi:10.1002/adts.201900135 fatcat:z66nrhorhrc4xjgklumjzwg6h4

Development of Polarizable Force Field Models for Transition Metal Ions

Jin Yu Xiang
2013
An Angular Overlap Model in the AMOEBA Polarizable Force Field In this chapter, we present an AOM for Cu 2+ ion in the AMOEBA polarizable force field.  ...  A Valence Bond Theory in the AMOEBAPolarizable Force FieldIn this chapter, a MM model is developed for aqueous Ni 2+ , Cu 2+ and Zn 2+ ions based on VB theory in conjunction with the AMOEBA (Atomic Multipole  ...  are on the right; only a single ligand is perturbed from the QM optimized geometry in each plot.  ... 
doi:10.7936/k73n21v3 fatcat:d3psglpa6rd77kn44d7wtxyv6y

Using Theoretical Chemistry to understand the Properties of Polyoxometalates and their potential as energy storage materials

EMANUELE FALBO
2022 figshare.com  
To this end, several polarizable FFs have been developed (class III), for example, the AMOEBA force field includes distributed multipoles and atom polarizabilities.  ...  This was also demonstrated by Zhang et al., who showed that the solvent effect is very important for [XW 12 O 40 ] n− (X = Fe(II), Co(III), Zn(II)) ions at high charge states. [134] In addition, in their  ...  For instance, this is the case of SiW 12 and PV 14 systems studied in Chapter 3.  ... 
doi:10.6084/m9.figshare.19701547.v1 fatcat:dyy7r5htwrgn5jlievfvieorry

Peptide-Cation Systems: Conformational Search, Benchmark Evaluation, and Force Field Parameter Adjustment Using Regularized Linear Regression

Markus Schneider
2018
Thereby calculated energies and IR spectra that are sufficiently accurate relied on DFT with computationally costly hybrid functionals, while for the structure search low-computationalcost force field  ...  As an example, the model system AcPheAla 5 LysH + is investigated in order to fully understand the forces that stabilize its helical structure.  ...  Here, the 2009 AMOEBA biopolymer force field, labeled AMOEBA-BIO09 (see Subsection 2.3.1), is applied, which is for two reasons: First, this polarizable force field provides a much "rougher" potential  ... 
doi:10.5075/epfl-thesis-8812 fatcat:osngb76o3bc5lbt2znlatfqmaq

DD(35)E [chapter]

2008 Encyclopedia of Genetics, Genomics, Proteomics and Informatics  
Single- stranded DNAs may become Zn 2+ /Cu 2+ or Pb 2+ metalloenzymes. The Zn 2+ /Cu 2+ enzymes may func- tion as DNA ligase.  ...  ▶blood groups Dielectrophoresis : Induced motion of polarizable particles in non-uniform fields, a method for the separation of bioparticles such as cells, viruses and proteins.  ...  Large scale and targeted mutagenesis and mutation testing in mice and other animals can reveal models for monogenic and complex human diseases.  ... 
doi:10.1007/978-1-4020-6754-9_4176 fatcat:zbpaeesjzrbp7lcezj6jyw36b4

Dowex Resins [chapter]

2008 Encyclopedia of Genetics, Genomics, Proteomics and Informatics  
Single- stranded DNAs may become Zn 2+ /Cu 2+ or Pb 2+ metalloenzymes. The Zn 2+ /Cu 2+ enzymes may func- tion as DNA ligase.  ...  ▶blood groups Dielectrophoresis : Induced motion of polarizable particles in non-uniform fields, a method for the separation of bioparticles such as cells, viruses and proteins.  ...  Large scale and targeted mutagenesis and mutation testing in mice and other animals can reveal models for monogenic and complex human diseases.  ... 
doi:10.1007/978-1-4020-6754-9_4859 fatcat:k32r3jc5pjaepcdaom2pgn5iue