One of the most important types of antioxidants are flavonoids which contain flavonols, flavonones, isoflavones, etc. Because of the importance of quercetin as an antioxidant, the present study pays special attention to this compound of flavonols. The main focus of this investigation is to explore structural properties of quercetin by molecular dynamics simulation. The results show that intermolecular hydrogen bonds between quercetin and water are stronger than water-water interactions. In addition, intramolecular hydrogen bond in quercetin is observed. Hydrogen bond interaction of water contains an enormous number, 930 hydrogen bonds in average though the number of hydrogen bonds between water and considered antioxidant is in average three. From dynamical point of view, RMSD of the system witnesses stability after a nanosecond of simulation which indicates the structure of quercetin finds its stable form and no conformational change is observed. However, Rg fluctuates around 0.37 nm that is also a sing of structural stability. The results of pair atomic correlations also designate that the interaction of alcoholic oxygen and hydrogen of target antioxidant with water are stronger than the interatomic interactions between etheric oxygen and corresponding carbon that confirms strong interaction between quercetin and water.

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