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Papers by P. J. van Maaren
Chemical Science, 2014
The concentration of hydronium and hydroxide at the water-air interface has been under debate for... more The concentration of hydronium and hydroxide at the water-air interface has been under debate for a long time. Recent evidence from a range of experiments and theoretical calculations strongly suggests the water surface is somewhat acidic. Using novel polarizable models we have performed potential of mean force calculations of a hydronium ion, a hydroxide ion and a water molecule in a water droplet and a water slab and we were able to rationalize that hydronium, but not hydroxide, is slightly enriched at the surface for two reasons. First, because the hydrogen-bond acceptance capacity of hydronium is weaker than water it is more favorable to have the hydronium oxygen on the surface. Second, hydroxide ions are expelled from the surface of droplets, due to the entropy being lower when a hydroxide ion is hydrated on the surface. As a result, the water dissociation constant pK w increases slightly near the surface. The results are corroborated by calculations of surface tension of NaOH solutions that are in reasonable agreement with experiment. The structural and thermodynamic interpretation of hydronium and hydroxide hydration provided by these calculations opens the route to a better understanding of atmospheric-and surface chemistry. † Electronic Supplementary Information (ESI) available: additional methods describing model development and validation and additional results. See
Proceedings of the National Academy of Sciences, 2011
Bioinformatics, 2012
Motivation: The molecular dynamics simulation package GROMACS is a widely used tool used in a bro... more Motivation: The molecular dynamics simulation package GROMACS is a widely used tool used in a broad range of different applications within physics, chemistry and biology. It is freely available, user friendly and extremely efficient. The GROMACS software is force field agnostic, and compatible with many molecular dynamics force fields; coarse-grained, unified atom, all atom as well as polarizable models based on the charge on a spring concept. To validate simulations, it is necessary to compare results from the simulations to experimental data. To ease the process of setting up topologies and structures for simulations, as well as providing pre-calculated physical properties along with experimental values for the same we provide a web-based database, containing 145 organic molecules at present. Results: Liquid properties of 145 organic molecules have been simulated using two different force fields, OPLS all atom and Generalized Amber Force Field. So far, eight properties have been calculated (the density, enthalpy of vaporization, surface tension, heat capacity at constant volume and pressure, isothermal compressibility, volumetric expansion coefficient and the static dielectric constant). The results, together with experimental values are available through the database, along with liquid structures and topologies for the 145 molecules, in the two force fields.
Journal of Chemical Theory and Computation, 2012
Journal of Physics-condensed Matter - J PHYS-CONDENS MATTER, 1994
The formation of colloids in alkali halides induced by ionizing radiation is studied by the Monte... more The formation of colloids in alkali halides induced by ionizing radiation is studied by the Monte Carlo simulation of aggregation of F centres. The model consists of the following mechanisms. (i) A two-dimensional lattice-gas Ising model is defined by a Hamiltonian that describes the thermally driven transition from gas (F centres) into the solid phase (condensed colloids). In addition two mechanisms specific for the irradiation of alkali halides are introduced. (ii) Highly mobile recombining centres (H centres) diffuse to the colloid with a flux approximately equal to the flux of F centres. After reaching the surface the H centre and one surface alkali-metal atom of the colloid recombine. (iii) The lattice is subject to a continuous generation of radiation-induced lattice excitations. At the surface of the colloid the excitations result in displacements, which distort the surface of the growing cluster. The morphology and growth kinetics are studied. It appears that the F centres d...
Chemical Science, 2014
ABSTRACT The concentration of hydronium and hydroxide at the water-air interface has been debated... more ABSTRACT The concentration of hydronium and hydroxide at the water-air interface has been debated for a long time. Recent evidence from a range of experiments and theoretical calculations strongly suggests the water surface to be somewhat acidic. Using novel polarizable models we have performed potential of mean force calculations of a hydronium ion, a hydroxide ion and a water molecule in a water droplet and a water slab and we were able to rationalize that hydronium, but not hydroxide, is slightly enriched at the surface for two reasons. First, because the hydrogen bond acceptance capacity of hydronium is weaker than water and it is more favorable to have the hydronium oxygen on the surface. Second, hydroxide ions are expelled from the surface of the droplets, due to the entropy being lower when a hydroxide ion is hydrated on the surface. As a result, the water dissociation constant pKw increases slightly near the surface. The results are corroborated by calculations of surface tension of NaOH solutions that are in reasonable agreement with the experiment. The structural and thermodynamic interpretation of hydronium and hydroxide hydration provided by these calculations opens the route to a better understanding of atmospheric and surface chemistry.
Journal of Chemical Theory and Computation, 2012
The chemical composition of small organic molecules is often very similar to amino acid side chai... more The chemical composition of small organic molecules is often very similar to amino acid side chains or the bases in nucleic acids, and hence there is no a priori reason why a molecular mechanics force field could not describe both organic liquids and biomolecules with a single parameter set. Here, we devise a benchmark for force fields in order to test the ability of existing force fields to reproduce some key properties of organic liquids, namely, the density, enthalpy of vaporization, the surface tension, the heat capacity at constant volume and pressure, the isothermal compressibility, the volumetric expansion coefficient, and the static dielectric constant. Well over 1200 experimental measurements were used for comparison to the simulations of 146 organic liquids. Novel polynomial interpolations of the dielectric constant (32 molecules), heat capacity at constant pressure (three molecules), and the isothermal compressibility (53 molecules) as a function of the temperature have been made, based on experimental data, in order to be able to compare simulation results to them. To compute the heat capacities, we applied the two phase thermodynamics method (Lin et al. J. Chem. Phys. 2003, 119, 11792), which allows one to compute thermodynamic properties on the basis of the density of states as derived from the velocity autocorrelation function. The method is implemented in a new utility within the GROMACS molecular simulation package, named g_dos, and a detailed expos e of the underlying equations is presented. The purpose of this work is to establish the state of the art of two popular force fields, OPLS/AA (all-atom optimized potential for liquid simulation) and GAFF (generalized Amber force field), to find common bottlenecks, i.e., particularly difficult molecules, and to serve as a reference point for future force field development. To make for a fair playing field, all molecules were evaluated with the same parameter settings, such as thermostats and barostats, treatment of electrostatic interactions, and system size (1000 molecules). The densities and enthalpy of vaporization from an independent data set based on simulations using the CHARMM General Force Field (CGenFF) presented by Vanommeslaeghe et al. (J. Comput. Chem. 2010, 31, 671) are included for comparison. We find that, overall, the OPLS/AA force field performs somewhat better than GAFF, but there are significant issues with reproduction of the surface tension and dielectric constants for both force fields.
Bioinformatics, 2012
The molecular dynamics simulation package GROMACS is a widely used tool used in a broad range of ... more The molecular dynamics simulation package GROMACS is a widely used tool used in a broad range of different applications within physics, chemistry and biology. It is freely available, user friendly and extremely efficient. The GROMACS software is force field agnostic, and compatible with many molecular dynamics force fields; coarse-grained, unified atom, all atom as well as polarizable models based on the charge on a spring concept. To validate simulations, it is necessary to compare results from the simulations to experimental data. To ease the process of setting up topologies and structures for simulations, as well as providing pre-calculated physical properties along with experimental values for the same we provide a web-based database, containing 145 organic molecules at present. Liquid properties of 145 organic molecules have been simulated using two different force fields, OPLS all atom and Generalized Amber Force Field. So far, eight properties have been calculated (the density, enthalpy of vaporization, surface tension, heat capacity at constant volume and pressure, isothermal compressibility, volumetric expansion coefficient and the static dielectric constant). The results, together with experimental values are available through the database, along with liquid structures and topologies for the 145 molecules, in the two force fields. The database is freely available under http://virtualchemistry.org.
Proceedings of the National Academy of Sciences, 2011
Water is a demanding partner. It strongly attracts ions, yet some halide anions-chloride, bromide... more Water is a demanding partner. It strongly attracts ions, yet some halide anions-chloride, bromide, and iodide-are expelled to the air/water interface. This has important implications for chemistry in the atmosphere, including the ozone cycle. We present a quantitative analysis of the energetics of ion solvation based on molecular simulations of all stable alkali and halide ions in water droplets. The potentials of mean force for Cl − ,Br − , and I − have shallow minima near the surface. We demonstrate that these minima derive from more favorable water-water interaction energy when the ions are partially desolvated. Alkali cations are on the inside because of the favorable ion-water energy, whereas F − is driven inside by entropy. Models attempting to explain the surface preference based on one or more ion properties such as polarizability or size are shown to lead to qualitative and quantitative errors, prompting a paradigm shift in chemistry away from such simplifications.
Chemical Science, 2014
The concentration of hydronium and hydroxide at the water-air interface has been under debate for... more The concentration of hydronium and hydroxide at the water-air interface has been under debate for a long time. Recent evidence from a range of experiments and theoretical calculations strongly suggests the water surface is somewhat acidic. Using novel polarizable models we have performed potential of mean force calculations of a hydronium ion, a hydroxide ion and a water molecule in a water droplet and a water slab and we were able to rationalize that hydronium, but not hydroxide, is slightly enriched at the surface for two reasons. First, because the hydrogen-bond acceptance capacity of hydronium is weaker than water it is more favorable to have the hydronium oxygen on the surface. Second, hydroxide ions are expelled from the surface of droplets, due to the entropy being lower when a hydroxide ion is hydrated on the surface. As a result, the water dissociation constant pK w increases slightly near the surface. The results are corroborated by calculations of surface tension of NaOH solutions that are in reasonable agreement with experiment. The structural and thermodynamic interpretation of hydronium and hydroxide hydration provided by these calculations opens the route to a better understanding of atmospheric-and surface chemistry. † Electronic Supplementary Information (ESI) available: additional methods describing model development and validation and additional results. See
Proceedings of the National Academy of Sciences, 2011
Bioinformatics, 2012
Motivation: The molecular dynamics simulation package GROMACS is a widely used tool used in a bro... more Motivation: The molecular dynamics simulation package GROMACS is a widely used tool used in a broad range of different applications within physics, chemistry and biology. It is freely available, user friendly and extremely efficient. The GROMACS software is force field agnostic, and compatible with many molecular dynamics force fields; coarse-grained, unified atom, all atom as well as polarizable models based on the charge on a spring concept. To validate simulations, it is necessary to compare results from the simulations to experimental data. To ease the process of setting up topologies and structures for simulations, as well as providing pre-calculated physical properties along with experimental values for the same we provide a web-based database, containing 145 organic molecules at present. Results: Liquid properties of 145 organic molecules have been simulated using two different force fields, OPLS all atom and Generalized Amber Force Field. So far, eight properties have been calculated (the density, enthalpy of vaporization, surface tension, heat capacity at constant volume and pressure, isothermal compressibility, volumetric expansion coefficient and the static dielectric constant). The results, together with experimental values are available through the database, along with liquid structures and topologies for the 145 molecules, in the two force fields.
Journal of Chemical Theory and Computation, 2012
Journal of Physics-condensed Matter - J PHYS-CONDENS MATTER, 1994
The formation of colloids in alkali halides induced by ionizing radiation is studied by the Monte... more The formation of colloids in alkali halides induced by ionizing radiation is studied by the Monte Carlo simulation of aggregation of F centres. The model consists of the following mechanisms. (i) A two-dimensional lattice-gas Ising model is defined by a Hamiltonian that describes the thermally driven transition from gas (F centres) into the solid phase (condensed colloids). In addition two mechanisms specific for the irradiation of alkali halides are introduced. (ii) Highly mobile recombining centres (H centres) diffuse to the colloid with a flux approximately equal to the flux of F centres. After reaching the surface the H centre and one surface alkali-metal atom of the colloid recombine. (iii) The lattice is subject to a continuous generation of radiation-induced lattice excitations. At the surface of the colloid the excitations result in displacements, which distort the surface of the growing cluster. The morphology and growth kinetics are studied. It appears that the F centres d...
Chemical Science, 2014
ABSTRACT The concentration of hydronium and hydroxide at the water-air interface has been debated... more ABSTRACT The concentration of hydronium and hydroxide at the water-air interface has been debated for a long time. Recent evidence from a range of experiments and theoretical calculations strongly suggests the water surface to be somewhat acidic. Using novel polarizable models we have performed potential of mean force calculations of a hydronium ion, a hydroxide ion and a water molecule in a water droplet and a water slab and we were able to rationalize that hydronium, but not hydroxide, is slightly enriched at the surface for two reasons. First, because the hydrogen bond acceptance capacity of hydronium is weaker than water and it is more favorable to have the hydronium oxygen on the surface. Second, hydroxide ions are expelled from the surface of the droplets, due to the entropy being lower when a hydroxide ion is hydrated on the surface. As a result, the water dissociation constant pKw increases slightly near the surface. The results are corroborated by calculations of surface tension of NaOH solutions that are in reasonable agreement with the experiment. The structural and thermodynamic interpretation of hydronium and hydroxide hydration provided by these calculations opens the route to a better understanding of atmospheric and surface chemistry.
Journal of Chemical Theory and Computation, 2012
The chemical composition of small organic molecules is often very similar to amino acid side chai... more The chemical composition of small organic molecules is often very similar to amino acid side chains or the bases in nucleic acids, and hence there is no a priori reason why a molecular mechanics force field could not describe both organic liquids and biomolecules with a single parameter set. Here, we devise a benchmark for force fields in order to test the ability of existing force fields to reproduce some key properties of organic liquids, namely, the density, enthalpy of vaporization, the surface tension, the heat capacity at constant volume and pressure, the isothermal compressibility, the volumetric expansion coefficient, and the static dielectric constant. Well over 1200 experimental measurements were used for comparison to the simulations of 146 organic liquids. Novel polynomial interpolations of the dielectric constant (32 molecules), heat capacity at constant pressure (three molecules), and the isothermal compressibility (53 molecules) as a function of the temperature have been made, based on experimental data, in order to be able to compare simulation results to them. To compute the heat capacities, we applied the two phase thermodynamics method (Lin et al. J. Chem. Phys. 2003, 119, 11792), which allows one to compute thermodynamic properties on the basis of the density of states as derived from the velocity autocorrelation function. The method is implemented in a new utility within the GROMACS molecular simulation package, named g_dos, and a detailed expos e of the underlying equations is presented. The purpose of this work is to establish the state of the art of two popular force fields, OPLS/AA (all-atom optimized potential for liquid simulation) and GAFF (generalized Amber force field), to find common bottlenecks, i.e., particularly difficult molecules, and to serve as a reference point for future force field development. To make for a fair playing field, all molecules were evaluated with the same parameter settings, such as thermostats and barostats, treatment of electrostatic interactions, and system size (1000 molecules). The densities and enthalpy of vaporization from an independent data set based on simulations using the CHARMM General Force Field (CGenFF) presented by Vanommeslaeghe et al. (J. Comput. Chem. 2010, 31, 671) are included for comparison. We find that, overall, the OPLS/AA force field performs somewhat better than GAFF, but there are significant issues with reproduction of the surface tension and dielectric constants for both force fields.
Bioinformatics, 2012
The molecular dynamics simulation package GROMACS is a widely used tool used in a broad range of ... more The molecular dynamics simulation package GROMACS is a widely used tool used in a broad range of different applications within physics, chemistry and biology. It is freely available, user friendly and extremely efficient. The GROMACS software is force field agnostic, and compatible with many molecular dynamics force fields; coarse-grained, unified atom, all atom as well as polarizable models based on the charge on a spring concept. To validate simulations, it is necessary to compare results from the simulations to experimental data. To ease the process of setting up topologies and structures for simulations, as well as providing pre-calculated physical properties along with experimental values for the same we provide a web-based database, containing 145 organic molecules at present. Liquid properties of 145 organic molecules have been simulated using two different force fields, OPLS all atom and Generalized Amber Force Field. So far, eight properties have been calculated (the density, enthalpy of vaporization, surface tension, heat capacity at constant volume and pressure, isothermal compressibility, volumetric expansion coefficient and the static dielectric constant). The results, together with experimental values are available through the database, along with liquid structures and topologies for the 145 molecules, in the two force fields. The database is freely available under http://virtualchemistry.org.
Proceedings of the National Academy of Sciences, 2011
Water is a demanding partner. It strongly attracts ions, yet some halide anions-chloride, bromide... more Water is a demanding partner. It strongly attracts ions, yet some halide anions-chloride, bromide, and iodide-are expelled to the air/water interface. This has important implications for chemistry in the atmosphere, including the ozone cycle. We present a quantitative analysis of the energetics of ion solvation based on molecular simulations of all stable alkali and halide ions in water droplets. The potentials of mean force for Cl − ,Br − , and I − have shallow minima near the surface. We demonstrate that these minima derive from more favorable water-water interaction energy when the ions are partially desolvated. Alkali cations are on the inside because of the favorable ion-water energy, whereas F − is driven inside by entropy. Models attempting to explain the surface preference based on one or more ion properties such as polarizability or size are shown to lead to qualitative and quantitative errors, prompting a paradigm shift in chemistry away from such simplifications.