Molecular dynamics simulation study of chlorophyll a in different organic solvents

TY - JOUR

T1 - Molecular dynamics simulation study of chlorophyll a in different organic solvents

AU - Karki, Khadga

AU - Roccatano, Danilo

PY - 2011/4/12

Y1 - 2011/4/12

N2 - Herein, we present a new model of chlorophyll a for molecular dynamics simulations based on the optimized potentials for liquid simulations force field. The new model was used to study the structural and dynamic properties of the molecule in three different solvents: water, methanol, and benzene. The results of the simulations show that structural and dynamic properties of the chlorin ring are similar in both methanol and benzene. In methanol and water, the magnesium in the chlorin ring binds the oxygen of the solvent molecules with residence times of 2566 and 1300 ps, respectively. In both methanol and benzene, the phytol tail shows a worm-like chain distribution with a larger persistence length for the molecule in benzene. On the contrary, chlorophyll a in water adopts a more compact structure with the phytol chain folded onto the chlorin ring. This conformation is consistent with the expected conformation of the aggregates of chlorophyll a in aqueous environments. Finally, the rotational time constants obtained with our model from the simulations in methanol (125 ps) and benzene (192 ps) are in good agreement with the value extrapolated from the experimental data.

AB - Herein, we present a new model of chlorophyll a for molecular dynamics simulations based on the optimized potentials for liquid simulations force field. The new model was used to study the structural and dynamic properties of the molecule in three different solvents: water, methanol, and benzene. The results of the simulations show that structural and dynamic properties of the chlorin ring are similar in both methanol and benzene. In methanol and water, the magnesium in the chlorin ring binds the oxygen of the solvent molecules with residence times of 2566 and 1300 ps, respectively. In both methanol and benzene, the phytol tail shows a worm-like chain distribution with a larger persistence length for the molecule in benzene. On the contrary, chlorophyll a in water adopts a more compact structure with the phytol chain folded onto the chlorin ring. This conformation is consistent with the expected conformation of the aggregates of chlorophyll a in aqueous environments. Finally, the rotational time constants obtained with our model from the simulations in methanol (125 ps) and benzene (192 ps) are in good agreement with the value extrapolated from the experimental data.

UR - http://www.scopus.com/inward/record.url?scp=84962377221&partnerID=8YFLogxK

U2 - 10.1021/ct1004627

DO - 10.1021/ct1004627

M3 - 文章

AN - SCOPUS:84962377221

SN - 1549-9618

VL - 7

SP - 1131

EP - 1140

JO - Journal of Chemical Theory and Computation

JF - Journal of Chemical Theory and Computation

IS - 4

ER -