Table 2.

Some articles related to studies of oxidation of phospholipids which use molecular dynamics simulations.

Phospholipid molecular systems	Simulation time lipid force field	Aim	Reference
30 molecules of O2 −, HO2, H2O2, HO, or O2 placed together at the aqueous phase surrounding a bilayer containing 128 2-oleoyl-1-palmitoyl-sn-glycero-3-phosphocholine (POPC) molecules.	50 ns Gromos 53A6	Studying the distribution, mobility, and permeation of ROS at phospholipid bilayers.	[25]
Coarse grained bilayer models containing different proportions of 1,2-dilinoleoyl-sn-glycero-3-phosphocholine (DUPC), cholesterol, and 1-palmitoyl-2-azelaoyl-sn-glycero-3-phosphocholine as oxidized lipid specie.	4–20 μs Martini coarse grained	Evaluate a protector role of cholesterol on phospholipid bilayers from disruption caused by lipid oxidation.	[26]
Bilayers, each one containing cholesterol and 128 phospholipids with varying POPC to 1-palmitoyl-2-glutaryl-sn-glycero-3-phosphocholine (PGPC); the last is an oxidized lipid, with a truncated carbon chain terminated with a carboxylic acid.	100 ns Berger's nonpolarizable united-atom	Evaluate overall changes of the membrane structural and dynamical properties once they become oxidized.	[27]
2 molecules of 16-doxyl stearic acid randomly placed in each leaflet of a bilayer containing 62 phospholipid molecules each of 1-palmitoyl-2-(13-hydroperoxy-9,11-octadecanedienoyl)-lecithin and 1-palmitoyl-2-linoleoyl-glycero-3-phosphocholine (PLPC).	200 ns modified Berger	Studying lipid peroxidation effects on bilayers properties.	[28]
Bilayers containing 128 molecules of POPC and oxidized phospholipids PoxnoPC and PazePC in different proportions. PoxnoPC has a carbonyl group, and PazePC has an anionic carboxyl group pendant at the end of the short, oxidized acyl chain.	100 ns united-atom Berger	Evaluate the perturbation of overall membrane structural and dynamic properties by oxidatively modified phospholipids.	[29]
Bilayers containing 72 molecules of PLPC and oxidized PLPC (oxPLPC) molecules in different proportions. OxPLPC contained modified linoleoyl residues: 12-oxo-cis-9-dodecenoate and 13-hydroperoxy-trans-11, cis-9-octadecadienoate.	25 ns OPLS	Observing the effect of oxidized lipids on the sensitivity of a bilayer to electroporating fields.	[30]
PLPC bilayers containing 72 lipids, replacing 2, 4, 8, 18, and 36 PLPC lipid molecules with each oxidized lipid. The oxidized lipid was modeled by addition of a hydroperoxide group at position C9 or C13 of the linoleate tail and shifting the double bonds.	180 ns united-atom	Studying the effect of lipid peroxidation on the properties of PLPC bilayers.	[31]