Prediction of partition coefficients and infinite dilution activity coefficients of 1-ethylpropylamine and 3-methyl-1-pentanol using force field methods

2009 ◽  
Vol 285 (1-2) ◽  
pp. 19-23 ◽  
Author(s):  
Yang Liu ◽  
Xiaofeng Li ◽  
Ling Wang ◽  
Huai Sun
2018 ◽  
Author(s):  
Guilherme Duarte Ramos Matos ◽  
Gaetano Calabró ◽  
David Mobley

<p>Molecular simulations see widespread use in calculating various physical properties of interest, with a key goal being predictive molecular design. These simulations, including molecular dynamics (MD) simulations, begin with a underlying energy model or force field and then, based on this model, use simulations to compute properties of interest. However, one of the most significant challenges in molecular dynamics and modeling studies is ensuring that the force field is a good enough approximation of the underlying physics that computed quantities can be used to reproduce experimental properties with the desired level of accuracy. Parameterization of force fields depend on various experimental properties including as much of the chemistry of interest as possible. Physicochemical properties measurable in a relatively straightforward manner are particularly interesting for developers. Such properties can be measured for a relatively diverse chemical set and used to expand the parameterization dataset as needed. Here, we examine infinite dilution activity coefficients (IDACs) which are experimental quantities that can play this role. We retrieved 237 empirical IDACs from NIST's ThermoML, a database of measured thermodynamic properties, and we estimated the corresponding values using solvation free energy calculations. We found that calculated IDAC values correlate strongly with experiment. Specifically, the natural logarithm of calculated and experimental IDAC values shows a Pearson correlation coefficient of 0.85+/-0.02. The calculated IDAC values allow us to identify strengths and potential weaknesses of force field parameters for specific functional groups in solutes and solvents, suggesting these may be a valuable source of data for force field parameterization, capturing some of the same type of information as hydration and solvation free energies and thus potentially providing a useful new source of experimental data.</p>


2019 ◽  
Author(s):  
Guilherme Duarte Ramos Matos ◽  
Gaetano Calabró ◽  
David Mobley

<p>Molecular simulations begin with an underlying energy model or force field, and from this, can predict diverse physical properties.<br></p> <p>However, force fields were often developed with relatively limited datasets, yet accuracy for diverse properties across a broad chemical space is desirable, so tests of such accuracy are particularly important. Here, to this end, we calculate 237 infinite dilution activity coefficients (IDACs), comparing with experimental values from NIST's ThermoML database. We found that calculated IDAC values correlate strongly with experiment (Pearson R of 0.92+/- 0.01), and allow us to identify specific functional groups which appear to present challenges to the force field employed. One potentially valuable aspect of IDACs, as compared to solvation free energies which have been frequently employed as force field tests, is that the same molecules serve both as solutes and solvents in different cases, allowing us to ensure force fields are not overly tuned to one particular environment or solvent.</p><br><p></p>


2018 ◽  
Author(s):  
Guilherme Duarte Ramos Matos ◽  
Gaetano Calabró ◽  
David Mobley

<p>Molecular simulations see widespread use in calculating various physical properties of interest, with a key goal being predictive molecular design. These simulations, including molecular dynamics (MD) simulations, begin with a underlying energy model or force field and then, based on this model, use simulations to compute properties of interest. However, one of the most significant challenges in molecular dynamics and modeling studies is ensuring that the force field is a good enough approximation of the underlying physics that computed quantities can be used to reproduce experimental properties with the desired level of accuracy. Parameterization of force fields depend on various experimental properties including as much of the chemistry of interest as possible. Physicochemical properties measurable in a relatively straightforward manner are particularly interesting for developers. Such properties can be measured for a relatively diverse chemical set and used to expand the parameterization dataset as needed. Here, we examine infinite dilution activity coefficients (IDACs) which are experimental quantities that can play this role. We retrieved 237 empirical IDACs from NIST's ThermoML, a database of measured thermodynamic properties, and we estimated the corresponding values using solvation free energy calculations. We found that calculated IDAC values correlate strongly with experiment. Specifically, the natural logarithm of calculated and experimental IDAC values shows a Pearson correlation coefficient of 0.85+/-0.02. The calculated IDAC values allow us to identify strengths and potential weaknesses of force field parameters for specific functional groups in solutes and solvents, suggesting these may be a valuable source of data for force field parameterization, capturing some of the same type of information as hydration and solvation free energies and thus potentially providing a useful new source of experimental data.</p>


2019 ◽  
Author(s):  
Guilherme Duarte Ramos Matos ◽  
Gaetano Calabró ◽  
David Mobley

<p>Molecular simulations begin with an underlying energy model or force field, and from this, can predict diverse physical properties.<br></p> <p>However, force fields were often developed with relatively limited datasets, yet accuracy for diverse properties across a broad chemical space is desirable, so tests of such accuracy are particularly important. Here, to this end, we calculate 237 infinite dilution activity coefficients (IDACs), comparing with experimental values from NIST's ThermoML database. We found that calculated IDAC values correlate strongly with experiment (Pearson R of 0.92+/- 0.01), and allow us to identify specific functional groups which appear to present challenges to the force field employed. One potentially valuable aspect of IDACs, as compared to solvation free energies which have been frequently employed as force field tests, is that the same molecules serve both as solutes and solvents in different cases, allowing us to ensure force fields are not overly tuned to one particular environment or solvent.</p><br><p></p>


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