Refined OPLS all-atom force field parameters for n-pentadecane, methyl acetate, and dimethyl phosphate
Krzysztof Murzyn1, Maciej Bratek, Marta Pasenkiewicz-Gierula
1Department of Computational Biophysics and Bioinformatics, Jagiellonian University , Kraków, Poland.
Abstract:
OPLS All-Atom (OPLS/AA) is a generic all-atom force field which was fine-tuned to accurately reproduce condensed phase properties of organic liquids. Its application in modeling of lipid membranes is, however, limited mainly due to the inability to correctly describe phase behavior and organization of the hydrophobic core of the model lipid bilayers. Here we report new OPLS/AA parameters for n-pentadecane, methyl acetate, and dimethyl phosphate anion. For the new force field parameters, we show very good agreement between calculated and numerous reference data, including liquid density, enthalpy of vaporization, free energy of hydration, and selected transport properties. The new OPLS/AA parameters have been used in successful submicrosecond MD simulations of bilayers made of bacterial glycolipids whose results will be published elsewhere shortly.
More Related Videos
Related Concept Videos
¹³C NMR: Distortionless Enhancement by Polarization Transfer (DEPT)
π Molecular Orbitals of 1,3-Butadiene
The simplest conjugated diene is 1,3-butadiene: a four-carbon system where each carbon is sp2-hybridized and has an unhybridized p orbital that contains an unpaired electron. According to molecular orbital theory, atomic orbitals combine to form molecular orbitals such that the...
Mass Spectrometry: Branched Alkane Fragmentation
Overview of Advanced Functional Groups
Functional groups are groups of atoms with specific chemical properties that occur within organic molecules and are sometimes denoted as “R”. Functional groups can “functionalize” a compound by enabling it to adopt different physical and chemical properties.
Types of Advanced Functional Groups
The table below summarizes some of the major functional groups in organic chemistry.
Comparing Intermolecular Forces: Melting Point, Boiling Point, and Miscibility
Temporary attractive forces like dispersion are present in all molecules, whether they are polar or nonpolar. They...
Nomenclature of Alkynes


