1
|
Hix MA, Walker AR. AutoParams: An Automated Web-Based Tool To Generate Force Field Parameters for Molecular Dynamics Simulations. J Chem Inf Model 2023; 63:6293-6301. [PMID: 37773638 DOI: 10.1021/acs.jcim.3c01049] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/01/2023]
Abstract
Many research questions benefit from molecular dynamics simulations to observe the motions and conformations of molecules over time, which rely on force fields that describe sets of common molecules by category. With the increase of importance for large data sets used in machine learning and growing computational efficiency, the ability to rapidly create large numbers of force field inputs is of high importance. Unusual molecules, such as nucleotide analogues, functionalized carbohydrates, and modified amino acids, are difficult to describe consistently using standard force fields, requiring the development of custom parameters for each unique molecule. While these parameters may be created by individual users, the process can become time-consuming or may introduce errors that may not be immediately apparent. We present an open-source automated parameter generation service, AutoParams, which requires minimal input from the user and creates useful Amber force field parameter sets for most molecules, particularly those that combine molecular types (e.g., a carbohydrate functionalized with a benzene). We include hierarchical atom-typing logic that makes it straightforward to expand with additional force fields and settings, and options for creating monomers in polymers, such as functionalized amino acids. It can be straightforwardly linked to any charge generation program and currently has interfaces to Psi4, PsiRESP, and TeraChem. It is open source and is available via GitHub. It includes error checking and testing protocols to ensure the parameters will be sufficient for subsequent molecular dynamics simulations and streamlines the creation of force field databases.
Collapse
Affiliation(s)
- Mark A Hix
- Department of Chemistry, Wayne State University, Detroit, Michigan 48202-3489, United States
| | - Alice R Walker
- Department of Chemistry, Wayne State University, Detroit, Michigan 48202-3489, United States
| |
Collapse
|
2
|
Anderson RL, Gunn DSD, Taddese T, Lavagnini E, Warren PB, Bray DJ. Phase Behavior of Alkyl Ethoxylate Surfactants in a Dissipative Particle Dynamics Model. J Phys Chem B 2023; 127:1674-1687. [PMID: 36786752 PMCID: PMC9969514 DOI: 10.1021/acs.jpcb.2c08834] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/15/2023]
Abstract
We present a dissipative particle dynamics (DPD) model capable of capturing the liquid state phase behavior of nonionic surfactants from the alkyl ethoxylate (CnEm) family. The model is based upon our recent work [Anderson et al. J. Chem. Phys. 2017, 147, 094503] but adopts tighter control of the molecular structure by setting the bond angles with guidance from molecular dynamics simulations. Changes to the geometry of the surfactants were shown to have little effect on the predicted micelle properties of sampled surfactants, or the water-octanol partition coefficients of small molecules, when compared to the original work. With these modifications the model is capable of reproducing the binary water-surfactant phase behavior of nine surfactants (C8E4, C8E5, C8E6, C10E4, C10E6, C10E8, C12E6, C12E8, and C12E12) with a good degree of accuracy.
Collapse
|
3
|
Minkara MS, Josephson TR, Venteicher CL, Greenvall BR, Lindsey RK, Koenig PH, Siepmann JI. Nonane and Hexanol Adsorption in the Lamellar Phase of a Nonionic Surfactant: Molecular Simulations and Comparison to Ideal Adsorbed Solution Theory. J Phys Chem B 2022; 126:3940-3949. [PMID: 35594369 DOI: 10.1021/acs.jpcb.2c02871] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Adsorption of n-nonane/1-hexanol (C9/C6OH) mixtures into the lamellar phase formed by a 50/50 w/w triethylene glycol mono-n-decyl ether (C10E3)/water system was studied using configurational-bias Monte Carlo simulations in the osmotic Gibbs ensemble. The interactions were described by the Shinoda-Devane-Klein coarse-grained force field. Prior simulations probing single-component adsorption indicated that C9 molecules preferentially load near the center of the bilayer, increasing the bilayer thickness, whereas C6OH molecules are more likely to be found near the interface of the polar and nonpolar moieties, swelling the bilayer in the lateral dimension. Here, we extend this work to binary C9/C6OH adsorption to probe whether the difference in the spatial preferences may lead to a synergistic effect and enhanced loadings for the mixture. Comparing loading trends and the thermodynamics of binary adsorption to unary adsorption reveals that C9-C9 interactions lead to the largest enhancement, whereas C9-C6OH and C6OH-C6OH interactions are less favorable for this bilayer system. Ideal adsorbed solution theory yields satisfactory predictions of the binary loading.
Collapse
Affiliation(s)
- Mona S Minkara
- Department of Bioengineering, Northeastern University, 360 Huntington Avenue, Boston, Massachusetts 02115, United States.,Department of Chemistry and Chemical Theory Center, University of Minnesota, 207 Pleasant Street SE, Minneapolis, Minnesota 55455-0431, United States
| | - Tyler R Josephson
- Department of Chemistry and Chemical Theory Center, University of Minnesota, 207 Pleasant Street SE, Minneapolis, Minnesota 55455-0431, United States.,Department of Chemical, Biochemical, and Environmental Engineering, University of Maryland, Baltimore County, 1000 Hilltop Circle, Baltimore, Maryland 21250, United States
| | - Connor L Venteicher
- Department of Chemistry and Chemical Theory Center, University of Minnesota, 207 Pleasant Street SE, Minneapolis, Minnesota 55455-0431, United States
| | - Benjamin R Greenvall
- Department of Bioengineering, Northeastern University, 360 Huntington Avenue, Boston, Massachusetts 02115, United States
| | - Rebecca K Lindsey
- Department of Chemistry and Chemical Theory Center, University of Minnesota, 207 Pleasant Street SE, Minneapolis, Minnesota 55455-0431, United States
| | - Peter H Koenig
- Computational Chemistry, Modeling and Simulation, The Procter and Gamble Company, 8256 Union Centre Blvd, West Chester, Ohio 45069, United States
| | - J Ilja Siepmann
- Department of Chemistry and Chemical Theory Center, University of Minnesota, 207 Pleasant Street SE, Minneapolis, Minnesota 55455-0431, United States.,Department of Chemical Engineering and Materials Science, University of Minnesota, 421 Washington Avenue SE, Minneapolis, Minnesota 55455-0132, United States
| |
Collapse
|
5
|
Swope WC, Johnston MA, Duff AI, McDonagh JL, Anderson RL, Alva G, Tek AT, Maschino AP. Challenge to Reconcile Experimental Micellar Properties of the CnEm Nonionic Surfactant Family. J Phys Chem B 2019; 123:1696-1707. [DOI: 10.1021/acs.jpcb.8b11568] [Citation(s) in RCA: 17] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- William C. Swope
- IBM Almaden Research Center, 650 Harry Road, San Jose, California 95120, United States
| | | | | | | | | | - Gabriela Alva
- IBM Almaden Research Center, 650 Harry Road, San Jose, California 95120, United States
| | - Andy T. Tek
- IBM Almaden Research Center, 650 Harry Road, San Jose, California 95120, United States
| | - Alexander P. Maschino
- Dr. TJ Owens Gilroy Early College Academy, 5055 Santa Teresa Blvd, Gilroy, California 95020, United States
| |
Collapse
|