PoreMS: a software tool for generating silica pore models with user-defined surface functionalisation and pore dimensions

References

• Margelefsky EL, Zeidan RK, Davis ME. Cooperative catalysis by silica-supported organic functional groups. Chem Soc Rev. 2008;37(6):1118–1126. Available from: http://xlink.rsc.org/?DOI=b710334b.
   PubMed Web of Science ®Google Scholar
• Marras F, Wang J, Coppens MO, et al. Ordered mesoporous materials as solid supports for rhodium–diphosphine catalysts with remarkable hydroformylation activity. Chem Commun. 2010;46(35):6587–6589. Available from: http://xlink.rsc.org/?DOI=c0cc00924e.
   PubMed Web of Science ®Google Scholar
• ALOthman Z. A review: fundamental aspects of silicate mesoporous materials. Materials. 2012;5(12):2874–2902. Available from: http://www.mdpi.com/1996-1944/5/12/2874.
   Web of Science ®Google Scholar
• Narayan R, Nayak U, Raichur A, et al. Mesoporous silica nanoparticles: a comprehensive review on synthesis and recent advances. Pharmaceutics. 2018;10(3):118. Available from: http://www.mdpi.com/1999-4923/10/3/118.
   PubMed Web of Science ®Google Scholar
• Diagboya PN, Dikio ED. Silica-based mesoporous materials; emerging designer adsorbents for aqueous pollutants removal and water treatment. Microporous Mesoporous Mater. 2018;266:252–267. Available from: https://linkinghub.elsevier.com/retrieve/pii/S138718111830132X.
   Web of Science ®Google Scholar
• Molaei S, Tamoradi T, Ghadermazi M, et al. Highly efficient oxidative coupling of thiols and oxidation of sulfides in the presence of MCM-41@tryptophan-Cd and MCM-41@tryptophan-Hg as novel and recoverable nanocatalysts. Catal Lett. 2018;148(7):1834–1847. Available from: http://link.springer.com/10.1007/s10562-018-2379-3.
   Web of Science ®Google Scholar
• Siefker J, Biehl R, Kruteva M, et al. Confinement facilitated protein stabilization as investigated by small-angle neutron scattering. J Am Chem Soc. 2018;140(40):12720–12723. Available from: https://pubs.acs.org/doi/10.1021/jacs.8b08454.
   PubMed Web of Science ®Google Scholar
• Dong B, Mansour N, Pei Y, et al. Single molecule investigation of nanoconfinement hydrophobicity in heterogeneous catalysis. J Am Chem Soc. 2020;142(31):13305–13309. Available from: https://pubs.acs.org/doi/10.1021/jacs.0c05905.
   PubMed Web of Science ®Google Scholar
• Melnikov SM, Höltzel A, Seidel-Morgenstern A, et al. Composition, structure, and mobility of water–acetonitrile mixtures in a silica nanopore studied by molecular dynamics simulations. Anal Chem. 2011;83(7):2569–2575. Available from: https://pubs.acs.org/doi/10.1021/ac102847m.
   PubMed Web of Science ®Google Scholar
• Lindsey RK, Rafferty JL, Eggimann BL, et al. Molecular simulation studies of reversed-phase liquid chromatography. J Chromatogr A. 2013;1287:60–82. Available from: https://linkinghub.elsevier.com/retrieve/pii/S0021967313003294.
   PubMed Web of Science ®Google Scholar
• Melnikov SM, Höltzel A, Seidel-Morgenstern A, et al. A molecular dynamics study on the partitioning mechanism in hydrophilic interaction chromatography. Angew Chem Int Ed. 2012;51(25):6251–6254. Available from: http://doi.wiley.com/10.1002/anie.201201096.
   PubMed Web of Science ®Google Scholar
• Melnikov SM, Höltzel A, Seidel-Morgenstern A, et al. A molecular dynamics view on hydrophilic interaction chromatography with polar-bonded phases: properties of the water-rich layer at a silica surface modified with diol-functionalized alkyl chains. J Phys Chem C. 2016;120(24):13126–13138. Available from: https://pubs.acs.org/doi/10.1021/acs.jpcc.6b03799.
   Web of Science ®Google Scholar
• Rybka J, Höltzel A, Melnikov SM, et al. A new view on surface diffusion from molecular dynamics simulations of solute mobility at chromatographic interfaces. Fluid Phase Equilib. 2016;407:177–187. Available from: https://linkinghub.elsevier.com/retrieve/pii/S0378381215003015.
   Web of Science ®Google Scholar
• Rybka J, Höltzel A, Tallarek U. Surface diffusion of aromatic hydrocarbon analytes in reversed-phase liquid chromatography. J Phys Chem C. 2017;121(33):17907–17920. Available from: https://pubs.acs.org/doi/10.1021/acs.jpcc.7b04746.
   Web of Science ®Google Scholar
• El Hage K, Gupta PK, Bemish R, et al. Molecular mechanisms underlying solute retention at heterogeneous interfaces. J Phys Chem Lett. 2017;8(18):4600–4607. Available from: https://pubs.acs.org/doi/10.1021/acs.jpclett.7b01966.
   PubMed Web of Science ®Google Scholar
• El Hage K, Bemish RJ, Meuwly M. From in silica to in silico: retention thermodynamics at solid–liquid interfaces. Phys Chem Chem Phys. 2018;20(27):18610–18622. Available from: http://xlink.rsc.org/?DOI=C8CP02899K.
   PubMed Web of Science ®Google Scholar
• Ziegler F, Teske J, Elser I, et al. Olefin metathesis in confined geometries: a biomimetic approach toward selective macrocyclization. J Am Chem Soc. 2019;141(48):19014–19022. Available from: https://pubs.acs.org/doi/10.1021/jacs.9b08776.
   PubMed Web of Science ®Google Scholar
• Zheng W, Yamada SA, Hung ST, et al. Enhanced Menshutkin S n2 reactivity in mesoporous silica: the influence of surface catalysis and confinement. J Am Chem Soc. 2020;142(12):5636–5648. Available from: https://pubs.acs.org/doi/10.1021/jacs.9b12666.
   PubMed Web of Science ®Google Scholar
• Kobayashi T, Kraus H, Hansen N, et al. Confined Ru-catalysts in a two phase heptane/ionic liquid solution: modeling aspects. Chem Cat Chem. 2020. Available from: https://doi.org/10.1002/cctc.202001596.
   Google Scholar
• Nejad MA, Urbassek HM. Diffusion of cisplatin molecules in silica nanopores: molecular dynamics study of a targeted drug delivery system. J Mol Graph Model. 2019;86:228–234. Available from: https://linkinghub.elsevier.com/retrieve/pii/S1093326318304376.
   PubMed Web of Science ®Google Scholar
• Bruix A, Margraf JT, Andersen M, et al. First-principles-based multiscale modelling of heterogeneous catalysis. Nature Catalysis. 2019;2(8):659–670. Available from: http://www.nature.com/articles/s41929-019-0298-3.
   Web of Science ®Google Scholar
• Žuvela P, Skoczylas M, Jay Liu J, et al. Column characterization and selection systems in reversed-phase high-performance liquid chromatography. Chem Rev. 2019;119(6):3674–3729. Available from: https://pubs.acs.org/doi/10.1021/acs.chemrev.8b00246.
   PubMed Web of Science ®Google Scholar
• Žuvela P, Skoczylas M, Liu JJ, et al. Addition: column characterization and selection systems in reversed-phase high-performance liquid chromatography. Chem Rev. 2019;119(7):4818–4818. Available from: https://pubs.acs.org/doi/10.1021/acs.chemrev.9b00167.
   PubMed Web of Science ®Google Scholar
• Rybka J, Höltzel A, Steinhoff A, et al. Molecular dynamics study of the relation between analyte retention and surface diffusion in reversed-phase liquid chromatography. J Phys Chem C. 2019;123(6):3672–3681. Available from: https://pubs.acs.org/doi/10.1021/acs.jpcc.8b11983.
   Web of Science ®Google Scholar
• Rybka J, Höltzel A, Trebel N, et al. Stationary-phase contributions to surface diffusion in reversed-phase liquid chromatography: chain length versus ligand density. J Phys Chem C. 2019;123(35):21617–21628. Available from: https://pubs.acs.org/doi/10.1021/acs.jpcc.9b06160.
   Web of Science ®Google Scholar
• Krishna R. Describing the diffusion of guest molecules inside porous structures. J Phys Chem C. 2009;113(46):19756–19781. Available from: https://pubs.acs.org/doi/10.1021/jp906879d.
   Web of Science ®Google Scholar
• Brkljča Z, Klimczak M, Miličević Z, et al. Complementary molecular dynamics and X-ray reflectivity study of an imidazolium-based ionic liquid at a neutral sapphire interface. J Phys Chem Lett. 2015;6(3):549–555. Available from: https://pubs.acs.org/doi/10.1021/jz5024493.
   PubMed Web of Science ®Google Scholar
• Stepić R, Wick CR, Strobel V, et al. Mechanism of the water–gas shift reaction catalyzed by efficient ruthenium–based catalysts: a computational and experimental study. Angew Chem Int Ed. 2019;58(3):741–745. Available from: https://onlinelibrary.wiley.com/doi/abs/10.1002/anie.201811627.
   PubMed Web of Science ®Google Scholar
• Vučemilović-Alagić N, Banhatti RD, Stepić R, et al. Insights from molecular dynamics simulations on structural organization and diffusive dynamics of an ionic liquid at solid and vacuum interfaces. J Colloid Interface Sci. 2019;553:350–363. Available from: https://linkinghub.elsevier.com/retrieve/pii/S0021979719306903.
   PubMed Web of Science ®Google Scholar
• García A, Slowing II, Evans JW. Pore diameter dependence of catalytic activity: p-nitrobenzaldehyde conversion to an aldol product in amine-functionalized mesoporous silica. J Chem Phys. 2018;149(2):024101. Available from: http://aip.scitation.org/doi/10.1063/1.5037618.
   PubMed Web of Science ®Google Scholar
• Apostolopoulou M, Santos MS, Hamza M, et al. Quantifying pore width effects on diffusivity via a novel 3D stochastic approach with input from atomistic molecular dynamics simulations. J Chem Theory Comput. 2019;15(12):6907–6922. Available from: https://pubs.acs.org/doi/10.1021/acs.jctc.9b00776.
   PubMed Web of Science ®Google Scholar
• Tallarek U, Hlushkou D, Rybka J, et al. Multiscale simulation of diffusion in porous media: from interfacial dynamics to hierarchical porosity. J Phys Chem C. 2019;123(24):15099–15112. Available from: https://pubs.acs.org/doi/10.1021/acs.jpcc.9b03250.
   Web of Science ®Google Scholar
• Zhuravlev L. The surface chemistry of amorphous silica. Zhuravlev model. Colloids Surf A. 2000;173(1–3):1–38. Available from: https://linkinghub.elsevier.com/retrieve/pii/S0927775700005562.
   Google Scholar
• Melnikov SM, Höltzel A, Seidel-Morgenstern A, et al. How ternary mobile phases allow tuning of analyte retention in hydrophilic interaction liquid chromatography. Anal Chem. 2013;85(18):8850–8856. Available from: https://pubs.acs.org/doi/10.1021/ac402123a.
   PubMed Web of Science ®Google Scholar
• Beck JS, Vartuli JC, Roth WJ, et al. A new family of mesoporous molecular sieves prepared with liquid crystal templates. J Am Chem Soc. 1992;114:10834–10843. Available from: https://doi.org/10.1021/ja00053a020.
   Web of Science ®Google Scholar
• Zhao D, Feng J, Huo Q, et al. Triblock copolymer syntheses of mesoporous silica with periodic 50 to 300 Angstrom pores. Science. 1998;279:548–552. Available from: https://www.sciencemag.org/lookup/doi/10.1126/science.279.5350.548.
   PubMed Web of Science ®Google Scholar
• Kleitz F, Choi SH, Ryoo R. Cubic Ia3d large mesoporous silica: synthesis and replication to platinum nanowires, carbon nanorods and carbon nanotubes. Chem Commun. 2003;17:2136–2137. Available from: https://doi.org/10.1039/B306504A.
   PubMed Web of Science ®Google Scholar
• Reich SJ, Svidrytski A, Hlushkou D, et al. Hindrance factor expression for diffusion in random mesoporous adsorbents obtained from pore-scale simulations in physical reconstructions. Ind Eng Chem Res. 2018;57(8):3031–3042. Available from: https://pubs.acs.org/doi/10.1021/acs.iecr.7b04840.
   Web of Science ®Google Scholar
• Reich SJ, Svidrytski A, Höltzel A, et al. Hindered diffusion in ordered mesoporous silicas: insights from pore-scale simulations in physical reconstructions of SBA-15 and KIT-6 silica. J Phys Chem C. 2018;122(23):12350–12361. Available from: https://pubs.acs.org/doi/10.1021/acs.jpcc.8b03630.
   Web of Science ®Google Scholar
• Rafferty JL, Siepmann J, Schure M. The effects of chain length, embedded polar groups, pressure, and pore shape on structure and retention in reversed-phase liquid chromatography: molecular-level insights from Monte Carlo simulations. J Chromatogr A. 2009;1216(12):2320–2331. Available from: https://linkinghub.elsevier.com/retrieve/pii/S0021967309000107.
   PubMed Web of Science ®Google Scholar
• Melnikov SM, Höltzel A, Seidel-Morgenstern A, et al. Adsorption of water–acetonitrile mixtures to model silica surfaces. J Phys Chem C. 2013;117(13):6620–6631. Available from: https://pubs.acs.org/doi/10.1021/jp312501b.
   Web of Science ®Google Scholar
• Williams JJ, Wiersum AD, Seaton NA, et al. Effect of surface group functionalization on the CO 2/N 2 separation properties of MCM-41: a grand-canonical Monte Carlo simulation study. J Phys Chem C. 2010;114(43):18538–18547. Available from: https://pubs.acs.org/doi/10.1021/jp105464u.
   Web of Science ®Google Scholar
• Williams JJ, Seaton NA, Düren T. Influence of surface groups on the diffusion of gases in MCM-41: a molecular dynamics study. J Phys Chem C. 2011;115(21):10651–10660. Available from: https://pubs.acs.org/doi/10.1021/jp112073z.
   Web of Science ®Google Scholar
• Lowry E, Piri M. Effect of surface chemistry on confined phase behavior in nanoporous media: an experimental and molecular modeling study. Langmuir. 2018;34(32):9349–9358. Available from: https://pubs.acs.org/doi/10.1021/acs.langmuir.8b00986.
   PubMed Web of Science ®Google Scholar
• Elola MD, Rodriguez J. Ionic mobility within functionalized silica nanopores. J Phys Chem C. 2019;123(6):3622–3633. Available from: https://pubs.acs.org/doi/10.1021/acs.jpcc.8b11444.
   Web of Science ®Google Scholar
• Coasne B, Di Renzo F, Galarneau A, et al. Adsorption of simple fluid on silica surface and nanopore: effect of surface chemistry and pore shape. Langmuir. 2008;24(14):7285–7293. Available from: https://pubs.acs.org/doi/10.1021/la800567g.
   PubMed Web of Science ®Google Scholar
• Williams CD, Travis KP, Burton NA, et al. A new method for the generation of realistic atomistic models of siliceous MCM-41. Microporous Mesoporous Mater. 2016;228:215–223. Available from: https://linkinghub.elsevier.com/retrieve/pii/S1387181116300609.
   Web of Science ®Google Scholar
• Geske J, Vogel M. Creating realistic silica nanopores for molecular dynamics simulations. Mol Simul. 2017;43(1):13–18. Available from: https://www.tandfonline.com/doi/full/10.1080/08927022.2016.1221072.
   Web of Science ®Google Scholar
• Keen DA, McGreevy RL. Structural modeling of glasses using reverse Monte-Carlo simulation. Nature. 1990;344:423–425. Available from: https://www.nature.com/articles/344423a0.
   Web of Science ®Google Scholar
• Siperstein FR, Gubbins KE. Synthesis and characterization of templated mesoporous materials using molecular simulation. Mol Simul. 2001;27:339–352. Available from: https://www.tandfonline.com/doi/abs/10.1080/08927020108031357.
   Web of Science ®Google Scholar
• Coasne B, Hung FR, Pellenq RJM, et al. Adsorption of simple gases in MCM-41 materials: the role of surface roughness. Langmuir. 2006;22):194–202. Available from: https://pubs.acs.org/doi/abs/10.1021/la051676g.
   PubMed Web of Science ®Google Scholar
• Bhattacharya S, Coasne B, Hung FR, et al. Modeling micelle-templated mesoporous material SBA-15: atomistic model and gas adsorption studies. Langmuir. 2009;25:5802–5813. Available from: https://pubs.acs.org/doi/10.1021/la801560e.
   PubMed Web of Science ®Google Scholar
• Schumacher C, Gonzalez J, Wright PA, et al. Generation of atomistic models of periodic mesoporous silica by kinetic Monte Carlo simulation of the synthesis of the material. J Phys Chem B. 2006;110(1):319–333. Available from: https://pubs.acs.org/doi/10.1021/jp0551871.
   PubMed Web of Science ®Google Scholar
• Ferreiro-Rangel CA, Lozinska MM, Wright PA, et al. Kinetic Monte Carlo simulation of the synthesis of periodic mesoporous silicas SBA-2 and STAC-1: generation of realistic atomistic models. J Phys Chem C. 2012;116:20966–20974. Available from: https://pubs.acs.org/doi/abs/10.1021/jp307610a.
   Web of Science ®Google Scholar
• Jorge M, Milne AW, Sobek ON, et al. Modelling the self-assembly of silica-based mesoporous materials. Mol Simul. 2018;44:435–452. Available from: https://www.tandfonline.com/doi/abs/10.1080/08927022.2018.1427237.
   Web of Science ®Google Scholar
• Han Y, Slowing II, Evans JW. Surface structure of linear nanopores in amorphous silica: comparison of properties for different pore generation algorithms. J Chem Phys. 2020;153:124708. Available from: https://aip.scitation.org/doi/abs/10.1063/5.0021317?journalCode=jcp.
   PubMed Web of Science ®Google Scholar
• Thompson MW, Gilmer JB, Matsumoto RA, et al. Towards molecular simulations that are transparent, reproducible, usable by others, and extensible (TRUE). Mol Phys. 2020;118:e1742938. Available from: https://www.tandfonline.com/doi/full/10.1080/00268976.2020.1742938.
   PubMed Web of Science ®Google Scholar
• Abraham MJ, Murtola T, Schulz R, et al. GROMACS: high performance molecular simulations through multi-level parallelism from laptops to supercomputers. SoftwareX. 2015;1–2:19–25. Available from: https://linkinghub.elsevier.com/retrieve/pii/S2352711015000059.
   Google Scholar
• Kraus H, Hansen N. PoreMS: v0.2.0; 2020. Available from: https://doi.org/10.5281/zenodo.3984865.
   Google Scholar
• Wyckoff RWG. Crystal structure of high temperature cristobalite. Am J Sci. 1925;s5-9(54):448–459. Available from: http://www.ajsonline.org/cgi/doi/10.2475/ajs.s5-9.54.448.
   Google Scholar
• Wyckoff RWG. Die Kristallstruktur von β-Cristobalit (bei hohen Temperaturen stabile Form). Z Kristallogr. 1925;62(1–6):189–200. Available from: http://www.degruyter.com/view/j/zkri.1925.62.issue-1-6/zkri.1925.62.1.189/zkri.1925.62.1.189.xml.
   Google Scholar
• Peacor DR. High-temperature single-crystal study of the cristobalite inversion. Z Kristallogr. 1973;138(1–4):274–298. Available from: http://www.degruyter.com/doi/10.1524/zkri.1973.138.1-4.274.
   Google Scholar
• Villars P, Calvert LD. Pearson's handbook of crystallographic data for intermetallic phases. 2nd ed. Materials Park (OH): ASM International; 1991.
   Google Scholar
• Unger KK. Porous silica, its properties and use as support in column liquid chromatography. Amsterdam: Elsevier; 1979. (Journal of chromatography library; v. 16).
   Google Scholar
• Vansant EF, Van Der Voort P, Vrancken KC. Characterization and chemical modification of the silica surface. Amsterdam: Elsevier; 1995. (Studies in surface science and catalysis; v. 93).
   Google Scholar
• Litton DA, Garofalini SH. Modeling of hydrophilic wafer bonding by molecular dynamics simulations. J Appl Phys. 2001;89(11):6013–6023. Available from: http://aip.scitation.org/doi/10.1063/1.1351538.
   Web of Science ®Google Scholar
• Wang J, Wang W, Kollman PA, et al. Automatic atom type and bond type perception in molecular mechanical calculations. J Mol Graph Model. 2006;25(2):247–260. Available from: https://linkinghub.elsevier.com/retrieve/pii/S1093326305001737.
   PubMed Web of Science ®Google Scholar
• Gulmen TS, Thompson WH. Testing a two-state model of nanoconfined liquids: conformational equilibrium of ethylene glycol in amorphous silica pores. Langmuir. 2006;22(26):10919–10923. Available from: https://pubs.acs.org/doi/10.1021/la062285k.
   PubMed Web of Science ®Google Scholar
• Abramov A, Iglauer S. Application of the CLAYFF and the DREIDING force fields for modeling of alkylated quartz surfaces. Langmuir. 2019;35(17):5746–5752. Available from: https://pubs.acs.org/doi/10.1021/acs.langmuir.9b00527.
   PubMed Web of Science ®Google Scholar
• Zhao XS, Lu GQ, Whittaker AK, et al. Comprehensive study of surface chemistry of MCM-41 using 29Si CP/MAS NMR, FTIR, pyridine-TPD, and TGA. J Phys Chem B. 1997;101(33):6525–6531. Available from: https://doi.org/10.1021/jp971366+.
   Web of Science ®Google Scholar
• Soler-Illia GJA, Crepaldi EL, Grosso D, et al. Block copolymer-templated mesoporous oxides. Curr Opin Colloid Interface Sci. 2003;8(1):109–126. Available from: https://linkinghub.elsevier.com/retrieve/pii/S1359029403000025.
   Web of Science ®Google Scholar
• Webb JD, Seki T, Goldston JF, et al. Selective functionalization of the mesopores of SBA-15. Microporous Mesoporous Mater. 2015;203:123–131. Available from: https://linkinghub.elsevier.com/retrieve/pii/S138718111400612X.
   Web of Science ®Google Scholar