Close contacts at the interface: Experimental-computational synergies for solving complexity problems

References

[1] Nilsson A, Petterson LGM, Norskov J. Chemical bonding at surfaces and interfaces. Oxford, U.K., Ed: Elsevier Ltd, 2008.10.1016/B978-044452837-7.50001-0Search in Google Scholar

[2] Eiswirth, M., Möller, P., Wetzl, K., Imbihl, R., Ertl, G. Mechanisms of spatial self‐organization in isothermal kinetic oscillations during the catalytic CO oxidation on Pt single crystal surfaces. J Chem Phys 1989;90:510.10.1063/1.456501Search in Google Scholar

[3] Higashi GS, Chabal J, Trucks GW, Raghavachari K. Ideal hydrogen termination of the Si (111) surface. Appl Phys Lett 1990;56:656.10.1063/1.102728Search in Google Scholar

[4] Muller DA. The electronic structure at the atomic scale of ultrathin gate oxides. Nature 1999;399:758–761.10.1038/21602Search in Google Scholar

[5] Garbassi F, Morra M, Occhiello E. Polymer surfaces: from physics to technology. Weinheim, Germany, Ed: Wiley-VCH, 1997.Search in Google Scholar

[6] Astruc D. Nanoparticles and catalysis. Weinheim, Germany, Ed: Wiley-VCH, 2008.Search in Google Scholar

[7] Carrasco J, Hodgson A, Michaelides A. A molecular perspective of water at metal interfaces. Nat Mater 2012;11:667.10.1038/nmat3354Search in Google Scholar PubMed

[8] Naoi K, Simon P. New materials and new configurations for advanced electrochemical capacitors. Electrochem J Soc 2008;17:34.10.1149/2.F04081IFSearch in Google Scholar

[9] Carchini G, Almora-Barrios N, Revilla-López G, Bellarosa L, García-Muelas R, García-Melchor M. How theoretical simulations can address the structure and activity of nanoparticles.Top Catal 2013;56:1262.10.1007/s11244-013-0093-3Search in Google Scholar

[10] Cölfen H. Biomineralization: a crystal-clear view. Nat Mater 2010;9:960.10.1038/nmat2911Search in Google Scholar PubMed

[11] Chorkendorff I, Niemanstverdriet JW. Concepts of modern catalysis and kinetics. Weinheim, Germany, Ed: Wiley-VCH, 2003.10.1002/3527602658Search in Google Scholar

[12] Martin RM. Electronic structure: basic theory and practical methods. Cambridge, Ed: Cambridge University Press, 2008.Search in Google Scholar

[13] Rapaport DC. The art of molecular dynamics simulations. Cambridge, Ed: Cambridge University Press, 2004.10.1017/CBO9780511816581Search in Google Scholar

[14] Vargel C. Corrosion of aluminium. Oxford, U.K.: Elsevier Ltd; 2004.10.1016/B978-008044495-6/50012-4Search in Google Scholar

[15] Ezuber H, El-Houd A, El-Shawesh F. A study on the corrosion behavior of aluminum alloys in seawater. Mater Des 2008;29:801–805.10.1016/j.matdes.2007.01.021Search in Google Scholar

[16] Tedim J, Poznyak SK, Kuznetsova A, Raps D, Hack T, Zheludkevich ML, et al. Enhancement of active corrosion protection via combination of inhibitor-loaded nanocontainers. ACS Appl Mater Inter 2010;2:1528–1535.10.1021/am100174tSearch in Google Scholar PubMed

[17] Jerman I, Vuk AS, Kozelj M, Orel B, Kovac J. A structural and corrosion study of triethoxysilyl functionalized POSS coatings on AA 2024 alloy. A Langmuir 2008;24:5029–5037.10.1021/la7037262Search in Google Scholar PubMed

[18] Liu J, Chudhury MK, Berry DH, Seebergh JE, Osborne JH, Blohowiak, KY. Effect of surface morphology on crack growth at a sol-gel reinforced epoxy/aluminum interface. J Adhes 2006;82:487–516.10.1080/00218460600713725Search in Google Scholar

[19] Warren SC, Perkins MR, Adams AM, Kamperman M, Burns AA, Arora H, et al. Nat Mater 2012;11:460–467.10.1038/nmat3274Search in Google Scholar PubMed

[20] Zheludkevich ML, Salvado IM, Ferreira MGS. Sol–gel coatings for corrosion protection of metals. J Mater Chem 2005;15:5099–5111.10.1039/b419153fSearch in Google Scholar

[21] Dalmoro V, dos Santos JHZ, Azambuja DS. Corrosion behavior of AA2024-T3 alloy treated with phosphonate-containing TEOS. J Solid State Electr 2012;16:403–414.10.1007/s10008-011-1346-3Search in Google Scholar

[22] Holzle LRB, Azambuja DS, Piatnicki CMS, Englert GE. Corrosion behaviour of aluminium in ethyleneglycol–water electrolytes containing phosphonic acid. Mater Chem Phy 2007;103:59–64.10.1016/j.matchemphys.2007.01.007Search in Google Scholar

[23] Lecollinet G, Delorme N, Edely M, Gibaud A, Bardeau J-F, Hindré F, et al. Self-assembled monolayers of bisphosphonates: influence of side chain steric hindrance. Langmuir 2009;25:7828–7835.10.1021/la8039576Search in Google Scholar PubMed

[24] Mutin PH, Guerrero G, Vioux A. Hybrid materials from organophosphorus coupling molecules. J Mater Chem 2005;15:3761–3768.10.1039/b505422bSearch in Google Scholar

[25] Khramov AN, Balbyshev VN, Kasten LS, Mantz RA. Sol–gel coatings with phosphonate functionalities for surface modification of magnesium alloys. Thin Solid Films 2006;514:174–181.10.1016/j.tsf.2006.02.023Search in Google Scholar

[26] Dalmoro V, dos Santos JHZ, Armelin E, Alemán C, Azambuja DS. A synergistic combination of tetraethylorthosilicate and multiphosphonic acid offers excellent corrosion protection to AA1100 aluminum alloy. Appl Surf Sci 2013;273:758–768.10.1016/j.apsusc.2013.02.131Search in Google Scholar

[27] Torras J, Azambuja DS, Wolf JM, Alemán C, Armelin E. How organophosphonic acid promotes silane deposition onto aluminum surface: a detailed investigation on adsorption mechanism. J Phys Chem C 2014;118:17724–17736.10.1021/jp5046707Search in Google Scholar

[28] Alexander MR, Thompson GE, Beamson G. Characterization of the oxide/hydroxide surface of aluminium using x‐ray photoelectron spectroscopy: a procedure for curve fitting the O 1s core level. Surf Interface Anal 2000;29:468–477.10.1002/1096-9918(200007)29:7<468::AID-SIA890>3.0.CO;2-VSearch in Google Scholar

[29] Zhang A, Okrasa L, Pakula T, Schlüter D. Homologous series of dendronized polymethacrylates with a methyleneoxycarbonyl spacer between the backbone and dendritic side chain: synthesis, characterization, and some bulk properties. J Am Chem Soc 2004;126:6658–6666.10.1021/ja0494205Search in Google Scholar

[30] Kim H-J, Young E-Y, Jin JY, Lee M. Solution behavior of dendrimer-coated rodlike coordination polymers. Macromolecules 2008;41:6066–6072.10.1021/ma8010203Search in Google Scholar

[31] Li W, Zhang A, Schlüter AD. Thermoresponsive dendronized polymers with tunable lower critical solution temperatures. Chem Commun 2008;5523–5525.10.1039/b811464aSearch in Google Scholar

[32] Bertran O, Zhang B, Schlüter AD, Kröger M, Alemán C. Modeling nanosized single molecule objects: dendronized polymers adsorbed onto mica. J Phys Chem C 2015;119:3746−3753.10.1021/jp510586rSearch in Google Scholar

[33] Guo Y, van Beek JD, Zhang B, Colussi M, Walsde P, Zhang A, et al. Tuning polymer thickness: synthesis and scaling theory of homologous series of dendronized polymers. J Am Chem Soc 2009;131:11841.10.1021/ja9032132Search in Google Scholar

[34] Zhang B, Wepf R, Fischer K, Schmidt M, Besse S, Lindner P, et al. The largest synthetic structure with molecular precision: towards a molecular object. Angew Chem 2011;50:763−766.10.1002/ange.201005164Search in Google Scholar

[35] Zhang B, Wepf R, Kröger M, Halperin A, Schlüter AD. Height and width of adsorbed dendronized polymers: electron and atomic force microscopy of homologous series. Macromolecules 2011;44:6785−6792.10.1021/ma2014707Search in Google Scholar

[36] Phillips JC, Braun R, Wang W, Gumbart J, Tajhordhid E, Villa E, et al. Scalable molecular dynamics with NAMD. J Comput Chem 2005;26:1781−1802.10.1002/jcc.20289Search in Google Scholar PubMed PubMed Central

[37] Cornell WD, Cieplak P, Bayly CI, Gould IR, Merz KM, Ferguson DM, et al. A second generation force field for the simulation of proteins, nucleic acids, and organic molecules. J Am Chem Soc 1995;117:5179−5197.10.1021/ja00124a002Search in Google Scholar

[38] Wang J, Wolf RM, Caldwell JM, Kollman PA, Case DA. Development and testing of a general amber force field. J Comput Chem 2004;15:1157−1174.10.1002/jcc.20035Search in Google Scholar PubMed

[39] Heinz H, Koermer H, Anderson KL, Vaia RA, Farmer BL. Force field for mica-type silicates and dynamics of octadecylammonium chains grafted to montmorillonite. Chem Mater 2005;17:5658−5669.10.1021/cm0509328Search in Google Scholar

[40] Bertran O, Zhang B, Schlüter AD, Halperin A, Kröger M, Alemán C. Computer simulation of dendronized polymers: organization and characterization at the atomistic level. RSC Adv 2013;3:126−140.10.1039/C2RA22034BSearch in Google Scholar

[41] Mecke A, Lee I, Baker jR, Banaszak MM, Orr BG. Deformability of poly (amidoamine) dendrimers. Eur Phys J E 2004;14:7−16.10.1140/epje/i2003-10087-5Search in Google Scholar PubMed

[42] Li D, Zheng Q, Wang Y. Combining surface topography with polymer chemistry: exploring new interfacial biological phenomena. Polym Chem 2014;5:14–24.10.1039/C3PY00739ASearch in Google Scholar

[43] Tretyakov N, Müller M. Directed transport of polymer drops on vibrating superhydrophobic substrates: a molecular dynamics study. Soft Matter 2014;10:4373–4386.10.1039/c3sm53156bSearch in Google Scholar PubMed

[44] Yin J, Yagüe JL, Boyce MC, Gleason KK. Biaxially mechanical tuning of 2-D reversible and irreversible surface topologies through simultaneous and sequential wrinkling. Appl Mater Interfaces 2014;6:2850−2857.10.1021/am4054207Search in Google Scholar PubMed

[45] Long YZ, Li M-M-, Gu C, Wan M, Duvail J-L, Liu Z, et al. Recent advances in synthesis, physical properties and applications of conducting polymer nanotubes and nanofibers. Prog Pol Scien 2011;36:1415.10.1016/j.progpolymsci.2011.04.001Search in Google Scholar

[46] Del Valle LJ, Estrany F, Armelin E, Oliver R, Alemán C. Cellular adhesion, proliferation and viability on conducting polymer substrates. Macromol Biosci 2008;8:1144.10.1002/mabi.200800101Search in Google Scholar

[47] Groenendaal L, Jonas F, Freitag D, Pielartzki H, Reynols JR. Poly (3, 4‐ethylenedioxythiophene) and its derivatives: past, present, and future. Adv Mater 2000;12:481.10.1002/(SICI)1521-4095(200004)12:7<481::AID-ADMA481>3.0.CO;2-CSearch in Google Scholar

[48] Kirchmeyer S, Reuter K. Polyfullerenes for organic photovoltaics. J Mater Chem 2005;15:2077.10.1039/b417803nSearch in Google Scholar

[49] Tamburri E, Orlanducci S, Toschi F, Terranova ML, Passeri D. Growth mechanisms, morphology, and electroactivity of PEDOT layers produced by electrochemical routes in aqueous médium. Synth Met 2009;159:406.10.1016/j.synthmet.2008.10.014Search in Google Scholar

[50] Aradilla D, Estrany F, Alemán C. Symmetric supercapacitors based on multilayers of conducting polymers. J Phys Chem C 2011;115:8430.10.1021/jp201108cSearch in Google Scholar

[51] Aradilla D, Azambuja DS, Estrany F, Casas MT, Ferreira CA, Alemán C. Hybrid polythiophene–clay exfoliated nanocomposites for ultracapacitor devices. J Mater Chem 2012;22:13110.10.1039/c2jm31372cSearch in Google Scholar

[52] Xuan Y, Sandberg M, Berggren M, Crispin X. An all-polymer-air PEDOT battery. Org Electron 2012;13:632.10.1016/j.orgel.2011.12.018Search in Google Scholar

[53] Aradilla D, Estrany F, Casellas F, Iribarren JI, Alemán C. All-polythiophene rechargeable batteries. Org Electron 2014;15:40.10.1016/j.orgel.2013.09.044Search in Google Scholar

[54] Aradilla D, Pérez-Madrigal MM, Estrany F, Azambuja D, Iribarren JI, Alemán, C. Nanometric ultracapacitors fabricated using multilayer of conducting polymers on self-assembled octanethiol monolayers. Org Electron 2013;14:1483.10.1016/j.orgel.2013.03.010Search in Google Scholar

[55] Aradilla D, Estrany F, Alemán C. Synergy of the redox pair in the capacitive properties of nanometric poly (3, 4-ethylenedioxythiophene). Org Electron 2013;14:131.10.1016/j.orgel.2012.10.026Search in Google Scholar

[56] Aradilla D, Estrany F, Armelin E, Alemán C. Ultraporous poly (3, 4-ethylenedioxythiophene) for nanometric electrochemical supercapacitor. Thin Solid Films 2012;520:4402.10.1016/j.tsf.2012.02.058Search in Google Scholar

[57] Zanuy D, Aleman C. Resolving the subnanometric structure of ultrathin films of poly (3, 4-ethylenedioxythiophene) on steel surfaces: a molecular modeling approach. Soft Matter 20139:11634.10.1039/c3sm52477aSearch in Google Scholar

[58] Ahumada O, Pérez-Madrigal MM, Ramírez J, Curcó D, Esteves C, Salvador-Mata G, et al. Sensitive thermal transitions of nanoscale polymer samples using the bimetallic effect: application to ultra-thin polythiophene. Rev Sci Instrum 2013;84:053904.10.1063/1.4804395Search in Google Scholar PubMed

[59] Ocampo C, Oliver R, Armelin E, Alemán C, Estrany F. Electrochemical synthesis of poly (3, 4-ethylenedioxythiophene) on steel electrodes: properties and characterization. J Polym Res 2006;13:193–200.10.1007/s10965-005-9025-7Search in Google Scholar

[60] Teixeira-Dias B, Zanuy D, del Valle LJ, Estrany F, Armelin E, Alemán C. Influence of the doping level on the interactions between poly (3, 4‐ethylenedioxythiophene) and plasmid DNA. Macromol Chem Phys 2010;211:1117–1126.10.1002/macp.200900599Search in Google Scholar

[61] Preat J, Zanuy D, Aleman C. Binding of Cationic Conjugated Polymers to DNA: Atomistic Simulations of Adducts Involving the Dickerson’s Dodecamer. J Comput Chem. 2011;12:1304–2012.10.1021/bm200022nSearch in Google Scholar PubMed

[62] Duan Y, Wu C, Chowdhury S, Lee MC, Xiong G, Zhang W, et al. A point-charge force field for molecular mechanics simulations of proteins based on condensed‐phase quantum mechanical calculations. J.Comput.Chem. 2003;24:1999–2012.10.1002/jcc.10349Search in Google Scholar PubMed

[63] Baaden M, Burgard M, Boehme C, Wipff G. Lanthanide cation binding to a phosphoryl-calix[4]arene: the importance of solvent and counterions investigated by molecular dynamicsand quantum mechanical simulations. Phys Chem Chem Phys 2001;3:1317–1322.10.1039/b009859kSearch in Google Scholar

[64] Savio D, Fillot N, Vergne P, Zaccheddu M. A model for wall slip prediction of confined n-alkanes: effect of wall-fluid interaction versus fluid resistance. Tribol Lett 2012;46:11–22.10.1007/s11249-011-9911-6Search in Google Scholar

[65] Toukmaji C, Sagui C, Board J, Darden T. Efficient particle-mesh Ewald based approach to fixed and induced dipolar interactions. J Chem Phys 2000;113:10913–10927.10.1063/1.1324708Search in Google Scholar

[67] Berendsen HJC, Postma PM, van Gunsteren WF, DiNola A, Haak GR. Molecular dynamics with coupling to an external bath. J Chem Phys. 1984;81:3684–3690.10.1063/1.448118Search in Google Scholar

[68] Martyna GJ, Tobias DL. Constant pressure molecular dynamics algorithms. Chem Phys. 1994;101:4177–4189.10.1063/1.467468Search in Google Scholar

[69] Feller SE, Zhang Y, Pastor RW. Constant pressure molecular dynamics simulation: The Langevin method. J Chem Phys. 1995;103:4613–4622.10.1063/1.470648Search in Google Scholar

[70] Toxvaer S. Molecular dynamics calculation of the equation of state of alkanes. J Chem Phys. 1990;93:4290–4295.10.1063/1.458709Search in Google Scholar

[71] Margolis HC, Beniash E, Fowler CE. Role of macromolecular assembly of enamel matrix proteins in enamel formation. J Dent Res 2006;85:775−793.10.1177/154405910608500902Search in Google Scholar PubMed

[72] Uskokovic V, Li W, Habelitz S. Amelogenin as a promoter of nucleation and crystal growth of apatite. J Cryst Growth 2011;316:106−117.10.1016/j.jcrysgro.2010.12.005Search in Google Scholar PubMed PubMed Central

[73] Wang L, Guan X, yin H., Moradian-Oldak J, Nancollas GH. Mimicking the self-organized microstructure of tooth enamel. J Phys Chem C 2008;112:5892−5899.10.1021/jp077105+Search in Google Scholar PubMed PubMed Central

[74] Gungormus M, Fong H, Kim IW, Evans JS, Tamerles C, Sarikaya M. Regulation of in vitro calcium phosphate mineralization by combinatorially selected hydroxyapatite-binding peptides. Biomacromolecules 2008;9:966−973.10.1021/bm701037xSearch in Google Scholar PubMed

[75] Zhu P, Masuda Y, Yonezawa T, Koumoto K. Investigation of apatite deposition onto charged surfaces in aqueous solutions using a quartz‐crystal microbalance. J Am Ceram Soc 2003;86:782−790.10.1111/j.1151-2916.2003.tb03375.xSearch in Google Scholar

[76] Zhu Z, tong H, Jiang T, Shen X, Wan P, Hu J. Studies on induction of l-aspartic acid modified chitosan to crystal growth of the calcium phosphate in supersaturated calcification solution by quartz crystal microbalance. Biosens Bioelectron 2006;22:291−297.10.1016/j.bios.2006.01.013Search in Google Scholar

[77] Ball V, Michel M, Boulmedais F, Hemmerles J, Haikel Y, Schaaf P, et al. Nucleation kinetics of calcium phosphates on polyelectrolyte multilayers displaying internal secondary structure. Cryst Growth Des 2006;6:327−334.10.1021/cg050044pSearch in Google Scholar

[78] Kakizawa Y, Miyata K, Furukawa S, Kataoka K. Size‐controlled formation of a calcium phosphate‐based organic–inorganic hybrid vector for gene delivery using poly (ethylene glycol)‐block‐poly (aspartic acid). Adv Mater 2004;16:699–702.10.1002/adma.200305782Search in Google Scholar

[79] Urabe M, Kume A, Toibita K, Ozawa K. DNA/calcium phosphate precipitates mixed with medium are stable and maintain high transfection efficiency. Biochem 2000;278:91–92.10.1006/abio.1999.4429Search in Google Scholar

[80] Ngourn SC, Butts HA, Petty AR, Anderson JE, Gerdon AE. Quartz crystal microbalance analysis of DNA-templated calcium phosphate mineralization. Langmuir 2012;28:12151–12158.10.1021/la300949ySearch in Google Scholar

[81] Sololova V, Radkte I, Heumenn R, Epple M. Effective transfection of cells with multi-shell calcium phosphate-DNA nanoparticles. Biomaterials 2006;27:3147–3153.10.1016/j.biomaterials.2005.12.030Search in Google Scholar

[82] Okazaki M, Yoshida Y, Yamaguchi S, Kaneo M, Elliott JC. Affinity binding phenomena of DNA onto apatite crystals. Biomaterials 2001;22:2459–2464.10.1016/S0142-9612(00)00433-6Search in Google Scholar

[83] Chen W-Y, Lin M-S, Lin P-H, Tasi P-S, Chang Y, Yamamoto S. Studies of the interaction mechanism between single strand and double-strand DNA with hydroxyapatite by microcalorimetry and isotherm measurements. Colloids Surf, A 2007;295:274−283.10.1016/j.colsurfa.2006.09.013Search in Google Scholar

[84] Del Valle LJ, Bertran O, Chaves G, Revilla-López G, Rivals M, Cassas MT, et al. DNA adsorbed on hydroxyapatite surfaces. J Mater Chem B 2014;2:6953–6966.10.1039/C4TB01184HSearch in Google Scholar PubMed

[85] Kostetsky EY. The possibility of the formation of protocells and their structural components on the basis of the apatite matrix and cocrystallizing minerals. J Biol Phys 2005;31:607–638.10.1007/s10867-005-2383-xSearch in Google Scholar PubMed PubMed Central

[86] Bertini I, Gray HB, Lippard SJ, Valentine JS. Bioinorganic Chemistry. Principles of bioinorganic chemistry. Mill Valley, CA: University Science Books, 1994.Search in Google Scholar

[87] Lukeman PS, Stevenson ML, Seeman NC. Morphology change of calcium carbonate in the presence of polynucleotides. Cryst Growth Des 2008;8:1200−1202.10.1021/cg700656rSearch in Google Scholar PubMed PubMed Central

[88] Revilla-López G, Casanovas J, Bertran O, Turón P, Puiggalí J, Alemán C. Modeling biominerals formed by apatites and DNA. Biointerphases 2013;8:10–25.10.1186/1559-4106-8-10Search in Google Scholar PubMed PubMed Central

[89] Casanovas J, Revilla-López G, Bertran O, del Valle LJ, Turón P, Puiggalí J. Restricted puckering of mineralized RNA-like riboses. J Phys Chem B 2014;118:5075–5081.10.1021/jp501714qSearch in Google Scholar PubMed

[90] Bertran O, del Valle LJ, Revilla-López G, Chaves G, Cardús L, Casas MT, et al. Mineralization of DNA into nanoparticles of hydroxyapatite. Dalton Trans 2014;43:317–327.10.1039/C3DT52112ESearch in Google Scholar

[91] Bertran O, del Valle LJ, Revilla-López G, Rivas M, Chaves G, Casas MT, et al. Synergistic approach to elucidate the incorporation of magnesium ions into hydroxyapatite. Chem Eur J 2015;21:2537–2546.10.1002/chem.201405428Search in Google Scholar PubMed

[92] Bertran O, Revilla-López G, Casanovas J, del Valle LJ, Turón P, Puiggalí J, et al. Dissolving hydroxyolite: a DNA molecule into its hydroxyapatite mold. Chem Eur J 2016;22:6631–6636.10.1002/chem.201600703Search in Google Scholar PubMed