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Chemical gradients in human enamel crystallites

A Publisher Correction to this article was published on 21 July 2020

This article has been updated


Dental enamel is a principal component of teeth1, and has evolved to bear large chewing forces, resist mechanical fatigue and withstand wear over decades2. Functional impairment and loss of dental enamel, caused by developmental defects or tooth decay (caries), affect health and quality of life, with associated costs to society3. Although the past decade has seen progress in our understanding of enamel formation (amelogenesis) and the functional properties of mature enamel, attempts to repair lesions in this material or to synthesize it in vitro have had limited success4,5,6. This is partly due to the highly hierarchical structure of enamel and additional complexities arising from chemical gradients7,8,9. Here we show, using atomic-scale quantitative imaging and correlative spectroscopies, that the nanoscale crystallites of hydroxylapatite (Ca5(PO4)3(OH)), which are the fundamental building blocks of enamel, comprise two nanometric layers enriched in magnesium flanking a core rich in sodium, fluoride and carbonate ions; this sandwich core is surrounded by a shell with lower concentration of substitutional defects. A mechanical model based on density functional theory calculations and X-ray diffraction data predicts that residual stresses arise because of the chemical gradients, in agreement with preferential dissolution of the crystallite core in acidic media. Furthermore, stresses may affect the mechanical resilience of enamel. The two additional layers of hierarchy suggest a possible new model for biological control over crystal growth during amelogenesis, and hint at implications for the preservation of biomarkers during tooth development.

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Fig. 1: The hierarchical architecture of human enamel.
Fig. 2: Atomic-scale structure and composition of human enamel crystallites.
Fig. 3: Chemical gradients in human enamel crystallites and the amorphous intergranular phase.
Fig. 4: Effect of substitution on mechanical and chemical properties of human enamel crystallites.
Fig. 5: A model for human enamel crystallite growth during amelogenesis.

Data availability

The data that support the findings of this study are available from the corresponding author upon reasonable request. Source data are provided with this paper.

Code availability

This manuscript primarily made use of commercial (IVAS, Origin, Matlab, MDI Jade, APEX2, Thermo Scientific Qtegra ISDS, COMSOL Multiphysics, TEM Imaging and Analysis, DigitalMicrograph, AZtec, Adobe Illustrator) and freely available (DEMETER, OLEX2, SHELX, Quantum ESPRESSO, Cornell Spectrum Imager, ImageJ) software packages for acquisition, processing and visualization of data. MCR was performed using custom code using the Matlab mcr.m package from the Eigenvector Research PLS_toolbox, as described elsewhere43. In addition, custom code written for the Mathematica and Matlab environments was used for file conversions, plotting and visualization. This code is available from the corresponding author upon reasonable request.

Change history


  1. 1.

    Nanci, A. Ten Cate’s Oral Histology: Development, Structure, and Function 7th edn (Mosby Elsevier, 2008).

  2. 2.

    Chai, H., Lee, J. J. W., Constantino, P. J., Lucas, P. W. & Lawn, B. R. Remarkable resilience of teeth. Proc. Natl Acad. Sci. USA 106, 7289–7293 (2009).

    ADS  CAS  PubMed  PubMed Central  Article  Google Scholar 

  3. 3.

    Klein, O. D. et al. Meeting report: a hard look at the state of enamel research. Int. J. Oral Sci. 9, e3 (2017).

    PubMed  PubMed Central  Article  Google Scholar 

  4. 4.

    Moradian-Oldak, J. Protein-mediated enamel mineralization. Front. Biosci. 17, 1996–2023 (2012).

    PubMed Central  Article  CAS  Google Scholar 

  5. 5.

    Lacruz, R. S., Habelitz, S., Wright, J. T. & Paine, M. L. Dental enamel formation and implications for oral health and disease. Physiol. Rev. 97, 939–993 (2017).

    PubMed  PubMed Central  Article  Google Scholar 

  6. 6.

    Robinson, C. Enamel maturation: a brief background with implications for some enamel dysplasias. Front. Physiol. 5, 388 (2014).

    PubMed  PubMed Central  Article  Google Scholar 

  7. 7.

    Gordon, L. M. et al. Amorphous intergranular phases control the properties of rodent tooth enamel. Science 347, 746–750 (2015).

    ADS  CAS  PubMed  Article  PubMed Central  Google Scholar 

  8. 8.

    La Fontaine, A. et al. Atomic-scale compositional mapping reveals Mg-rich amorphous calcium phosphate in human dental enamel. Sci. Adv. 2, e1601145 (2016).

    ADS  PubMed  PubMed Central  Article  CAS  Google Scholar 

  9. 9.

    Gordon, L. M. & Joester, D. Mapping residual organics and carbonate at grain boundaries and in the amorphous interphase in mouse incisor enamel. Front. Physiol. 6, 57 (2015).

    PubMed  PubMed Central  Article  Google Scholar 

  10. 10.

    Zhang, Y.-R., Du, W., Zhou, X.-D. & Yu, H.-Y. Review of research on the mechanical properties of the human tooth. Int. J. Oral Sci. 6, 61–69 (2014).

    PubMed  PubMed Central  Article  Google Scholar 

  11. 11.

    Robinson, C. et al. The chemistry of enamel caries. Crit. Rev. Oral Biol. Med. 11, 481–495 (2000).

    CAS  PubMed  Article  Google Scholar 

  12. 12.

    Yanagisawa, T. & Miake, Y. High-resolution electron microscopy of enamel-crystal demineralization and remineralization in carious lesions. J. Electron Microsc. 52, 605–613 (2003).

    CAS  Article  Google Scholar 

  13. 13.

    Reyes-Gasga, J., Hemmerle, J. & Bres, E. F. Aberration-corrected transmission electron microscopy study of the central dark line defect in human tooth enamel crystals. Microsc. Microanal. 22, 1047–1055 (2016).

    ADS  CAS  PubMed  Article  PubMed Central  Google Scholar 

  14. 14.

    Hart, J. L. et al. Direct detection electron energy-loss spectroscopy: a method to push the limits of resolution and sensitivity. Sci. Rep. 7, 8243 (2017).

    ADS  PubMed  PubMed Central  Article  CAS  Google Scholar 

  15. 15.

    de Juan, A. & Tauler, R. Multivariate curve resolution (MCR) from 2000: progress in concepts and applications. Crit. Rev. Anal. Chem. 36, 163–176 (2006).

    Article  CAS  Google Scholar 

  16. 16.

    Gordon, L. M., Tran, L. & Joester, D. Atom probe tomography of apatites and bone-type mineralized tissues. ACS Nano 6, 10667–10675 (2012).

    CAS  PubMed  Article  PubMed Central  Google Scholar 

  17. 17.

    Gault, B., Moody, M. P., Cairney, J. M. & Ringer, S. P. Atom Probe Microscopy (Springer, 2012).

  18. 18.

    Robinson, C., Kirkham, J., Brookes, S. J., Bonass, W. A. & Shore, R. C. Int. J. Dev. Biol. The chemistry of enamel development. 39, 145–152 (1995).

    CAS  Google Scholar 

  19. 19.

    Robinson, C., Weatherell, J. A. & Hallsworth, A. S. Distribution of magnesium in mature human enamel. Caries Res. 15, 70–77 (1981).

    CAS  PubMed  Article  PubMed Central  Google Scholar 

  20. 20.

    Laurencin, D. et al. Magnesium incorporation into hydroxyapatite. Biomaterials 32, 1826–1837 (2011).

    CAS  PubMed  Article  PubMed Central  Google Scholar 

  21. 21.

    Shannon, R. D. & Prewitt, C. T. Effective ionic radii in oxides and fluorides. Acta Crystallogr. B 25, 925–946 (1969).

    CAS  Article  Google Scholar 

  22. 22.

    Hughes, J. M., Cameron, M. & Crowley, K. D. Structural variations in natural F, OH, and Cl apatites. Am. Mineral. 74, 870–876 (1989).

    CAS  Google Scholar 

  23. 23.

    LeGeros, R. Z., Sakae, T., Bautista, C., Retino, M. & LeGeros, J. P. Magnesium and carbonate in enamel and synthetic apatites. Adv. Dent. Res. 10, 225–231 (1996).

    CAS  PubMed  Article  Google Scholar 

  24. 24.

    Ben Abdelkader, S., Khattech, I., Rey, C. & Jemal, M. Synthése, caractérisation et thermochimie d’apatites calco-magnésiennes hydroxylées et fluorées. Thermochim. Acta 376, 25–36 (2001).

    Article  Google Scholar 

  25. 25.

    Deymier, A. C. et al. Protein-free formation of bone-like apatite: new insights into the key role of carbonation. Biomaterials 127, 75–88 (2017).

    CAS  PubMed  PubMed Central  Article  Google Scholar 

  26. 26.

    Voegel, J. C. & Frank, R. M. Stages in dissolution of human enamel crystals in dental caries. Calcif. Tissue Res. 24, 19–27 (1977).

    CAS  PubMed  Article  PubMed Central  Google Scholar 

  27. 27.

    Tohda, H., Takuma, S. & Tanaka, N. Intercrystalline structure of enamel crystals affected by caries. J. Dent. Res. 66, 1647–1653 (1987).

    CAS  PubMed  Article  Google Scholar 

  28. 28.

    Gao, H. J., Ji, B. H., Jager, I. L., Arzt, E. & Fratzl, P. Materials become insensitive to flaws at nanoscale: lessons from nature. Proc. Natl Acad. Sci. USA 100, 5597–5600 (2003).

    ADS  CAS  PubMed  PubMed Central  Article  Google Scholar 

  29. 29.

    Yahyazadehfar, M. et al. On the mechanics of fatigue and fracture in teeth. Appl. Mech. Rev. 66, 030803 (2014).

    ADS  Article  Google Scholar 

  30. 30.

    Yilmaz, E. D., Schneider, G. A. & Swain, M. V. Influence of structural hierarchy on the fracture behaviour of tooth enamel. Phil. Trans. R. Soc. A 373, 1–20 (2015).

    CAS  Article  Google Scholar 

  31. 31.

    Langelier, B., Wang, X. & Grandfield, K. Atomic scale chemical tomography of human bone. Sci. Rep. 7, 39958 (2017).

    ADS  CAS  PubMed  PubMed Central  Article  Google Scholar 

  32. 32.

    Stoffers, A. et. al. Correlating atom probe tomography with atomic-resolved scanning transmission electron microscopy: example of segregation at silicon grain boundaries. Microsc. Microanal. 23, 291–299 (2017).

    ADS  CAS  PubMed  Article  Google Scholar 

  33. 33.

    Daculsi, G. & Kerebel, B. High-resolution electron-microscope study of human enamel crystallites — size, shape, and growth. J. Ultrastruct. Res. 65, 163–172 (1978).

    CAS  PubMed  Article  Google Scholar 

  34. 34.

    Beniash, E., Metzler, R. A., Lam, R. S. & Gilbert, P. U. Transient amorphous calcium phosphate in forming enamel. J. Struct. Biol. 166, 133–143 (2009).

    CAS  PubMed  PubMed Central  Article  Google Scholar 

  35. 35.

    Robinson, C., Fuchs, P. & Weatherell, J. A. The appearance of developing rat incisor enamel using a freeze fracturing technique. J. Cryst. Growth 53, 160–165 (1981).

    ADS  CAS  Article  Google Scholar 

  36. 36.

    Kirkham, J. et al. Self-assembling peptide scaffolds promote enamel remineralization. J. Dent. Res. 86, 426–430 (2007).

    CAS  PubMed  Article  Google Scholar 

  37. 37.

    Luder, H. U., Gerth-Kahlert, C., Ostertag-Benzinger, S. & Schorderet, D. F. Dental phenotype in Jalili syndrome due to a c.1312 dupC homozygous mutation in the CNNM4 gene. PLoS ONE 8, e78529 (2013).

    ADS  CAS  PubMed  PubMed Central  Article  Google Scholar 

  38. 38.

    Yamazaki, D. et al. Basolateral Mg2+ extrusion via CNNM4 mediates transcellular Mg2+ transport across epithelia: a mouse model. PLoS Genet. 9, e1003983 (2013).

    PubMed  PubMed Central  Article  CAS  Google Scholar 

  39. 39.

    Nakano, Y. et al. A critical role of TRPM7 as an ion channel protein in mediating the mineralization of the craniofacial hard tissues. Front. Physiol. 7, 258 (2016).

    PubMed  PubMed Central  Article  Google Scholar 

  40. 40.

    Aoba, T., Shimoda, S. & Moreno, E. C. Labile or surface pools of magnesium, sodium, and potassium in developing porcine enamel mineral. J. Dent. Res. 71, 1826–1831 (1992).

    CAS  PubMed  Article  PubMed Central  Google Scholar 

  41. 41.

    Hubbard, M. J., Mangum, J. E., Perez, V. A., Nervo, G. J. & Hall, R. K. Molar hypomineralisation: a call to arms for enamel researchers. Front. Physiol. 8, 546 (2017).

    PubMed  PubMed Central  Article  Google Scholar 

  42. 42.

    Park, Y. C. et al. Use of permanent marker to deposit a protection layer against FIB damage in TEM specimen preparation. J. Microsc. 255, 180–187 (2014).

    CAS  PubMed  Article  Google Scholar 

  43. 43.

    Zachman, M. J., Tu, Z. Y., Choudhury, S., Archer, L. A. & Kourkoutis, L. F. Cryo-STEM mapping of solid-liquid interfaces and dendrites in lithium-metal batteries. Nature 560, 345–349 (2018).

    ADS  CAS  PubMed  Article  Google Scholar 

  44. 44.

    Ravel, B. & Newville, M. ATHENA, ARTEMIS, HEPHAESTUS: data analysis for X-ray absorption spectroscopy using IFEFFIT. J. Synchrotron Radiat. 12, 537–541 (2005).

    CAS  Article  Google Scholar 

  45. 45.

    Antao, S. M., Mulder, W. H., Hassan, I., Crichton, W. A. & Parise, J. B. Cation disorder in dolomite, CaMg(CO3)2, and its influence on the aragonite + magnesite ↔ dolomite reaction boundary. Am. Mineral. 89, 1142–1147 (2004).

    ADS  CAS  Article  Google Scholar 

  46. 46.

    Dollase, W. A. & Reeder, R. J. Crystal-structure refinement of huntite, CaMg3(CO3)4, with X-ray powder data. Am. Mineral. 71, 163–166 (1986).

    CAS  Google Scholar 

  47. 47.

    Calvo, C. & Gopal, R. Crystal structure of whitlockite from Palermo Quarry. Am. Mineral. 60, 120–133 (1975).

    CAS  Google Scholar 

  48. 48.

    Rehr, J. J. & Albers, R. C. Theoretical approaches to X-ray absorption fine structure. Rev. Mod. Phys. 72, 621–654 (2000).

    ADS  CAS  Article  Google Scholar 

  49. 49.

    Reeder, R. J., Lamble, G. M. & Northrup, P. A. XAFS study of the coordination and local relaxation around Co2+, Zn2+, Pb2+, and Ba2+ trace elements. Am. Mineral. 84, 1049–1060 (1999).

    ADS  CAS  Article  Google Scholar 

  50. 50.

    Holt, C. et al. Preparation of amorphous calcium-magnesium phosphates at pH 7 and characterization by x-ray absorption and fourier transform infrared spectroscopy. J. Cryst. Growth 92, 239–252 (1988).

    ADS  CAS  Article  Google Scholar 

  51. 51.

    Harries, J. E., Hukins, D. W. L., Holt, C. & Hasnain, S. S. Conversion of amorphous calcium phosphate into hydroxyapatite investigated by EXAFS spectroscopy. J. Cryst. Growth 84, 563–570 (1987).

    ADS  CAS  Article  Google Scholar 

  52. 52.

    Larson, D. J., Prosa, T. J., Ulfig, R. M., Geiser, B. P. & Kelly, T. F. Local Electrode Atom Probe Tomography: A User’s Guide (Springer Science and Business Media, 2013).

  53. 53.

    Thompson, K. et al. In situ site-specific specimen preparation for atom probe tomography. Ultramicroscopy 107, 131–139 (2007).

    CAS  PubMed  Article  Google Scholar 

  54. 54.

    Qi, M.-l., Xiao, G.-y. & Lu, Y.-p. Rapid hydrothermal synthesis of submillimeter ultralong flexible hydroxyapatite fiber using different pH regulators. Acta Metall. Sinica Engl. Lett. 29, 609–613 (2016).

    CAS  Article  Google Scholar 

  55. 55.

    Dolomanov, O. V., Bourhis, L. J., Gildea, R. J., Howard, J. A. K. & Puschmann, H. OLEX2: a complete structure solution, refinement and analysis program. J. Appl. Crystallogr. 42, 339–341 (2009).

    CAS  Article  Google Scholar 

  56. 56.

    Sheldrick, G. M. Crystal structure refinement with SHELXL. Acta Crystallogr. C 71, 3–8 (2015).

    MATH  Article  CAS  Google Scholar 

  57. 57.

    Perdew, J. P. et al. Restoring the density-gradient expansion for exchange in solids and surfaces. Phys. Rev. Lett. 100, 136406 (2008).

    ADS  PubMed  Article  CAS  PubMed Central  Google Scholar 

  58. 58.

    Giannozzi, P. et al. QUANTUM EXPRESSO: a modular and open-source software project for quantum simulations of materials. J. Phys. Condens. Matter 21, 395502 (2009).

    PubMed  Article  PubMed Central  Google Scholar 

  59. 59.

    Vanderbilt, D. Soft self-consistent pseudopotentials in a generalized eigenvalue formalism. Phys. Rev. B 41, 7892–7895 (1990).

    ADS  CAS  Article  Google Scholar 

  60. 60.

    Dal Corso, A. Pseudopotentials periodic table: from H to Pu. Comput. Mater. Sci 95, 337–350 (2014).

    CAS  Article  Google Scholar 

  61. 61.

    Babushkin, O., Lindbäck, T., Holmgren, A., Li, J. & Hermansson, L. Thermal expansion of hot isostatically pressed hydroxyapatite. J. Mater. Chem. 4, 413–415 (1994).

    CAS  Article  Google Scholar 

  62. 62.

    Rohatgi, A. WebPlotDigitizer Version 4.2 (2019).

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This work was supported in part by the National Institute of Health–National Institute of Dental and Craniofacial Research (NIH-NIDCR R03 DE025303-01, R01 DE025702-01), the National Science Foundation (DMR-1508399), the NSF Platform for the Accelerated Realization, Analysis and Discovery of Interface Materials (PARADIM) under Cooperative Agreement no. DMR-1539918, and the University of Virginia. K.A.D. was in part supported by a 3M fellowship. The Canadian National Sciences and Engineering Research Council in part supported L.M.G. K.A.D. and M.J.C. were supported in part by the Northwestern University Graduate School Cluster in Biotechnology, Systems and Synthetic Biology, which is affiliated with the Biotechnology Training Program. L.S. was supported by a Deutsche Forschungsgemeinschaft research fellowship (STE2689/1-1). This work made use of the following core facilities operated by Northwestern University: NUCAPT, which received support from NSF (DMR-0420532), ONR (N00014-0400798, N00014-0610539, N00014-0910781 and N00014-1712870), and the Initiative for Sustainability and Energy at Northwestern University (ISEN); MatCI; NUANCE and EPIC, which received support from the International Institute for Nanotechnology (IIN), the Keck Foundation, and the State of Illinois, through the IIN; IMSERC; the Jerome B. Cohen X-Ray Diffraction Facility; QBIC, which received support from NASA Ames Research Center (NNA06CB93G). NUCAPT, MatCI, NUANCE and EPIC were further supported by the MRSEC programme (NSF DMR-1720139) at the Materials Research Center; NUCAPT, NUANCE, EPIC and IMSERC were also supported by the Soft and Hybrid Nanotechnology Experimental (SHyNE) Resource (NSF ECCS-1542205). This work made use of the Cornell Center for Materials Research (CCMR) Shared Facilities supported through the NSF MRSEC Program (no. DMR-1719875). The Titan Themis 300 was acquired through NSF-MRI-1429155, with additional support from Cornell University, the Weill Institute, and the Kavli Institute at Cornell. This work made use of the Rivanna cluster maintained by the Advanced Research Computing Services at the University of Virginia. Portions of this work were performed at the Canadian Light Source (CLS), which received support from The Natural Sciences and Engineering Research Council of Canada, the National Research Council of Canada, the Canadian Institutes of Health Research, the Province of Saskatchewan, Western Economic Diversification Canada, and the University of Saskatchewan. The authors thank P. Akers, M. Stohle and G. Borden for providing de-identified human premolars, and C. Malliakas, K. MacRenaris, M. Thomas and especially K. Rice for technical support.

Author information




The experiments and simulations were designed by K.A.D., P.J.M.S., L.S., P.V.B., J.M.R., D.J. STEM experiments were performed by P.J.M.S., B.H.G. and M.J.Z., with additional help in analysis and simulations provided by M.J.Z. and L.F.K. APT data were collected and analysed by K.A.D., with D.J. assisting the analysis. The finite-element model was developed by K.A.D. and D.J. using DFT calculations performed by P.V.B., and synthetic Mg-rich OHAp crystals made and analysed by L.S. XAS data were collected and analysed by L.M.G. and M.J.C. K.A.D., P.J.M.S., B.H.G., P.V.B., M.J.Z., L.F.K., J.M.R. and D.J. were all involved in preparing the manuscript.

Corresponding author

Correspondence to Derk Joester.

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The authors declare no competing interests.

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Supplementary information

Supplementary Information

This file contains Supplementary Methods, Tables, Discussion, and References, organized by experimental technique (1: STEM; 2: XAS; 3: APT; 4: FEM; 5: SEM) with an additional chapter that details the proposed model for amelogenesis in greater detail. This section contains 21 Supplementary Figures, 9 Supplementary Tables, and 40 references.

Reporting Summary

Supplementary Data

This zipped file contains source data for Supplementary Figures 4–7 and 14–17.

Video 1

Ion positions in a human enamel crystallite. All 24Mg2+ (magenta), 40Ca19F+ (blue), 23Na+ (turquoise), and COxHy+ ions (red) are rendered for a 30 nm thick slice through a human enamel crystallite (crystallite D in Supplementary Fig. S10a). Note that dataset was rotated such that view direction (x axis) is approximately parallel to the Mg layers. The animation shows rotation about the z axis, which is normal to the Mg layers. This visualization was scripted using the Matlab R2019b platform (The MathWorks).

Video 2

Core-shell and sandwich structure of human enamel crystallite. The reconstruction was rotated as in Video 1, voxelized (1 nm isotropic voxels) and smoothed. Iso-concentration surfaces and iso-caps for 24Mg2+ (magenta, ciso = 0.1 nm−3), 23Na+ (turquoise, 0.3 nm−3), and COxHy+ ions (red, 0.12 nm−3) were rendered together with that for 40Ca19F+ (blue, 0.07 nm−3) for the same slice as in Video 1, but ions outside the central crystallite are not shown. The animation shows one revolution about the z axis, followed by an oscillatory tilt series about the y axis. This visualization was scripted using the Matlab R2019b platform (The MathWorks).

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DeRocher, K.A., Smeets, P.J.M., Goodge, B.H. et al. Chemical gradients in human enamel crystallites. Nature 583, 66–71 (2020).

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