Theoretical Study of Alkylsulfonic Acids: Force-Field Development and Molecular Dynamics Simulations

Potential model descriptions for alkylsulfonic acids, methanesulfonic, ethanesulfonic, and propanesulfonic acids, are developed based on CHARMM and OPLS parameters and protocols. Thermodynamic, structural, and transport properties of these alkylsulfonic acids, including density, heat of vaporization, radial and spatial distribution functions, hydrogen bond structure, shear viscosity, and translational diffusion coefficients, are examined via molecular dynamics simulations using these potential models. The results are compared with the predictions of ab initio molecular dynamics simulations as well as with available experimental information. A good overall agreement indicates that the force-field descriptions developed here provide a reliable framework to study liquid systems containing alkylsulfonic acids

Theoretical Study of Alkylsulfonic Acids: Force-Field Development and Molecular Dynamics Simulations

Potential model descriptions for alkylsulfonic acids, methanesulfonic, ethanesulfonic, and propanesulfonic acids, are developed based on CHARMM and OPLS parameters and protocols. Thermodynamic, structural, and transport properties of these alkylsulfonic acids, including density, heat of vaporization, radial and spatial distribution functions, hydrogen bond structure, shear viscosity, and translational diffusion coefficients, are examined via molecular dynamics simulations using these potential models. The results are compared with the predictions of ab initio molecular dynamics simulations as well as with available experimental information. A good overall agreement indicates that the force-field descriptions developed here provide a reliable framework to study liquid systems containing alkylsulfonic acids

Theoretical Study of Alkylsulfonic Acids: Force-Field Development and Molecular Dynamics Simulations

Potential model descriptions for alkylsulfonic acids, methanesulfonic, ethanesulfonic, and propanesulfonic acids, are developed based on CHARMM and OPLS parameters and protocols. Thermodynamic, structural, and transport properties of these alkylsulfonic acids, including density, heat of vaporization, radial and spatial distribution functions, hydrogen bond structure, shear viscosity, and translational diffusion coefficients, are examined via molecular dynamics simulations using these potential models. The results are compared with the predictions of ab initio molecular dynamics simulations as well as with available experimental information. A good overall agreement indicates that the force-field descriptions developed here provide a reliable framework to study liquid systems containing alkylsulfonic acids

Theoretical Study of Alkylsulfonic Acids: Force-Field Development and Molecular Dynamics Simulations

Potential model descriptions for alkylsulfonic acids, methanesulfonic, ethanesulfonic, and propanesulfonic acids, are developed based on CHARMM and OPLS parameters and protocols. Thermodynamic, structural, and transport properties of these alkylsulfonic acids, including density, heat of vaporization, radial and spatial distribution functions, hydrogen bond structure, shear viscosity, and translational diffusion coefficients, are examined via molecular dynamics simulations using these potential models. The results are compared with the predictions of ab initio molecular dynamics simulations as well as with available experimental information. A good overall agreement indicates that the force-field descriptions developed here provide a reliable framework to study liquid systems containing alkylsulfonic acids

Theoretical Study of Alkylsulfonic Acids: Force-Field Development and Molecular Dynamics Simulations

Potential model descriptions for alkylsulfonic acids, methanesulfonic, ethanesulfonic, and propanesulfonic acids, are developed based on CHARMM and OPLS parameters and protocols. Thermodynamic, structural, and transport properties of these alkylsulfonic acids, including density, heat of vaporization, radial and spatial distribution functions, hydrogen bond structure, shear viscosity, and translational diffusion coefficients, are examined via molecular dynamics simulations using these potential models. The results are compared with the predictions of ab initio molecular dynamics simulations as well as with available experimental information. A good overall agreement indicates that the force-field descriptions developed here provide a reliable framework to study liquid systems containing alkylsulfonic acids

Theoretical Study of Alkylsulfonic Acids: Force-Field Development and Molecular Dynamics Simulations

Potential model descriptions for alkylsulfonic acids, methanesulfonic, ethanesulfonic, and propanesulfonic acids, are developed based on CHARMM and OPLS parameters and protocols. Thermodynamic, structural, and transport properties of these alkylsulfonic acids, including density, heat of vaporization, radial and spatial distribution functions, hydrogen bond structure, shear viscosity, and translational diffusion coefficients, are examined via molecular dynamics simulations using these potential models. The results are compared with the predictions of ab initio molecular dynamics simulations as well as with available experimental information. A good overall agreement indicates that the force-field descriptions developed here provide a reliable framework to study liquid systems containing alkylsulfonic acids

MD and X-ray results for distances between binding sites of PDC109 and PhC.

<p>Distances are in Å and were determined by averaging through MD trajectories (protomer A) and from the crystal structure (protomers A and B, *PDB ID: 1h8p). Distances for tryptophans were calculated between the six-carbon ring centers of sidechain indoles and the PhC quaternary ammonium nitrogen. Distances for tyrosines were calculated between sidechain hydroxyl oxygens and the average position of three PhC phosphate oxygens. Average MD distances and standard deviations were calculated using the initial 230 ns trajectories because PhC started to detach from the binding pocket of PDC109/a at about 240 ns.</p

X-ray structure of BSP-A1.

<p>(A) Sequence and associated secondary structure organization of PDC109. Cystine bridges are indicated by black lines. (B) Crystal structure of PDC109 <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0009180#pone.0009180-Wah1" target="_blank">[24]</a>. The N-terminal Fn2 domain (PDC109/a, residues 24–61) and the C-terminal Fn2 domain (PDC109/b, residues 69–109) are connected by a linker peptide (residues 62–68) shown in blue. The net charges are 1, 1, and 2 for PDC109/a, linker, and PDC109/b, respectively. Loop 1 (H41-L44) between 2 and 3 strands in PDC109/a and loop 2 (G87-M91) between the 2 and 3 strands in PDC109/b are denoted by green arrows <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0009180#pone.0009180-Molecular1" target="_blank">[74]</a>.</p

Comparison of the first three normal modes and principal components.

<p>Overlapping ribbon conformations for the three lowest normal modes are shown at t = 0 (red) and (blue) with the normalized eigenvector vibrational amplitudes scaled by a factor of 200. The normal mode index corresponds to specific vibrational frequencies as follows:  = 1 (hinge-bend), 0.80 cm;  = 2 (twist), 1.72 cm;  = 3 (tilt), 3.08 cm. Overlapping ribbon conformations for the three largest amplitude principal components (p = 1, 2, 3) are shown with the reference structure (red) as displacements scaled by a factor of 200 standard deviations along each principal component (blue) <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0009180#pone.0009180-Molecular1" target="_blank">[74]</a>.</p

Distances between the ligand and protein interaction sites in PDC109 domains.

<p>Time series are shown for distances between the quaternary ammonium nitrogen of PhC and the center of geometry of six carbon atoms in indole rings of W47 (A), W93 (B), W58 (C), W106 (D); and between the average position of anionic PhC phosphoryl oxygens and the hydroxyl oxygens of Y30 (E), Y75 (F), Y54 (G), Y100 (H), Y60 (I), Y108 (J).</p