Publication

Study of the structural and dynamical properties of a biomimetic compound of diiron proteins via ab initio and hybrid molecular dynamics simulations

2002
Conference Papers

Abstract

A biomimetic four-helix bundle with a binuclear active site (DF1), bearing Zn, Mn or Fe as transition metals, has been synthesized and characterized. The carboxylate bridged binuclear motif of DF1 resembles the active site of numerous binuclear enzymes, such as Manganese Catalase, Methane Monoxygenase (MMO), etc. Due to the crucial chem. and biol. relevance of binuclear enzymes in hydrolytic as well as redox active processes, we have performed a systematic study of the structural properties of the dizinc analog of DF1 through ab initio and hybrid QM/MM Car-Parrinello mol. dynamics simulations. Different quantum mech. models of the active site have been chosen in order to gain a qual. view of how the first and second shell ligands can tune structural and dynamical properties of the active site. In addn., the geometrical restraints and the electrostatic stabilization provided by the whole structure have been explicitly considered, performing QM/MM mol. dynamics simulations. [on SciFinder (R)]

Official source

https://infoscience.epfl.ch/entities/publication/cab5d6f9-ccca-4f6f-b82f-954ec9cc0a51

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2002
Conference Papers

Abstract

Official source

https://infoscience.epfl.ch/entities/publication/cab5d6f9-ccca-4f6f-b82f-954ec9cc0a51

About this result

Related concepts (32)

Molecular dynamics

Molecular dynamics (MD) is a computer simulation method for analyzing the physical movements of atoms and molecules. The atoms and molecules are allowed to interact for a fixed period of time, giving a view of the dynamic "evolution" of the system. In the most common version, the trajectories of atoms and molecules are determined by numerically solving Newton's equations of motion for a system of interacting particles, where forces between the particles and their potential energies are often calculated using interatomic potentials or molecular mechanical force fields.

Computational chemistry

Computational chemistry is a branch of chemistry that uses computer simulation to assist in solving chemical problems. It uses methods of theoretical chemistry, incorporated into computer programs, to calculate the structures and properties of molecules, groups of molecules, and solids. It is essential because, apart from relatively recent results concerning the hydrogen molecular ion (dihydrogen cation, see references therein for more details), the quantum many-body problem cannot be solved analytically, much less in closed form.

Transition metal

In chemistry, a transition metal (or transition element) is a chemical element in the d-block of the periodic table (groups 3 to 12), though the elements of group 12 (and less often group 3) are sometimes excluded. The lanthanide and actinide elements (the f-block) are called inner transition metals and are sometimes considered to be transition metals as well. Since they are metals, they are lustrous and have good electrical and thermal conductivity.