A Drude Polarizable Model for Liquid Hydrogen Sulfide

Riahi, Saleh; Rowley, Christopher N.

doi:10.1021/jp401847s

Cited by 24 publications

(58 citation statements)

References 44 publications

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“…This is consistent with previous studies that concluded that thiol sulfurs are poor hydrogen bond acceptors due to their large radius and modest electronegativity. 19,39 These rdfs are consistent with the thiols being hydrophobic solutes, with very limited hydrogen bonding interactions with the aqueous solvent.…”

Section: Methylthiolsupporting

confidence: 59%

The hydration structure of methylthiolate from QM/MM molecular dynamics

Awoonor-Williams

Rowley

2018

The Journal of Chemical Physics

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Thiols are widely present in biological systems, most notably as the side chain of cysteine amino acids in proteins. Thiols can be deprotonated to form a thiolate which affords a diverse range of enzymatic activity and modes for chemical modification of proteins. Parameters for modeling thiolates using molecular mechanical force fields have not yet been validated, in part due to the lack of structural data on thiolate solvation. Here, the CHARMM36 and Amber models for thiolates in aqueous solutions are assessed using free energy perturbation and hybrid quantum mechanics/molecular mechanics (QM/MM) molecular dynamics (MD) simulations. The hydration structure of methylthiolate was calculated from 1 ns of QM/MM MD (PBE0-D3/def2-TZVP//TIP3P), which shows that the water-S distances are approximately 2 Å with a coordination number near 6. The CHARMM thiolate parameters predict a thiolate S radius close to the QM/MM value and predict a hydration Gibbs energy of -329.2 kJ/mol, close to the experimental value of -318 kJ/mol. The cysteine thiolate model in the Amber force field underestimates the thiolate radius by 0.2 Å and overestimates the thiolate hydration energy by 119 kJ/mol because it uses the same Lennard-Jones parameters for thiolates as for thiols. A recent Drude polarizable model for methylthiolate with optimized thiolate parameters also performs well. SAPT2+ [Symmetry Adapted Perturbation Theory (SAPT)] analysis indicates that exchange repulsion is larger for the methylthiolate, consistent with it having a more diffuse electron density distribution in comparison with the parent thiol. These data demonstrate that it is important to define distinct non-bonded parameters for the protonated/deprotonated states of amino acid side chains in molecular mechanical force fields.

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Section: Methylthiolsupporting

confidence: 59%

The hydration structure of methylthiolate from QM/MM molecular dynamics

Awoonor-Williams

Rowley

2018

The Journal of Chemical Physics

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“…Beyond this conventional nonpolarizable model, the Drude polarizable force field is also supported by CHARMM . This model has been parameterized for water, ions, sulfur‐containing compounds, aromatics, amides, alkanes, alcohols, proteins, and nucleic acids …”

Section: Introductionmentioning

confidence: 99%

The CHARMM–TURBOMOLE interface for efficient and accurate QM/MM molecular dynamics, free energies, and excited state properties

Riahi

Rowley

2014

J Comput Chem

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The quantum mechanical (QM)/molecular mechanical (MM) interface between Chemistry at HARvard Molecular Mechanics (CHARMM) and TURBOMOLE is described. CHARMM provides an extensive set of simulation algorithms, like molecular dynamics (MD) and free energy perturbation, and support for mature nonpolarizable and Drude polarizable force fields. TURBOMOLE provides fast QM calculations using density functional theory or wave function methods and excited state properties. CHARMM-TURBOMOLE is well-suited for extended QM/MM MD simulations using first principles methods with large (triple-ζ) basis sets. We demonstrate these capabilities with a QM/MM simulation of Mg(2+) (aq), where the MM outer sphere water molecules are represented using the SWM4-NDP Drude polarizable force field and the ion and inner coordination sphere are represented using QM PBE, PBE0, and MP2 methods. The relative solvation free energies of Mg(2+) and Zn(2+) were calculated using thermodynamic integration. We also demonstrate the features for excited state properties. We calculate the time-averaged solution absorption spectrum of indole, the emission spectrum of the indole 1La excited state, and the electronic circular dichroism spectrum of an oxacepham.

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“…The approach was proposed by Paul Drude in 1900 26 as a simple way to describe the dispersive properties of materials and introduced into CHARMM (Chemistry at HARvard Molecular Mechanics) back in 2003. 22,27 Ever since, force field parameters based on Drude oscillator models have been developed for water, 22,28 alkanes, 29 alcohols, 30 ethers, 31 amides, 32 aromatics, 33 nitrogen-containing heteroaromatics, 34 sulfur-containing compounds, 35,36 and ions. 37,38 Those for biomolecules, such as proteins, nucleic acids, lipids, and carbohydrates, 39 are under active development.…”

Section: Introductionmentioning

confidence: 99%

Kirkwood-Buff analysis of aqueous N-methylacetamide and acetamide solutions modeled by the CHARMM additive and Drude polarizable force fields

Lin

Lopes

Roux

et al. 2013

The Journal of Chemical Physics

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Kirkwood-Buff analysis was performed on aqueous solutions of N-methylacetamide and acetamide using the Chemistry at HARvard Molecular Mechanics additive and Drude polarizable all-atom force fields. Comparison of a range of properties with experimental results, including Kirkwood-Buff integrals, excess coordination numbers, solution densities, partial molar values, molar enthalpy of mixing, showed both models to be well behaved at higher solute concentrations with the Drude model showing systematic improvement at lower solution concentrations. However, both models showed difficulties reproducing experimental activity derivatives and the excess Gibbs energy, with the Drude model performing slightly better. At the molecular level, the improved agreement of the Drude model at low solute concentrations is due to increased structure in the solute-solute and solute-solvent interactions. The present results indicate that the explicit inclusion of electronic polarization leads to improved modeling of dilute solutions even when those properties are not included as target data during force field optimization.

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A Drude Polarizable Model for Liquid Hydrogen Sulfide

Cited by 24 publications

References 44 publications

The hydration structure of methylthiolate from QM/MM molecular dynamics

The hydration structure of methylthiolate from QM/MM molecular dynamics

The CHARMM–TURBOMOLE interface for efficient and accurate QM/MM molecular dynamics, free energies, and excited state properties

Kirkwood-Buff analysis of aqueous N-methylacetamide and acetamide solutions modeled by the CHARMM additive and Drude polarizable force fields

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