1932

Abstract

Biominerals are crucial materials that play a vital role in many forms of life. Understanding the various steps through which ions in aqueous environment associate to form increasingly structured particles that eventually transform into the final crystalline or amorphous poly(a)morph in the presence of biologically active molecules is therefore of great significance. In this context, computer modeling is now able to provide an accurate atomistic picture of the dynamics and thermodynamics of possible association events in solution, as well as to make predictions as to particle stability and possible alternative nucleation pathways, as a complement to experiment. This review provides a general overview of the most significant computational methods and of their achievements in this field, with a focus on calcium carbonate as the most abundant biomineral.

Loading

Article metrics loading...

/content/journals/10.1146/annurev-matsci-070317-124327
2018-07-01
2024-04-22
Loading full text...

Full text loading...

/deliver/fulltext/48/1/annurev-matsci-070317-124327.html?itemId=/content/journals/10.1146/annurev-matsci-070317-124327&mimeType=html&fmt=ahah

Literature Cited

  1. 1.  Dubois P, Ameye L 2001. Regeneration of spines and pedicellariae in echinoderms: a review. Microsc. Res. Tech. 55:6427–37
    [Google Scholar]
  2. 2.  Franceschi VR, Horner HT 1980. Calcium oxalate crystals in plants. Bot. Rev. 46:4361–427
    [Google Scholar]
  3. 3.  Horner HT, Wagner BL 1995. Calcium oxalate crystal formation in higher plants. Calcium Oxalate in Biological Systems SR Khan 53–72 Boca Raton, FL: CRC
    [Google Scholar]
  4. 4.  Falini G, Fermani S, Vanzo S, Miletic M, Zaffino G 2005. Influence on the formation of aragonite or vaterite by otolith macromolecules. Eur. J. Inorg. Chem. 2005:1162–67
    [Google Scholar]
  5. 5.  Mann S, Frankel RB, Blakemore RP 1984. Structure, morphology and crystal growth of bacterial magnetite. Nature 310:5976405–7
    [Google Scholar]
  6. 6.  Kamennaya N, Ajo-Franklin C, Northen T, Jansson C 2012. Cyanobacteria as biocatalysts for carbonate mineralization. Minerals 2:4338–64
    [Google Scholar]
  7. 7. Natl. Inst. Diabetes Dig. Kidney Dis. 2017. Definition and facts for kidney stones: What are kidney stones? https://www.niddk.nih.gov/health-information/urologic-diseases/kidney-stones/definition-facts; accessed July 18, 2017
  8. 8. Harvard Women's Health Watch. 2010. Calcium beyond the bones http://www.health.harvard.edu/womens-health/calcium-beyond-the-bones; accessed July 18, 2017
  9. 9. Osteoporos. Relat. Bone Dis. Nat. Resour. Cent. 2017. Osteoporosis overview https://www.niams.nih.gov/Health_Info/Bone/Osteoporosis/overview.asp; accessed July 18, 2017
  10. 10.  Weiner S, Dove PM 2003. An overview of biomineralization processes and the problem of the vital effect. Rev. Mineral. 54:11–29
    [Google Scholar]
  11. 11.  Dove PM 2010. The rise of skeletal biominerals. Elements 6:137–42
    [Google Scholar]
  12. 12.  Frankel RB, Bazylinski DA 2003. Biologically induced mineralization by bacteria. Rev. Mineral. 54:95–114
    [Google Scholar]
  13. 13.  Araki Y, Tsukamoto K, Takagi R, Miyashita T, Oyabu N et al. 2014. Direct observation of the influence of additives on calcite hydration by frequency modulation atomic force microscopy. Cryst. Growth Des. 14:126254–60
    [Google Scholar]
  14. 14.  De Yoreo JJ, Sommerdijk NAJM 2016. Investigating materials formation with liquid-phase and cryogenic TEM. Nat. Rev. Mater. 1:816035
    [Google Scholar]
  15. 15.  Sun S, Chevrier DM, Zhang P, Gebauer D, Cölfen H 2016. Distinct short-range order is inherent to small amorphous calcium carbonate clusters (<2nm). Angew. Chem. Int. Ed. 55:4012206–9
    [Google Scholar]
  16. 16.  Kubicki JD 2016. Molecular Modeling of Geochemical Reactions: An Introduction Chichester, UK: John Wiley & Sons
  17. 17.  De La Pierre M, Demichelis R, Wehrmeister U, Jacob DE, Raiteri P et al. 2014. Probing the multiple structures of vaterite through combined computational and experimental Raman spectroscopy. J. Phys. Chem. C 118:27493–501
    [Google Scholar]
  18. 18.  Rimola A, Aschi M, Orlando R, Ugliengo P 2012. Does adsorption at hydroxyapatite surfaces induce peptide folding? Insights from large-scale B3LYP calculations. J. Am. Chem. Soc. 134:2610899–910
    [Google Scholar]
  19. 19.  Zhao W, Sharma N, Jones F, Raiteri P, Gale JD, Demichelis R 2016. Anhydrous calcium oxalate polymorphism: a combined computational and synchrotron X-ray diffraction study. Cryst. Growth Des. 16:105954–65
    [Google Scholar]
  20. 20.  Parvaneh LS, Donadio D, Sulpizi M 2016. Molecular mechanism of crystal growth inhibition at the calcium oxalate/water interfaces. J. Phys. Chem. C 120:84410–17
    [Google Scholar]
  21. 21.  Malavasi G, Menziani MC, Pedone A, Civalleri B, Corno M, Ugliengo P 2007. A computational multiscale strategy to the study of amorphous materials. Theor. Chem. Acc. 117:5–6933–42
    [Google Scholar]
  22. 22.  Demichelis R, Raiteri P, Gale JD, Dovesi R 2013. Examining the accuracy of Density Functional Theory for predicting the thermodynamics of water incorporation into minerals: the hydrates of calcium carbonate. J. Phys. Chem. C 117:17814–23
    [Google Scholar]
  23. 23.  Chaka AM, Felmy AR 2014. Ab initio thermodynamic model for magnesium carbonates and hydrates. J. Phys. Chem. A 118:357469–88
    [Google Scholar]
  24. 24.  DiStasio RA, Santra B, Li Z, Wu X, Car R 2014. The individual and collective effects of exact exchange and dispersion interactions on the ab initio structure of liquid water. J. Chem. Phys. 141:8084502
    [Google Scholar]
  25. 25.  Ruiz Pestana L, Mardirossian N, Head-Gordon M, Head-Gordon T 2017. Ab initio molecular dynamics simulations of liquid water using high quality meta-GGA functionals. Chem. Sci. 8:53554–65
    [Google Scholar]
  26. 26.  Zen A, Luo Y, Mazzola G, Guidoni L, Sorella S 2015. Ab initio molecular dynamics simulation of liquid water by quantum Monte Carlo. J. Chem. Phys. 142:14144111
    [Google Scholar]
  27. 27.  Demichelis R, Raiteri P, Gale JD, Quigley D, Gebauer D 2011. Stable prenucleation mineral clusters are liquid-like ionic polymers. Nat. Commun. 2:590
    [Google Scholar]
  28. 28.  Wallace AF, Hedges LO, Fernandez-Martinez A, Raiteri P, Gale JD et al. 2013. Microscopic evidence for liquid-liquid separation in supersaturated CaCO3 solutions. Science 341:885–89
    [Google Scholar]
  29. 29.  van Duin ACT, Dasgupta S, Lorant FA, Goddard WA III 2001. ReaxFF: a reactive force field for hydrocarbons. J. Phys. Chem. A 105:419396–409
    [Google Scholar]
  30. 30.  Wu Y, Chen H, Wang F, Paesani F, Voth GA 2008. An improved multistate empirical valence bond model for aqueous proton solvation and transport. J. Phys. Chem. B 112:2467–82
    [Google Scholar]
  31. 31.  Molinari M, Brukhno AV, Parker SC, Spagnoli D 2016. Force field application and development. See Ref 16 33–75
  32. 32.  Raiteri P, Demichelis R, Gale JD 2013. Development of accurate force fields for the simulation of biomineralisation. Methods Enzymol. 532:3–23
    [Google Scholar]
  33. 33.  Raiteri P, Demichelis R, Gale JD, Kellermeier M, Gebauer D et al. 2012. Exploring the influence of organic species on pre- and post-nucleation calcium carbonate. Faraday Discuss 159:61–85
    [Google Scholar]
  34. 34.  MacKerell AD, Bashford D, Bellott M, Dunbrack RL, Evanseck JD et al. 1998. All-atom empirical potential for molecular modeling and dynamics studies of proteins. J. Phys. Chem. B 102:183586–3616
    [Google Scholar]
  35. 35.  Cornell WD, Cieplak P, Bayly CI, Gould IR et al. 1995. A second generation force field for the simulation of proteins, nucleic acids, and organic molecules. J. Am. Chem. Soc. 117:195179–97
    [Google Scholar]
  36. 36.  Jorgensen WL, Maxwell DS, Tirado-Rives J 1996. Development and testing of the OPLS all-atom force field on conformational energetics and properties of organic liquids. J. Am. Chem. Soc. 118:4511225–36
    [Google Scholar]
  37. 37.  Oostenbrink C, Villa A, Mark AE, van Gunsteren WF 2004. A biomolecular force field based on the free enthalpy of hydration and solvation: the GROMOS force-field parameter sets 53A5 and 53A6. J. Comput. Chem. 25:131656–76
    [Google Scholar]
  38. 38.  Lopez-Berganza JA, Diao Y, Pamidighantam S, Espinosa-Marzal RM 2015. Ab initio studies of calcium carbonate hydration. J. Phys. Chem. A 119:4711591–600
    [Google Scholar]
  39. 39.  Dewar MJS, Thiel W 1977. MINDO/3 study of the addition of singlet oxygen (1ΔgO2) to 1,3-butadiene. J. Am. Chem. Soc. 99:72338–39
    [Google Scholar]
  40. 40.  Ponder JW, Wu C, Ren P, Pande VS, Chodera JD et al. 2010. Current status of the AMOEBA polarizable force field. J. Phys. Chem. B 114:82549–64
    [Google Scholar]
  41. 41.  De La Pierre M, Raiteri P, Gale JD 2016. Structure and dynamics of water at step edges on the calcite surface. Cryst. Growth Des. 16:105907–14
    [Google Scholar]
  42. 42.  Chipot C, Pohorille A 2007. Free Energy Calculations (Springer Series in Chemical Physics, Vol. 86) Berlin/Heidelberg: Springer
  43. 43.  Matlahov I, Iline-Vul T, Abayev M, Lee EMY, Nadav-Tsubery M et al. 2015. Interfacial mineral-peptide properties of a mineral binding peptide from osteonectin and bone-like apatite. Chem. Mater. 27:165562–69
    [Google Scholar]
  44. 44.  Arnarez C, Uusitalo JJ, Masman MF, Ingólfsson HI, de Jong DH et al. 2015. Dry Martini, a coarse-grained force field for lipid membrane simulations with implicit solvent. J. Chem. Theory Comput. 11:1260–75
    [Google Scholar]
  45. 45.  Gebauer D, Volkel A, Cölfen H 2008. Stable prenucleation calcium carbonate clusters. Science 322:1819–22
    [Google Scholar]
  46. 46.  Stirling A 2011. HCO3 formation from CO2 at high pH: ab initio molecular dynamics study. J. Phys. Chem. B 115:4914683–87
    [Google Scholar]
  47. 47.  Andersson MP, Rodriguez-Blanco JD, Stipp SLS 2016. Is bicarbonate stable in and on the calcite surface?. Geochim. Cosmochim. Acta 176:198–205
    [Google Scholar]
  48. 48.  Fuoss RM, Kraus CA 1933. Properties of electrolytic solutions. III. The dissociation constant. J. Am. Chem. Soc. 55:31019–28
    [Google Scholar]
  49. 49.  Fuoss RM, Hsia KL 1967. Association of 1–1 salts in water. PNAS 57:61550–57
    [Google Scholar]
  50. 50.  Masterton WL, Bierly T 1976. Ion association in 2:2 complex ion electrolytes: [Co(NH3)5NO2]SO4 in water-dioxane mixtures. J. Solut. Chem. 5:10721–31
    [Google Scholar]
  51. 51.  Geissler P, Dellago C, Chandler D 1999. Kinetic pathways of ion pair dissociation in water. J. Phys. Chem. B 103:183706–10
    [Google Scholar]
  52. 52.  Raiteri P, Gale JD, Quigley D, Rodger PM 2010. Derivation of an accurate force-field for simulating the growth of calcium carbonate from aqueous solution: a new model for the calcite−water interface. J. Phys. Chem. C 114:135997–6010
    [Google Scholar]
  53. 53.  Raiteri P, Demichelis R, Gale JD 2015. Thermodynamically consistent force field for molecular dynamics simulations of alkaline-earth carbonates and their aqueous speciation. J. Phys. Chem. C 119:4324447–58
    [Google Scholar]
  54. 54.  Pegado L, Marsalek O, Jungwirth P, Wernersson E 2012. Solvation and ion-pairing properties of the aqueous sulfate anion: explicit versus effective electronic polarization. Phys. Chem. Chem. Phys. 14:2910248
    [Google Scholar]
  55. 55.  Kohagen M, Pluhařová E, Mason PE, Jungwirth P 2015. Exploring ion-ion interactions in aqueous solutions by a combination of molecular dynamics and neutron scattering. J. Phys. Chem. Lett. 6:91563–67
    [Google Scholar]
  56. 56.  Baer MD, Mundy CJ 2016. Local aqueous solvation structure around Ca2+ during Ca2+⋅⋅⋅Cl pair formation. J. Phys. Chem. B 120:81885–93
    [Google Scholar]
  57. 57.  Torrie G, Valleau J 1977. Nonphysical sampling distributions in Monte Carlo free-energy estimation: umbrella sampling. J. Comput. Phys. 23:2187–99
    [Google Scholar]
  58. 58.  Jarzynski C 1997. Nonequilibrium equality for free energy differences. Phys. Rev. Lett. 78:142690–93
    [Google Scholar]
  59. 59.  Laio A, Parrinello M 2002. Escaping free-energy minima. PNAS 99:2012562–66
    [Google Scholar]
  60. 60.  Bruneval F, Donadio D, Parrinello M 2007. Molecular dynamics study of the solvation of calcium carbonate in water. J. Phys. Chem. B 111:12219–27
    [Google Scholar]
  61. 61.  Tribello GA, Bruneval F, Liew C, Parrinello M 2009. A molecular dynamics study of the early stages of calcium carbonate growth. J. Phys. Chem. B 113:3411680–87
    [Google Scholar]
  62. 62.  De Visscher A, Vanderdeelen J, Königsberger E, Churagulov BR, Ichikuni M, Tsurumi M 2012. IUPAC-NIST Solubility Data Series. 95. Alkaline earth carbonates in aqueous systems. Part 1. Introduction, Be and Mg. J. Phys. Chem. Ref. Data 41:1013105
    [Google Scholar]
  63. 63.  Kellermeier M, Raiteri P, Berg JK, Kempter A, Gale JD, Gebauer D 2016. Entropy drives calcium carbonate ion association. ChemPhysChem 17:213535–41
    [Google Scholar]
  64. 64.  Frenkel JA 1939. A general theory of heterophase fluctuations and pretransition phenomena. J. Chem. Phys. 7:7538–47
    [Google Scholar]
  65. 65.  Pouget EM, Bomans PHH, Goos JACM, Frederik PM, de With G 2009. The initial stages of template-controlled CaCo3 formation revealed by cryo-TEM. Science 323:59201455–58
    [Google Scholar]
  66. 66.  Habraken WJEM, Tao J, Brylka LJ, Friedrich H, Bertinetti L et al. 2013. Ion-association complexes unite classical and non-classical theories for the biomimetic nucleation of calcium phosphate. Nat. Commun. 4:1507
    [Google Scholar]
  67. 67.  Kellermeier M, Gebauer D, Melero-García E, Drechsler M, Talmon Y et al. 2012. Colloidal stabilization of calcium carbonate prenucleation clusters with silica. Adv. Funct. Mater. 22:204301–11
    [Google Scholar]
  68. 68.  Raiteri P, Gale JD 2010. Water is the key to nonclassical nucleation of amorphous calcium carbonate. J. Am. Chem. Soc. 132:4917623–34
    [Google Scholar]
  69. 69.  Finney AR, Rodger PM 2012. Probing the structure and stability of calcium carbonate pre-nucleation clusters. Faraday Discuss 159:47–14
    [Google Scholar]
  70. 70.  Kawska A, Brickmann J, Kniep R, Hochrein O, Zahn D 2006. An atomistic simulation scheme for modeling crystal formation from solution. J. Chem. Phys. 124:2024513
    [Google Scholar]
  71. 71.  Lin S-T, Maiti PK, Goddard WA III 2010. Two-phase thermodynamic model for efficient and accurate absolute entropy of water from molecular dynamics simulations. J. Phys. Chem. B 114:248191–98
    [Google Scholar]
  72. 72.  Duffy DM, Harding JH 2004. Simulation of organic monolayers as templates for the nucleation of calcite crystals. Langmuir 20:187630–36
    [Google Scholar]
  73. 73.  Faatz M, Gröhn F, Wegner G 2004. Amorphous calcium carbonate: synthesis and potential intermediate in biomineralization. Adv. Mater. 16:12996–1000
    [Google Scholar]
  74. 74.  Andersson MP, Stipp SLS 2016. Insight into CaCO3 nucleation from the liquid-liquid phase diagram predicted by COSMO-RS Goldschmidt Conf. Abstr. https://goldschmidtabstracts.info/2016/70.pdf
  75. 75.  ten Wolde PR, Frenkel D 1997. Enhancement of protein crystal nucleation by critical density fluctuations. Science 277:53341975–78
    [Google Scholar]
  76. 76.  Addadi L, Raz S, Weiner S 2003. Taking advantage of disorder: amorphous calcium carbonate and its roles in biomineralization. Adv. Mater. 15:12959–70
    [Google Scholar]
  77. 77.  Cartwright JHE, Checa AG, Gale JD, Gebauer D, Sainz-Díaz CI 2012. Calcium carbonate polyamorphism and its role in biomineralization: How many amorphous calcium carbonates are there?. Angew. Chem. Int. Ed. 51:11960–70
    [Google Scholar]
  78. 78.  Goodwin AL, Michel FM, Phillips BL, Keen DA, Dove MT, Reeder RJ 2010. Nanoporous structure and medium-range order in synthetic amorphous calcium carbonate. Chem. Mater. 22:103197–205
    [Google Scholar]
  79. 79.  Singer JW, Yazaydin , Kirkpatrick RJ, Bowers GM 2012. Structure and transformation of amorphous calcium carbonate: a solid-state 43Ca NMR and computational molecular dynamics investigation. Chem. Mater. 24:101828–36
    [Google Scholar]
  80. 80.  Navrotsky A 2004. Energetic clues to pathways to biomineralization: Precursors, clusters, and nanoparticles. PNAS 101:3312096–101
    [Google Scholar]
  81. 81.  Bano AM, Rodger PM, Quigley D 2014. New insight into the stability of CaCO3 surfaces and nanoparticles via molecular simulation. Langmuir 30:257513–21
    [Google Scholar]
  82. 82.  Quigley D, Rodger PM 2008. Free energy and structure of calcium carbonate nanoparticles during early stages of crystallization. J. Chem. Phys. 128:22221101
    [Google Scholar]
  83. 83.  Freeman CL, Harding JH, Quigley D, Rodger PM 2010. Structural control of crystal nuclei by an eggshell protein. Angew. Chem. Int. Ed. 49:305135–37
    [Google Scholar]
  84. 84.  De La Pierre M, Carteret C, Maschio L, André E, Orlando R, Dovesi R 2014. The Raman spectrum of CaCO3 polymorphs calcite and aragonite: a combined experimental and computational study. J. Chem. Phys. 140:16164509
    [Google Scholar]
  85. 85.  Carteret C, De La Pierre M, Dossot M, Pascale F, Erba A, Dovesi R 2013. The vibrational spectrum of CaCO3 aragonite: a combined experimental and quantum-mechanical investigation. J. Chem. Phys. 138:1014201
    [Google Scholar]
  86. 86.  Christy AG 2017. A review of the structures of vaterite: the impossible, the possible, and the likely. Cryst. Growth Des. 17:63567–78
    [Google Scholar]
  87. 87.  Demichelis R, Raiteri P, Gale JD, Dovesi R 2012. A new structural model for disorder in vaterite from first-principles calculations. CrystEngComm 14:44–47
    [Google Scholar]
  88. 88.  Demichelis R, Raiteri P, Gale JD, Dovesi R 2013. The multiple structures of vaterite. Cryst. Growth Des. 13:62247–51
    [Google Scholar]
  89. 89.  Burgess KMN, Bryce DL 2014. On the crystal structure of the vaterite polymorph of CaCO3: a calcium-43 solid-state NMR and computational assessment. Solid State Nucl. Magn. Reson. 65:75–83
    [Google Scholar]
  90. 90.  Jiang W, Pacella MS, Athanasiadou D, Nelea V, Vali H et al. 2017. Chiral acidic amino acids induce chiral hierarchical structure in calcium carbonate. Nat. Commun. 8:15066
    [Google Scholar]
  91. 91.  Swainson IP 2008. The structure of monohydrocalcite and the phase composition of the beachrock deposits of Lake Butler and Lake Fellmongery, South Australia. Am. Mineral. 93:1014–18
    [Google Scholar]
  92. 92.  Demichelis R, Raiteri P, Gale JD 2014. Structure of hydrated calcium carbonates: a first-principles study. J. Cryst. Growth 401:33–37
    [Google Scholar]
  93. 93.  Señorale-Pose M, Chalar C, Dauphin Y, Massard P, Pradel P, Marín M 2008. Monohydrocalcite in calcareous corpuscles of Mesocestoides corti. . Exp. Parasitol. 118:154–58
    [Google Scholar]
  94. 94.  Neumann M, Epple M 2007. Monohydrocalcite and its relationship to hydrated amorphous calcium carbonate in biominerals. Eur. J. Inorg. Chem. 2007:1953–57
    [Google Scholar]
  95. 95.  Swainson IP, Hammond RP 2003. Hydrogen bonding in ikaite, CaCO3·6H2O. Mineral. Mag. 67:555–62
    [Google Scholar]
  96. 96.  Tang CC, Thompson SP, Parker JE, Lennie AR, Azoughc F, Katod K 2009. The ikaite-to-vaterite transformation: new evidence from diffraction and imaging. J. Appl. Cryst. 42:225–33
    [Google Scholar]
  97. 97.  Gebauer D, Gunawidjaja PN, Ko JYP, Bacsik Z, Aziz B et al. 2010. Proto-calcite and proto-vaterite in amorphous calcium carbonates. Angew. Chem. Int. Ed. 49:8889–91
    [Google Scholar]
  98. 98.  Weber E, Pokroy B 2015. Intracrystalline inclusions within single crystalline hosts: from biomineralization to bio-inspired crystal growth. CrystEngComm 17:315873–83
    [Google Scholar]
  99. 99.  Kim Y-Y, Carloni JD, Demarchi B, Sparks D, Reid DG et al. 2016. Tuning hardness in calcite by incorporation of amino acids. Nat. Mater. 15:8903–10
    [Google Scholar]
  100. 100.  Sun J, Bhushan B 2012. Hierarchical structure and mechanical properties of nacre: a review. RSC Adv 2:207617–32
    [Google Scholar]
  101. 101.  Ghosh P, Katti DR, Katti KS 2007. Mineral proximity influences mechanical response of proteins in biological mineral–protein hybrid systems. Biomacromolecules 8:3851–56
    [Google Scholar]
  102. 102.  Xiao S, Edwards SA, Gräter F 2011. A new transferable forcefield for simulating the mechanics of CaCO3 crystals. J. Phys. Chem. C 115:4120067–75
    [Google Scholar]
  103. 103.  Qu T, Verma D, Alucozai M, Tomar V 2015. Influence of interfacial interactions on deformation mechanism and interface viscosity in α-chitin-calcite interfaces. Acta Biomater 25:325–38
    [Google Scholar]
  104. 104.  Bhowmik R, Katti KS, Katti DR 2007. Mechanics of molecular collagen is influenced by hydroxyapatite in natural bone. J. Mater. Sci. 42:218795–8803
    [Google Scholar]
  105. 105.  De Yoreo JJ, Vekilov PG 2003. Principles of crystal nucleation and growth. Rev. Mineral. Geochem. 54:157–93
    [Google Scholar]
  106. 106.  de Leeuw NH, Parker SC 1997. Atomistic simulation of the effect of molecular adsorption of water on the surface structure and energies of calcite surfaces. Faraday Trans 93:3467–75
    [Google Scholar]
  107. 107.  de Leeuw NH, Parker SC 1998. Surface structure and morphology of calcium carbonate polymorphs calcite, aragonite, and vaterite: an atomistic approach. J. Phys. Chem. B 102:162914–22
    [Google Scholar]
  108. 108.  Kerisit S, Parker SC, Harding JH 2003. Atomistic simulation of the dissociative adsorption of water on calcite surfaces. J. Phys. Chem. B 107:317676–82
    [Google Scholar]
  109. 109.  Kerisit S, Parker SC 2004. Free energy of adsorption of water and metal ions on the calcite surface. J. Am. Chem. Soc. 126:3210152–61
    [Google Scholar]
  110. 110.  Geissbuhler P, Fenter P, DiMasi E, Srajer G, Sorensen LB, Sturchio NC 2004. Three-dimensional structure of the calcite-water interface by surface X-ray scattering. Surf. Sci. 573:2191–203
    [Google Scholar]
  111. 111.  Imada H, Kimura K, Onishi H 2013. Water and 2-propanol structured on calcite (104) probed by frequency-modulation atomic force microscopy. Langmuir 29:3410744–51
    [Google Scholar]
  112. 112.  Marutschke C, Walters D, Cleveland J, Hermes I, Bechstein R, Kühnle A 2014. Three-dimensional hydration layer mapping on the (10.4) surface of calcite using amplitude modulation atomic force microscopy. Nanotechnology 25:33335703
    [Google Scholar]
  113. 113.  Fenter P, Kerisit S, Raiteri P, Gale JD 2013. Is the calcite-water interface understood? Direct comparisons of molecular dynamics simulations with specular X-ray reflectivity data. J. Phys. Chem. C 117:5028–42
    [Google Scholar]
  114. 114.  Wolthers M, di Tommaso D, Du Z, de Leeuw NH 2013. Variations in calcite growth kinetics with surface topography: molecular dynamics simulations and process-based growth kinetics modelling. CrystEngComm 15:275506–14
    [Google Scholar]
  115. 115.  Wolthers M, Di Tommaso D, Du Z, de Leeuw NH 2012. Calcite surface structure and reactivity: molecular dynamics simulations and macroscopic surface modelling of the calcite-water interface. Phys. Chem. Chem. Phys. 14:4315145–57
    [Google Scholar]
  116. 116.  Andersson MP, Stipp SLS 2012. How acidic is water on calcite?. J. Phys. Chem. C 116:3518779–87
    [Google Scholar]
  117. 117.  Lardge JS, Duffy DM, Gillan MJ 2009. Investigation of the interaction of water with the calcite (10.4) surface using ab initio simulation. J. Phys. Chem. C 113:177207–12
    [Google Scholar]
  118. 118.  Lardge JS, Duffy DM, Gillan MJ, Watkins M 2010. Ab initio simulations of the interaction between water and defects on the calcite surface. J. Phys. Chem. C 114:62664–68
    [Google Scholar]
  119. 119.  Kerisit S, Parker SC 2004. Free energy of adsorption of water and calcium on the calcite surface. Chem. Commun. 2004:152–53
    [Google Scholar]
  120. 120.  Kerisit S, Cooke DJ, Spagnoli D, Parker SC 2005. Molecular dynamics simulations of the interactions between water and inorganic solids. J. Mater. Chem. 15:141454–62
    [Google Scholar]
  121. 121.  Gratz AJ, Hillner PE, Hansma PK 1993. Step dynamics and spiral growth on calcite. Geochim. Cosmochim. Acta 57:491–95
    [Google Scholar]
  122. 122.  De La Pierre M, Raiteri P, Stack AG, Gale JD 2017. Uncovering the atomistic mechanism for calcite step growth. Angew. Chem. Int. Ed. 56:298464–67
    [Google Scholar]
  123. 123.  De Yoreo JJ, Zepeda-Ruiz LA, Friddle RW, Qiu SR, Wasylenki LE et al. 2009. Rethinking classical crystal growth models through molecular scale insights: consequences of kink-limited kinetics. Cryst. Growth Des. 9:125135–44
    [Google Scholar]
  124. 124.  Tribello GA, Ceriotti M, Parrinello M 2010. A self-learning algorithm for biased molecular dynamics. PNAS 107:4117509–14
    [Google Scholar]
  125. 125.  Pfaendtner J, Bonomi M 2015. Efficient sampling of high-dimensional free-energy landscapes with parallel bias metadynamics. J. Chem. Theory Comput. 11:115062–67
    [Google Scholar]
  126. 126.  Allen RJ, Warren PB, ten Wolde PR 2005. Sampling rare switching events in biochemical networks. Phys. Rev. Lett. 94:1018104
    [Google Scholar]
  127. 127.  Straub JE, Berne BJ 1985. A rapid method for determining rate constants by molecular dynamics. J. Chem. Phys. 83:31138–39
    [Google Scholar]
  128. 128.  Stack AG, Raiteri P, Gale JD 2012. Accurate rates of the complex mechanisms for growth and dissolution of minerals using a combination of rare-event theories. J. Am. Chem. Soc. 134:111–14
    [Google Scholar]
  129. 129.  Darkins RDW 2016. Computational insight into the molecular mechanisms that control the growth of inorganic crystals PhD Thesis, UCL
  130. 130.  Piana S, Reyhani M, Gale JD 2005. Simulating micrometre-scale crystal growth from solution. Nature 438:706470–73
    [Google Scholar]
  131. 131.  McCoy JM, LaFemina JP 1997. Kinetic Monte Carlo investigation of pit formation at the surface-water interface. Surf. Sci. 373:2–3288–99
    [Google Scholar]
  132. 132.  Kurganskaya I, Luttge A 2016. Kinetic Monte Carlo approach to study carbonate dissolution. J. Phys. Chem. C 120:126482–92
    [Google Scholar]
  133. 133.  Anderson MW, Gebbie-Rayet JT, Hill AR, Farida N, Attfield MP et al. 2017. Predicting crystal growth via a unified kinetic three-dimensional partition model. Nature 544:7651456–59
    [Google Scholar]
  134. 134.  Sikirić MD, Füredi-Milhofer H 2006. The influence of surface active molecules on the crystallization of biominerals in solution. Adv. Colloid Interface Sci. 128–130:135–58
    [Google Scholar]
  135. 135.  Nancollas GH, Gardner GL 1974. Kinetics of crystal growth of calcium oxalate monohydrate. J. Cryst. Growth 21:2267–76
    [Google Scholar]
  136. 136.  Elhadj S, De Yoreo JJ, Hoyer JR, Dove PM 2006. Role of molecular charge and hydrophilicity in regulating the kinetics of crystal growth. PNAS 103:5119237–42
    [Google Scholar]
  137. 137.  Westin KJ, Rasmuson ÅC 2005. Nucleation of calcium carbonate in presence of citric acid, DTPA, EDTA and pyromellitic acid. J. Colloid Interface Sci. 282:2370–79
    [Google Scholar]
  138. 138.  Nygren MA, Gay DH, Catlow CRA, Wilson MP, Rohl AL 1998. Incorporation of growth-inhibiting diphosphonates into steps on the calcite cleavage plane surface. Faraday Trans 94:243685–93
    [Google Scholar]
  139. 139.  Ukrainczyk M, Greiner M, Elts E, Briesen H 2015. Simulating preferential sorption of tartrate on prismatic calcite surfaces. CrystEngComm 17:1149–59
    [Google Scholar]
  140. 140.  Sommerdijk NAJM, de With G 2008. Biomimetic CaCO3 mineralization using designer molecules and interfaces. Chem. Rev. 108:114499–550
    [Google Scholar]
  141. 141.  Freeman CL, Harding JH, Cooke DJ, Elliott JA, Lardge JS, Duffy DM 2007. New forcefields for modeling biomineralization processes. J. Phys. Chem. C 111:3211943–51
    [Google Scholar]
  142. 142.  Remko M, Rode BM 2006. Effect of metal ions (Li+, Na+, K+, Mg2+, Ca2+, Ni2+, Cu2+, and Zn2+) and water coordination on the structure of glycine and zwitterionic glycine. J. Phys. Chem. A 110:51960–67
    [Google Scholar]
  143. 143.  Tang N, Skibsted LH 2016. Calcium binding to amino acids and small glycine peptides in aqueous solution: toward peptide design for better calcium bioavailability. J. Agric. Food Chem. 64:214376–89
    [Google Scholar]
  144. 144.  Kahlen J, Salimi L, Sulpizi M, Peter C, Donadio D 2014. Interaction of charged amino-acid side chains with ions: an optimization strategy for classical force fields. J. Phys. Chem. B 118:143960–72
    [Google Scholar]
  145. 145.  Nada H 2014. Difference in the conformation and dynamics of aspartic acid on the flat regions, step edges, and kinks of a calcite surface: a molecular dynamics study. J. Phys. Chem. C 118:2614335–45
    [Google Scholar]
  146. 146.  Freeman CL, Harding JH 2014. Entropy of molecular binding at solvated mineral surfaces. J. Phys. Chem. C 118:31506–14
    [Google Scholar]
  147. 147.  Shen J-W, Li C, van der Vegt NFA, Peter C 2013. Understanding the control of mineralization by polyelectrolyte additives: simulation of preferential binding to calcite surfaces. J. Phys. Chem. C 117:136904–13
    [Google Scholar]
  148. 148.  Duffy DM, Harding JH 2002. Modelling the interfaces between calcite crystals and Langmuir monolayers. J. Mater. Chem. 12:123419–25
    [Google Scholar]
  149. 149.  Quigley D, Rodger PM, Freeman CL, Harding JH, Duffy DM 2009. Metadynamics simulations of calcite crystallization on self-assembled monolayers. J. Chem. Phys. 131:9094703
    [Google Scholar]
  150. 150.  Sumper MA 2002. Phase separation model for the nanopatterning of diatom biosilica. Science 295:2430–33
    [Google Scholar]
/content/journals/10.1146/annurev-matsci-070317-124327
Loading
/content/journals/10.1146/annurev-matsci-070317-124327
Loading

Data & Media loading...

  • Article Type: Review Article
This is a required field
Please enter a valid email address
Approval was a Success
Invalid data
An Error Occurred
Approval was partially successful, following selected items could not be processed due to error