Conformations of 1,2-Dimethoxyethane in Gas and Solution Phase from Molecular Mechanics and Monte Carlo/Stochastic Dynamics Simulations

and, D. Jeremy Williams; Hall, Kathleen B.

doi:10.1021/jp952581y

Cited by 34 publications

(21 citation statements)

References 21 publications

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“…Also, the relative energies of all stable conformers of pentane, sec ‐butanol, cyclohexanol, diethyl ether, isopropyl methyl ether, methoxyethanol, and isopropyl formate were included along with the data on low‐energy conformers of THPOH, HMOP, GTHP, and GTHPO. This set was supplemented with reliable experimental data or recently published ab initio energies for ethane,50, 51 butane,42 cyclohexane,52 cyclooctane,53 methylcyclohexane,54 cyclohexanol,32 dimethyl ether,55 ethyl methyl ether,56 oxane,57, 58 dimethoxyethane,59 methyl formate,60 methyl acetate,61 and ethyl formate 62. Finally, torsional profiles and conformational energies for diketones and ketoamides studied by us previously63 were included.…”

Section: Methodsmentioning

confidence: 99%

Parameterization of OPLS–AA force field for the conformational analysis of macrocyclic polyketides

2002

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The parameters for the OPLS-AA potential energy function have been extended to include some functional groups that are present in macrocyclic polyketides. Existing OPLS-AA torsional parameters for alkanes, alcohols, ethers, hemiacetals, esters, and ketoamides were improved based on MP2/aug-cc-pVTZ and MP2/aug-cc-pVDZ calculations. Nonbonded parameters for the sp(3) carbon and oxygen atoms were refined using Monte Carlo simulations of bulk liquids. The resulting force field predicts conformer energies and torsional barriers of alkanes, alcohols, ethers, and hemiacetals with an overall RMS deviation of 0.40 kcal/mol as compared to reference data. Densities of 19 bulk liquids are predicted with an average error of 1.1%, and heats of vaporization are reproduced within 2.4% of experimental values. The force field was used to perform conformational analysis of smaller analogs of the macrocyclic polyketide drug FK506. Structures that adopted low-energy conformations similar to that of bound FK506 were identified. The results show that a linker of four ketide units constitutes the shortest effector domain that allows binding of the ketide drugs to FKBP proteins. It is proposed that the exact chemical makeup of the effector domain has little influence on the conformational preference of tetraketides.

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Section: Methodsmentioning

confidence: 99%

Parameterization of OPLS–AA force field for the conformational analysis of macrocyclic polyketides

2002

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“…10 Because of the widespread importance of PEO in aqueous solutions, we [11][12][13][14][15] and other groups [16][17][18][19][20] have conducted molecular dynamics (MD) simulation studies in order to gain atomistic level insight into the thermodynamics and dynamics of PEO and its oligomers in aqueous solutions. This paper is the third in a series dealing with the dynamic properties of PEO/water solutions from MD simulations.…”

Section: Introductionmentioning

confidence: 99%

Concentration Dependence of Water Dynamics in Poly(Ethylene Oxide)/Water Solutions from Molecular Dynamics Simulations

2002

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We have performed molecular dynamics simulations of aqueous solutions of poly(ethylene oxide) (PEO) in order to investigate the influence of the polymer on water dynamics. Simulations were performed on 12 repeat unit CH 3 -capped PEO chains (530 Da) at 318 K covering a composition range (polymer weight fraction) from 0.17 to 1.0. The simulations employed an ab initio quantum-chemistry-based PEO/water and PEO/PEO force field together with the TIP4P (four-point transferable intermolecular potential) water model. Water translational and rotational diffusion were found to slow monotonically, whereas water-water and waterether hydrogen bond lifetimes increased with increasing polymer concentration. The slowing of water dynamics in PEO/water solutions was associated with PEO-water interactions that are moderated in concentrated solutions by the formation of water clusters. Water translational motion could be ascribed to a combination of free water (water not involved with PEO hydration) that exhibited bulklike water dynamics and bound (hydrating water) whose motion was strongly correlated with that of the PEO molecule. Water rotational motion was found to be strongly correlated with translation motion and exhibited increasing anisotropy with increasing PEO concentration indicative of preferred rotation of the water molecules around their dipole moment vector. At high PEO concentration, water and ether oxygen atoms exhibited well pronounced subdiffusive behavior occurring on a picosecond time scale that disappears upon dilution. The characteristic length scale for the water subdiffusive behavior associated with water caging correlates well with nearestneighbor ether oxygen-ether oxygen distance.

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“…These approaches have the advantage that in addition to capturing the mean structural effects of the solvent on the solute, the free energy of solvation can also be accurately predicted, often as precisely as can be done with explicit solvent simulations (Jean-Charles et al, 1991). The GB/SA model in particular has been used successfully in the simulation of peptides (Guarnieri and Weinstein, 1996) and organic molecules (Smith and Vijayakumar, 1991;Williams and Hall, 1996), although it has only recently been applied to nucleic acid systems in which charge-charge interactions are of critical importance (Jayaram et al, 1998;Srinivasan et al, 1998). These recent studies used the GB/SA model to calculate the solvation energy for various nucleic acid conformers generated from explicit solvent molecular dynamics simulations.…”

Section: Introductionmentioning

confidence: 99%

Unrestrained Stochastic Dynamics Simulations of the UUCG Tetraloop Using an Implicit Solvation Model

Williams¹,

Hall²

1999

Biophysical Journal

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Three unrestrained stochastic dynamics simulations have been carried out on the RNA hairpin GGAC[UUCG] GUCC, using the AMBER94 force field (Cornell et al., 1995. J. Am. Chem. Soc. 117:5179-5197) in MacroModel 5.5 (Mohamadi et al., 1990. J. Comp. Chem. 11:440-467) and either the GB/SA continuum solvation model (Still et al., 1990. J. Am. Chem. Soc. 112:6127-6129) or a linear distance-dependent dielectric (1/R) treatment. The linear distance-dependent treatment results in severe distortion of the nucleic acid structure, restriction of all hydroxyl dihedrals, and collapse of the counterion atmosphere over the course of a 5-ns simulation. An additional vacuum simulation without counterions shows somewhat improved behavior. In contrast, the two GB/SA simulations (1.149 and 3.060 ns in length) give average structures within 1.2 A of the initial NMR structure and in excellent agreement with results of an earlier explicit solvent simulation (Miller and Kollman, 1997. J. Mol. Biol. 270:436-450). In a 3-ns GB/SA simulation starting with the incorrect UUCG tetraloop structure (Cheong et al., 1990. Nature. 346:680-682), this loop conformation converts to the correct loop geometry (Allain and Varani, 1995. J. Mol. Biol. 250:333-353), suggesting enhanced sampling relative to the previous explicit solvent simulation. Thermodynamic effects of 2'-deoxyribose substitutions of loop nucleotides were experimentally determined and are found to correlate with the fraction of time the ribose 2'-OH is hydrogen bonded and the distribution of the hydroxyl dihedral is observed in the GB/SA simulations. The GB/SA simulations thus appear to faithfully represent structural features of the RNA without the computational expense of explicit solvent.

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Conformations of 1,2-Dimethoxyethane in Gas and Solution Phase from Molecular Mechanics and Monte Carlo/Stochastic Dynamics Simulations

Cited by 34 publications

References 21 publications

Parameterization of OPLS–AA force field for the conformational analysis of macrocyclic polyketides

Parameterization of OPLS–AA force field for the conformational analysis of macrocyclic polyketides

Concentration Dependence of Water Dynamics in Poly(Ethylene Oxide)/Water Solutions from Molecular Dynamics Simulations

Unrestrained Stochastic Dynamics Simulations of the UUCG Tetraloop Using an Implicit Solvation Model

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