Application of molecular dynamics and free energy perturbation methods to metalloporphyrin-ligand systems. 1. CO and dioxygen binding to four heme systems

Journal Article · Wed Aug 02 04:00:00 EDT 1989 · Journal of the American Chemical Society; (USA)

DOI:https://doi.org/10.1021/ja00198a036· OSTI ID:7155507

Lopez, M A; Kollman, P A ^[1]

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1. Univ. of California, San Francisco (USA)

The authors present the application of molecular mechanics/dynamics and free energy perturbation computational techniques to simulation of iron(II) porphyrin systems. Force field parameters were developed by modeling the geometry of four systems whose crystal structure is known. This force field was then used in molecular dynamics/free energy perturbation calculations at 300 K in vacuo, on a separate set of four iron(II) porphyrin systems including models of 5,5-pyridine cyclophane heme (1,5-DCI) (I), picket fence heme(2-MeIm) (II), monochelated heme (III), and 7,7-durene cyclophane heme(1,5-DCI) (IV). The perturbation calculations reproduced reasonably well the trend in the partition coefficient, M value, of this set. Their simplified model indicates that the electrostatic component of both I and II factors the binding of O{sub 2} over CO, whereas the electrostatic component of III and IV favors CO over O{sub 2}. The preference of O{sub 2} over CO binding from the nonbonded steric component was I > II > III > IV. Molecular dynamics simulations showed that the Fe atom of the O{sub 2} and CO complexes of I oscillated 0.06 and 0.16 {angstrom}, respectively, lower than those of II, even though the crystal structure and the simulation of the O{sub 2} complex of II shows the Fe atom 0.087 {angstrom} below the porphyrin plane: this result suggests that the ratios of R state to T state CO/O{sub 2} binding affinities will be extremely low for system 1. The simulations also showed that even with a 7,7-strap as in IV, there is still more interaction with a bound CO than with a bound O{sub 2}.

• OSTI ID: 7155507
• Journal Information: Journal of the American Chemical Society; (USA), Journal Name: Journal of the American Chemical Society; (USA) Vol. 111:16; ISSN 0002-7863; ISSN JACSA
• Country of Publication: United States
• Language: English

Related Subjects

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CHEMISTRY
400500* -- Photochemistry
550000 -- Biomedical Sciences
Basic Studies
59 BASIC BIOLOGICAL SCIENCES
99 GENERAL AND MISCELLANEOUS
990200 -- Mathematics & Computers
CALCULATION METHODS
CARBOXYLIC ACIDS
COMPUTERIZED SIMULATION
ELEMENTS
HETEROCYCLIC ACIDS
HETEROCYCLIC COMPOUNDS
IRON
LIGANDS
MATHEMATICAL MODELS
METALLOPROTEINS
METALS
MOLECULAR MODELS
ORGANIC ACIDS
ORGANIC COMPOUNDS
ORGANIC NITROGEN COMPOUNDS
PERTURBATION THEORY
PORPHYRINS
PROTEINS
SIMULATION
TRANSITION ELEMENTS