Reliable computational design of biological-inorganic materials to the large nanometer scale using Interface-FF

References

• Li MF, Zhao ZP, Cheng T, et al. Ultrafine jagged platinum nanowires enable ultrahigh mass activity for the oxygen reduction reaction. Science. 2016;354:1414–1419.10.1126/science.aaf9050
   PubMed Web of Science ®Google Scholar
• Smeets PJM, Cho KR, Kempen RGE, et al. Calcium carbonate nucleation driven by ion binding in a biomimetic matrix revealed by in situ electron microscopy. Nat Mater. 2015;14:394–399.10.1038/nmat4193
   PubMed Web of Science ®Google Scholar
• Bonaccorso F, Colombo L, Yu G, et al. Graphene, related two-dimensional crystals, and hybrid systems for energy conversion and storage. Science. 2015;347, 1246501.
   PubMed Web of Science ®Google Scholar
• Wegst UGK, Bai H, Saiz E, et al. Bioinspired structural materials. Nat Mater. 2015;14:23–36.
   PubMed Web of Science ®Google Scholar
• Nicolosi V, Chhowalla M, Kanatzidis MG, et al. Liquid exfoliation of layered materials. Science. 2013;340:1226419.10.1126/science.1226419
   Web of Science ®Google Scholar
• Heinz H, Ramezani-Dakhel H. Simulations of inorganic–bioorganic interfaces to discover new materials: insights, comparisons to experiment, challenges, and opportunities. Chem Soc Rev. 2016;45:412–448.10.1039/C5CS00890E
   PubMed Web of Science ®Google Scholar
• Dreaden EC, Alkilany AM, Huang XH, et al. The golden age: gold nanoparticles for biomedicine. Chem Soc Rev. 2012;41:2740–2779.10.1039/C1CS15237H
   PubMed Web of Science ®Google Scholar
• Heinz H, Pramanik C, Heinz O, et al. Nanoparticle decoration with surfactants: molecular interactions, assembly, and applications. Surf Sci Rep. 2017;72:1–58.10.1016/j.surfrep.2017.02.001
   Web of Science ®Google Scholar
• Jeon NJ, Noh JH, Yang WS, et al. Compositional engineering of perovskite materials for high-performance solar cells. Nature. 2015;517:476–480.10.1038/nature14133
   PubMed Web of Science ®Google Scholar
• Liu H, Espe M, Modarelli DA, et al. Interaction of substituted poly(phenyleneethynylene)s with ligand-stabilized CdS nanoparticles. J Mater Chem A. 2014;2:8705–8711.10.1039/c4ta01280a
   Web of Science ®Google Scholar
• Xu J, Wu J, Luo L, et al. Co3O4 nanocubes homogeneously assembled on few-layer graphene for high energy density lithium-ion batteries. J Power Sources. 2015;274:816–822.10.1016/j.jpowsour.2014.10.106
   Web of Science ®Google Scholar
• Kirklin S, Meredig B, Wolverton C. High-throughput computational screening of new Li-ion battery anode materials. Adv Energy Mater. 2013;3:252–262.10.1002/aenm.v3.2
   Web of Science ®Google Scholar
• Huang XQ, Zhao ZP, Cao L, et al. High-performance transition metal-doped Pt3Ni octahedra for oxygen reduction reaction. Science. 2015;348:1230–1234.10.1126/science.aaa8765
   PubMed Web of Science ®Google Scholar
• Auyeung E, Morris W, Mondloch JE, et al. Controlling structure and porosity in catalytic nanoparticle superlattices with DNA. J Am Chem Soc. 2015;137:1658–1662.10.1021/ja512116p
   PubMed Web of Science ®Google Scholar
• Sun M, Yang C, Zheng J, et al. Enhanced efficacy of chemotherapy for breast cancer stem cells by simultaneous suppression of multidrug resistance and antiapoptotic cellular defense. Acta Biomater. 2015;28:171–182.10.1016/j.actbio.2015.09.029
   PubMed Web of Science ®Google Scholar
• Suter JL, Groen D, Coveney PV. Chemically specific multiscale modeling of clay-polymer nanocomposites reveals intercalation dynamics, tactoid self-assembly and emergent materials properties. Adv Mater. 2015;27:966–984.10.1002/adma.201403361
   PubMed Web of Science ®Google Scholar
• Kaushik A, Kumar R, Arya SK, et al. Organic-inorganic hybrid nanocomposite-based gas sensors for environmental monitoring. Chem Rev. 2015;115:4571–4606. Epub 2015 May 02.10.1021/cr400659h
   PubMed Web of Science ®Google Scholar
• Fu YT, Heinz H. Cleavage energy of alkylammonium-modified montmorillonite and relation to exfoliation in nanocomposites: Influence of cation density, head group structure, and chain length. Chem Mater. 2010;22:1595–1605.10.1021/cm902784r
   Web of Science ®Google Scholar
• Booth GH, Grueneis A, Kresse G, et al. Towards an exact description of electronic wavefunctions in real solids. Nature. 2013;493:365–370.
   PubMed Web of Science ®Google Scholar
• Heinz H, Lin T-J, Mishra RK, et al. Thermodynamically consistent force fields for the assembly of inorganic, organic, and biological nanostructures: the interface force field. Langmuir. 2013;29:1754–1765.10.1021/la3038846
   PubMed Web of Science ®Google Scholar
• Chenoweth K, van Duin ACT, Goddard WA. ReaxFF reactive force field for molecular dynamics simulations of hydrocarbon oxidation. J Phys Chem A. 2008;112:1040–1053.10.1021/jp709896w
   PubMed Web of Science ®Google Scholar
• Heinz H, Koerner H, Anderson KL, et al. Force field for mica-type silicates and dynamics of octadecylammonium chains grafted to montmorillonite. Chem Mater. 2005;17:5658–5669.10.1021/cm0509328
   Web of Science ®Google Scholar
• Emami FS, Puddu V, Berry RJ, et al. Force field and a surface model database for silica to simulate interfacial properties in atomic resolution. Chem Mater. 2014;26:2647–2658.10.1021/cm500365c
   Web of Science ®Google Scholar
• Mishra RK, Fernández-Carrasco L, Flatt RJ, et al. A force field for tricalcium aluminate to characterize surface properties, initial hydration, and organically modified interfaces in atomic resolution. Dalton Trans. 2014;43:10602–10616.10.1039/c4dt00438h
   PubMed Web of Science ®Google Scholar
• Mishra RK, Flatt RJ, Heinz H. Force field for tricalcium silicate and insight into nanoscale properties: cleavage, initial hydration, and adsorption of organic molecules. J Phys Chem C. 2013;117:10417–10432.10.1021/jp312815g
   Web of Science ®Google Scholar
• Heinz H, Vaia RA, Farmer BL, et al. Accurate simulation of surfaces and interfaces of face-centered cubic metals using 12−6 and 9−6 Lennard-Jones potentials. J Phys Chem C. 2008;112:17281–17290.10.1021/jp801931d
   Web of Science ®Google Scholar
• Lin TZ, Heinz H. Accurate force field parameters and pH resolved surface models for hydroxyapatite to understand structure, mechanics, hydration, and biological interfaces. J Phys Chem C. 2016;120:4975–4992.10.1021/acs.jpcc.5b12504
   Web of Science ®Google Scholar
• Heinz H, Suter UW. Atomic charges for classical simulations of polar systems. J Phys Chem B. 2004;108:18341–18352.10.1021/jp048142t
   Web of Science ®Google Scholar
• Gross KC, Seybold PG, Hadad CM. Comparison of different atomic charge schemes for predicting pKa variations in substituted anilines and phenols. Int J Quantum Chem. 2002;90:445–458.10.1002/(ISSN)1097-461X
   Web of Science ®Google Scholar
• Singh-Miller NE, Marzari N. Surface energies, work functions, and surface relaxations of low-index metallic surfaces from first principles. Phys Rev B. 2009;80:235407.10.1103/PhysRevB.80.235407
   Web of Science ®Google Scholar
• Valero R, Gomes JR, Truhlar DG, et al. Density functional study of CO and NO adsorption on Ni-doped MgO(100). J Chem Phys. 2010;132:104701. Epub 2010 Mar 18.10.1063/1.3340506
   PubMed Web of Science ®Google Scholar
• Zhao Y, Truhlar D. The M06 suite of density functionals for main group thermochemistry, thermochemical kinetics, noncovalent interactions, excited states, and transition elements: two new functionals and systematic testing of four M06-class functionals and 12 other functionals. Theoret Chem Acc. 2008;120:215–241.10.1007/s00214-007-0310-x
   Web of Science ®Google Scholar
• Xu R, Chen C-C, Wu L, et al. Three-dimensional coordinates of individual atoms in materials revealed by electron tomography. Nat Mater. 2015;14:1099–1103.10.1038/nmat4426
   PubMed Web of Science ®Google Scholar
• Sanders MJ, Leslie M, Catlow CRA. Interatomic potentials for SiO2. J Chem Soc-Chem Commun. 1984:1271-1273.
   Google Scholar
• Cygan RT, Liang J-J, Kalinichev AG. Molecular models of hydroxide, oxyhydroxide, and clay phases and the development of a general force field. J Phys Chem B. 2004;108:1255–1266.10.1021/jp0363287
   Web of Science ®Google Scholar
• Berendsen HJC, Grigera JR, Straatsma TP. The missing term in effective pair potentials. J Phys Chem. 1987;91:6269–6271.10.1021/j100308a038
   Web of Science ®Google Scholar
• Mahoney MW, Jorgensen WL. A five-site model for liquid water and the reproduction of the density anomaly by rigid, Nonpolarizable Potential Functions. J Chem Phys. 2000;112:8910–8922.
   Web of Science ®Google Scholar
• Heinz H, Farmer BL, Pandey RB, et al. Nature of molecular interactions of peptides with gold, palladium, and Pd-Au bimetal surfaces in aqueous solution. J Am Chem Soc. 2009;131:9704–9714.10.1021/ja900531f
   PubMed Web of Science ®Google Scholar
• Coppage R, Slocik JM, Briggs BD, et al. Crystallographic recognition controls peptide binding for bio-based nanomaterials. J Am Chem Soc. 2011;133:12346–12349.10.1021/ja203726n
   PubMed Web of Science ®Google Scholar
• Heinz H, Jha KC, Luettmer-Strathmann J, et al. Polarization at metal-biomolecular interfaces in solution. J R Soc Interface. 2011;8:220–232 . Epub 2010/07/16.10.1098/rsif.2010.0318
   PubMed Web of Science ®Google Scholar
• Jha KC, Liu H, Bockstaller MR, et al. Facet recognition and molecular ordering of ionic liquids on metal surfaces. J Phys Chem C. 2013;117:25969–25981.10.1021/jp4032404
   Web of Science ®Google Scholar
• Feng J, Pandey RB, Berry RJ, et al. Adsorption mechanism of single amino acid and surfactant molecules to Au 111 surfaces in aqueous solution: design rules for metal-binding molecules. Soft Matter. 2011;7:2113–2120.10.1039/c0sm01118e
   Web of Science ®Google Scholar
• Feng J, Slocik JM, Sarikaya M, et al. Influence of the shape of nanostructured metal surfaces on adsorption of single peptide molecules in aqueous solution. Small. 2012;8:1049–1059.10.1002/smll.201102066
   PubMed Web of Science ®Google Scholar
• Ramezani-Dakhel H, Ruan LY, Huang Y, et al. Molecular mechanism of specific recognition of cubic Pt nanocrystals by peptides and the concentration-dependent formation from seed crystals. Adv Func Mater. 2015;25:1374–1384.10.1002/adfm.v25.9
   Web of Science ®Google Scholar
• Briggs B, Bedford N, Seifert S, et al. Atomic-scale identification of Pd leaching in nanoparticle catalyzed CC coupling: effects of particle surface disorder. Chem Sci. 2015;6:6413–6419.10.1039/C5SC01424G
   Web of Science ®Google Scholar
• Ruan L, Ramezani-Dakhel H, Chiu C-Y, et al. Tailoring molecular specificity toward a crystal facet: a lesson from biorecognition toward Pt{1 1 1}. Nano Lett. 2013;13:840–846.10.1021/nl400022g
   PubMed Web of Science ®Google Scholar
• Ruan LY, Ramezani-Dakhel H, Lee C, et al. A rational biomimetic approach to structure defect generation in colloidal nanocrystals. ACS Nano. 2014;8:6934–6944.10.1021/nn501704k
   PubMed Web of Science ®Google Scholar
• Ramezani-Dakhel H, Mirau PA, Naik RR, et al. Stability, surface features, and atom leaching of palladium nanoparticles: toward prediction of catalytic functionality. Phys Chem Chem Phys. 2013;15:5488–5492.10.1039/c3cp00135k
   PubMed Web of Science ®Google Scholar
• Bedford NM, Ramezani-Dakhel H, Slocik JM, et al. Elucidation of peptide-directed palladium surface structure for biologically tunable nanocatalysts. ACS Nano. 2015;9:5082–5092.10.1021/acsnano.5b00168
   PubMed Web of Science ®Google Scholar
• Coppage R, Slocik JM, Ramezani-Dakhel H, et al. Exploiting localized surface binding effects to enhance the catalytic reactivity of peptide-capped nanoparticles. J Am Chem Soc. 2013;135:11048–11054.10.1021/ja402215t
   PubMed Web of Science ®Google Scholar
• Gupta A, Boekfa B, Sakurai H, et al. Structure, interaction, and dynamics of Au/Pd bimetallic nanoalloys dispersed in aqueous ethylpyrrolidone, a monomeric moiety of polyvinylpyrrolidone. J Phys Chem C. 2016;120:17454–17464.10.1021/acs.jpcc.6b05097
   Web of Science ®Google Scholar
• Pacardo DB, Sethi M, Jones SE, et al. Biomimetic synthesis of Pd nanocatalysts for the stille coupling reaction. ACS Nano. 2009;3:1288–1296.10.1021/nn9002709
   PubMed Web of Science ®Google Scholar
• Tyson WR, Miller WA. Surface free energies of solid metals: estimation from liquid surface tension measurements. Surf Sci. 1977;62:267–276.10.1016/0039-6028(77)90442-3
   Web of Science ®Google Scholar
• Love JC, Estroff LA, Kriebel JK, et al. Self-assembled monolayers of thiolates on metals as a form of nanotechnology. Chem Rev. 2005;105:1103–1170.10.1021/cr0300789
   PubMed Web of Science ®Google Scholar
• Heinz H. Adsorption of biomolecules and polymers on silicates, glasses, and oxides: mechanisms, predictions, and opportunities by molecular simulation. Curr Opin Chem Eng. 2016;11:34–41.10.1016/j.coche.2015.12.003
   Web of Science ®Google Scholar
• Heinz H. The role of chemistry and pH of solid surfaces for specific adsorption of biomolecules in solution – accurate computational models and experiment. J Phys: Condens Matter. 2014;26:244105.
   PubMed Web of Science ®Google Scholar
• Patwardhan SV, Emami FS, Berry RJ, et al. Chemistry of aqueous silica nanoparticle surfaces and the mechanism of selective peptide adsorption. J Am Chem Soc. 2012;134:6244–6256.10.1021/ja211307u
   PubMed Web of Science ®Google Scholar
• Bolt GH. Determination of the charge density of silica sols. J Phys Chem. 1957;61:1166–1169.10.1021/j150555a007
   Web of Science ®Google Scholar
• Emami FS, Puddu V, Berry RJ, et al. Prediction of specific biomolecule adsorption on silica surfaces as a function of pH and particle size. Chem Mater. 2014;26:5725–5734.10.1021/cm5026987
   Web of Science ®Google Scholar
• Scott MC, Chen CC, Mecklenburg M, et al. Electron tomography at 2.4-ångström resolution. Nature. 2012;483:444–447.10.1038/nature10934
   PubMed Web of Science ®Google Scholar
• Chen CC, Zhu C, White ER, et al. Three-dimensional imaging of dislocations in a nanoparticle at atomic resolution. Nature. 2013;496:74–77.10.1038/nature12009
   PubMed Web of Science ®Google Scholar
• Miao J, Ercius P, Billinge SJL. Atomic electron tomography: 3D structures without crystals. Science. 2016;353:1380.
   Web of Science ®Google Scholar
• Yang Y, Chen C-C, Scott MC, et al. Deciphering chemical order/disorder and material properties at the single-atom level. Nature. 2017;542:75–79.10.1038/nature21042
   PubMed Web of Science ®Google Scholar
• Ritt P, Sakidja R, Perepezko JH. Mo–Si–B based coating for oxidation protection of SiC–C composites. Surf Coat Technol. 2012;206:4166–4172.10.1016/j.surfcoat.2012.04.016
   Web of Science ®Google Scholar
• Lemberg JA, Ritchie RO. Mo-Si-B alloys for ultrahigh-temperature structural applications. Adv Mater. 2012;24:3445–3480.10.1002/adma.201200764
   PubMed Web of Science ®Google Scholar
• Rioult FA. Transient oxidation of Mo–Si–B alloys: effect of the microstructure size scale. Acta Mater. 2009;57:4600–4613.10.1016/j.actamat.2009.06.036
   Web of Science ®Google Scholar
• Miao JW, Förster F, Levi O. Equally sloped tomography with oversampling reconstruction. Phys Rev B. 2005;72:052103.10.1103/PhysRevB.72.052103
   Web of Science ®Google Scholar
• Ma JC, Dougherty DA. The cation–π Interaction. Chem Rev. 1997;97:1303–1324.10.1021/cr9603744
   PubMed Web of Science ®Google Scholar
• Hunter CA, Sanders JKM. The nature of π–π interactions. J Am Chem Soc. 1990;112:5525–5534.10.1021/ja00170a016
   Web of Science ®Google Scholar
• Sinnokrot MO, Sherrill CD. High-accuracy quantum mechanical studies of π–π interactions in benzene dimers. J Phys Chem A. 2006;110:10656–10668.10.1021/jp0610416
   PubMed Web of Science ®Google Scholar