SHAPES empirical force field: new treatment of angular potentials and its application to square-planar transition-metal complexes

Allured, Viloya S.; Kelly, Christine; Landis, Clark R.

doi:10.1021/ja00001a001

Cited by 145 publications

(61 citation statements)

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“…The TRIPOS valence force-field expresses the total potential energy of a molecule as the sum of the bond-stretching, anglebending, out-of-plane-bending, torsional and non-bonded (van der Waals, and electrostatic) terms. The application of empirical force-field computations to metal co-ordination compounds is problematic because ofthe large variation ofligand-metal-ligand bond angles observed at transition-metal centres (Lauher, 1986;Allured et al, 1991). Energy minimization of the CdZnMT was therefore carried out keeping the sulphur-metal-sulphur angles constrained to the values found in the crystal structure.…”

Section: Discussionmentioning

confidence: 99%

A putative glutathione-binding site in CdZn-metallothionein identified by equilibrium binding and molecular-modelling studies

Brouwer

Hoexum-Brouwer

Cashon

1993

Biochemical Journal

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Section: Discussionmentioning

confidence: 99%

A putative glutathione-binding site in CdZn-metallothionein identified by equilibrium binding and molecular-modelling studies

Brouwer

Hoexum-Brouwer

Cashon

1993

Biochemical Journal

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“…In existing simulation codes based on classical potentials, the angular terms are usually either ignored [2][3][4], on the assumption that direct ligand-ligand interactions can take up most of the "slack", or they are treated with simple assumed angular forms. The latter range from quadratic or higher order expansions about observed equilibrium bond angles [5][6][7][8] to more sophisticated expansions in trigonometric functions [9][10][11][12]. However, there has been no derivation of the angular form of classical potentials from quantum mechanics.…”

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confidence: 99%

Angular Forces Around Transition Metals in Biomolecules

Carlsson

1998

Phys. Rev. Lett.

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Quantum-mechanical analysis based on an exact sum rule is used to extract an semiclassical angle-dependent energy function for transition metal ions in biomolecules. The angular dependence is simple but different from existing classical potentials. Comparison of predicted energies with a computergenerated database shows that the semiclassical energy function is remarkably accurate, and that its angular dependence is optimal.

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“…A wide variety of force fields that can be applied to zeolites exist. Among them, we find universal force field (UFF) [31], Discover (CFF) [32], MM2 [33], MM3 [34,35], MM4 [36,37], Dreiding [38], SHARP [39], VALBON [40], AMBER [41], CHARMM [42], OPLS [43], Tripos [44], ECEPP/2 [45], GROMOS [46], MMFF [47], Burchart [48], BKS [48], and specialty force fields for morphology predictions [49] or for computing adsorption [50]. In one approach, force fields are designed to be generic, providing a broad coverage of the periodic table, including inorganic compounds, metals, and transition metals.…”

Section: Modeling Zeolites and Nonframework Cationsmentioning

confidence: 99%

Modeling of Transport and Accessibility in Zeolites

Calero¹

2010

Zeolites and Catalysis

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IntroductionModeling plays an important role in the field of zeolites and related porous materials. The use of molecular simulations allows the prediction of adsorption and diffusion coefficients in these materials and also provides important information about the processes taking place inside the porous structures at the molecular level [1-10]. Hence, molecular modeling is a very good complement to experimental work in the understanding of the molecular behavior inside the pores.Despite the great interest and the applicability of zeolites, there are still many facets of the molecular mechanisms for a given reaction inside their pores that are poorly understood. These mechanisms are important for (i) the way the zeolite adsorbs, diffuses, and concentrates the adsorbates near the specific active sites; (ii) the interactions between the zeolite and the adsorbates and the effect on the electronic properties of the system; (iii) the chemical conversion at the active site; and (iv) the way the zeolite disperses the final product. Detailed knowledge on the molecular mechanisms involved will eventually lead to an increase in the reaction efficiency.This chapter focuses on molecular modeling of transport and accessibility in zeolites. It describes how simulations have contributed to a better understanding of these materials and provides a summary of the state of the art as well as of current challenges. The chapter is organized as follows. First, common models and potentials are briefly described. This is followed by a general overview on current simulation methods to compute adsorption, diffusion, free energies, surface areas, and pore volumes. The chapter continues with some examples on applications of molecular modeling to processes of interest from the industrial and environmental point of view. Finally, the chapter closes with a summary and some remarks on future challenges.

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SHAPES empirical force field: new treatment of angular potentials and its application to square-planar transition-metal complexes

Cited by 145 publications

References 1 publication

A putative glutathione-binding site in CdZn-metallothionein identified by equilibrium binding and molecular-modelling studies

A putative glutathione-binding site in CdZn-metallothionein identified by equilibrium binding and molecular-modelling studies

Angular Forces Around Transition Metals in Biomolecules

Modeling of Transport and Accessibility in Zeolites

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