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Slidedeck Doctoral Defense - Public

SobrinoM
November 01, 2017

Slidedeck Doctoral Defense - Public

Slidedeck on confinement induced assembly of anisotropic particles

SobrinoM

November 01, 2017
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  1. Confinement induced assembly of anisotropic particles: patchy colloids and water

    molecules Mario Sobrino Fern´ andez Supervised by: Prof. Dr. Francois Peeters Dr. Mehdi Neek-Amal Dr. Vyacheslav Misko
  2. Anisotropic particles Directed assemblies (JPs) Confinement induced assembly of anisotropic

    particles: patchy colloids and water molecules List of publications: 9/36
  3. Anisotropic particles Directed assemblies (JPs) Confinement induced assembly of anisotropic

    particles: patchy colloids and water molecules List of publications: 1. Self-assembly of Janus particles confined in a channel, M. Sobrino Fern´ andez, V. R. Misko, and F. M. Peeters, Physical Review E, 2014, 89, 022306. 9/36
  4. Anisotropic particles Directed assemblies (JPs) Confinement induced assembly of anisotropic

    particles: patchy colloids and water molecules List of publications: 1. Self-assembly of Janus particles confined in a channel, M. Sobrino Fern´ andez, V. R. Misko, and F. M. Peeters, Physical Review E, 2014, 89, 022306. 2. Self-assembly of Janus particles into helices with tunable pitch, M. Sobrino Fern´ andez, V. R. Misko, and F. M. Peeters, Physical Review E, 2015, 92, 042309. 9/36
  5. Anisotropic particles Directed assemblies (JPs) Confinement induced assembly of anisotropic

    particles: patchy colloids and water molecules List of publications: 1. Self-assembly of Janus particles confined in a channel, M. Sobrino Fern´ andez, V. R. Misko, and F. M. Peeters, Physical Review E, 2014, 89, 022306. 2. Self-assembly of Janus particles into helices with tunable pitch, M. Sobrino Fern´ andez, V. R. Misko, and F. M. Peeters, Physical Review E, 2015, 92, 042309. 3. AA-stacked bilayer square ice between graphene layers, M. Sobrino Fern´ andez, M. Neek-Amal, and F. M. Peeters, Physical Review B, 2015, 92, 245428. 9/36
  6. Anisotropic particles Directed assemblies (JPs) Confinement induced assembly of anisotropic

    particles: patchy colloids and water molecules List of publications: 1. Self-assembly of Janus particles confined in a channel, M. Sobrino Fern´ andez, V. R. Misko, and F. M. Peeters, Physical Review E, 2014, 89, 022306. 2. Self-assembly of Janus particles into helices with tunable pitch, M. Sobrino Fern´ andez, V. R. Misko, and F. M. Peeters, Physical Review E, 2015, 92, 042309. 3. AA-stacked bilayer square ice between graphene layers, M. Sobrino Fern´ andez, M. Neek-Amal, and F. M. Peeters, Physical Review B, 2015, 92, 245428. 4. Electric-field-induced structural changes in water confined between two graphene layers, M. Sobrino Fern´ andez, F. M. Peeters, and M. Neek-Amal, Physical Review B, 2016, 94, 045436. 9/36
  7. Anisotropic particles Directed assemblies (JPs) Confinement induced assembly of anisotropic

    particles: patchy colloids and water molecules List of publications: 1. Self-assembly of Janus particles confined in a channel, M. Sobrino Fern´ andez, V. R. Misko, and F. M. Peeters, Physical Review E, 2014, 89, 022306. 2. Self-assembly of Janus particles into helices with tunable pitch, M. Sobrino Fern´ andez, V. R. Misko, and F. M. Peeters, Physical Review E, 2015, 92, 042309. 3. AA-stacked bilayer square ice between graphene layers, M. Sobrino Fern´ andez, M. Neek-Amal, and F. M. Peeters, Physical Review B, 2015, 92, 245428. 4. Electric-field-induced structural changes in water confined between two graphene layers, M. Sobrino Fern´ andez, F. M. Peeters, and M. Neek-Amal, Physical Review B, 2016, 94, 045436. 5. Reversible structural transition in nanoconfined ice, V. Satarifard, M. Mousaei, M. Sobrino Fern´ andez, J. Dix, J. Beheshtian, P. Carbone, F. M. Peeters, and M. Neek-Amal, under review. 9/36
  8. Anisotropic particles Directed assemblies (JPs) Confinement induced assembly of anisotropic

    particles: patchy colloids and water molecules List of publications: 1. Self-assembly of Janus particles confined in a channel, M. Sobrino Fern´ andez, V. R. Misko, and F. M. Peeters, Physical Review E, 2014, 89, 022306. 2. Self-assembly of Janus particles into helices with tunable pitch, M. Sobrino Fern´ andez, V. R. Misko, and F. M. Peeters, Physical Review E, 2015, 92, 042309. 3. AA-stacked bilayer square ice between graphene layers, M. Sobrino Fern´ andez, M. Neek-Amal, and F. M. Peeters, Physical Review B, 2015, 92, 245428. 4. Electric-field-induced structural changes in water confined between two graphene layers, M. Sobrino Fern´ andez, F. M. Peeters, and M. Neek-Amal, Physical Review B, 2016, 94, 045436. 5. Reversible structural transition in nanoconfined ice, V. Satarifard, M. Mousaei, M. Sobrino Fern´ andez, J. Dix, J. Beheshtian, P. Carbone, F. M. Peeters, and M. Neek-Amal, under review. 9/36
  9. Anisotropic particles Directed assemblies (JPs) Confinement induced assembly of anisotropic

    particles: patchy colloids and water molecules List of publications: 1. Self-assembly of Janus particles confined in a channel, M. Sobrino Fern´ andez, V. R. Misko, and F. M. Peeters, Physical Review E, 2014, 89, 022306. 2. Self-assembly of Janus particles into helices with tunable pitch, M. Sobrino Fern´ andez, V. R. Misko, and F. M. Peeters, Physical Review E, 2015, 92, 042309. 3. AA-stacked bilayer square ice between graphene layers, M. Sobrino Fern´ andez, M. Neek-Amal, and F. M. Peeters, Physical Review B, 2015, 92, 245428. 4. Electric-field-induced structural changes in water confined between two graphene layers, M. Sobrino Fern´ andez, F. M. Peeters, and M. Neek-Amal, Physical Review B, 2016, 94, 045436. 5. Reversible structural transition in nanoconfined ice, V. Satarifard, M. Mousaei, M. Sobrino Fern´ andez, J. Dix, J. Beheshtian, P. Carbone, F. M. Peeters, and M. Neek-Amal, under review. 9/36
  10. Table of contents 1. Introduction Graphene Molecular structure of ice

    2. Experiment: Square ice in graphene nanocapillaries 3. Molecular dynamics 4. Square ice? Ice monolayer Ice bilayer Multi-layered ice 5. Concluding remarks 10/36
  11. Introduction Graphene What is graphene? Graphene can be isolated from

    graphite Graphite → pencil lead • Layered, planar structure 11/36
  12. Introduction Graphene What is graphene? Graphene can be isolated from

    graphite Graphite → pencil lead • Layered, planar structure • Within layers: covalent bonds form a honeycomb lattice 11/36
  13. Introduction Graphene What is graphene? Graphene can be isolated from

    graphite Graphite → pencil lead • Layered, planar structure • Within layers: covalent bonds form a honeycomb lattice • Weak vdW bonds between layers 11/36
  14. Introduction Graphene What is graphene? Graphene can be isolated from

    graphite Graphite → pencil lead • Layered, planar structure • Within layers: covalent bonds form a honeycomb lattice • Weak vdW bonds between layers Single graphite layer = Graphene 11/36
  15. Introduction Graphene What is graphene? Graphene can be isolated from

    graphite Graphite → pencil lead • Layered, planar structure • Within layers: covalent bonds form a honeycomb lattice • Weak vdW bonds between layers Single graphite layer = Graphene • Thinnest, lightest, strongest compound 11/36
  16. Introduction Graphene What is graphene? Graphene can be isolated from

    graphite Graphite → pencil lead • Layered, planar structure • Within layers: covalent bonds form a honeycomb lattice • Weak vdW bonds between layers Single graphite layer = Graphene • Thinnest, lightest, strongest compound • Best conductor of heat & electricity (at T=300K) 11/36
  17. Introduction Fabrication of graphene 2004: Graphene isolated from graphite using

    mechanical exfoliation Also known as the ”scotch tape method” 12/36
  18. Introduction Fabrication of graphene 2004: Graphene isolated from graphite using

    mechanical exfoliation Also known as the ”scotch tape method” 1. placed flake of graphite onto plastic tape 12/36
  19. Introduction Fabrication of graphene 2004: Graphene isolated from graphite using

    mechanical exfoliation Also known as the ”scotch tape method” 1. placed flake of graphite onto plastic tape 2. folded sticky side over the flake 12/36
  20. Introduction Fabrication of graphene 2004: Graphene isolated from graphite using

    mechanical exfoliation Also known as the ”scotch tape method” 1. placed flake of graphite onto plastic tape 2. folded sticky side over the flake 3. Pulled apart, cleaving the flake in two 12/36
  21. Introduction Fabrication of graphene 2004: Graphene isolated from graphite using

    mechanical exfoliation Also known as the ”scotch tape method” 1. placed flake of graphite onto plastic tape 2. folded sticky side over the flake 3. Pulled apart, cleaving the flake in two 4. Repeat...until receiving a Nobel prize (2010) 12/36
  22. Introduction Molecular structure of ice Bulk ice Naturally formed ice

    (Ih) Crystalline structure based on water molecules 15/36
  23. Introduction Molecular structure of ice Bulk ice Naturally formed ice

    (Ih) Crystalline structure based on water molecules 16 crystalline forms 15/36
  24. Introduction Molecular structure of ice Bulk ice Naturally formed ice

    (Ih) Crystalline structure based on water molecules 16 crystalline forms 17/36
  25. Introduction Molecular structure of ice Bulk ice Naturally formed ice

    (Ih) Crystalline structure based on water molecules 16 crystalline forms Hydrogen bonds between adjacent oxygen and hydrogen atoms 17/36
  26. Introduction Molecular structure of ice Bulk ice Naturally formed ice

    (Ih) Crystalline structure based on water molecules 16 crystalline forms Hydrogen bonds between adjacent oxygen and hydrogen atoms Bernal-Fowler Ice-rules 17/36
  27. Introduction Molecular structure of ice Bulk ice Naturally formed ice

    (Ih) Crystalline structure based on water molecules 16 crystalline forms Hydrogen bonds between adjacent oxygen and hydrogen atoms Bernal-Fowler Ice-rules 1. Each oxygen is covalently bonded to two hydrogen atoms and forms two hydrogen bonds between other oxygen atoms. 17/36
  28. Introduction Molecular structure of ice Bulk ice Naturally formed ice

    (Ih) Crystalline structure based on water molecules 16 crystalline forms Hydrogen bonds between adjacent oxygen and hydrogen atoms Bernal-Fowler Ice-rules 1. Each oxygen is covalently bonded to two hydrogen atoms and forms two hydrogen bonds between other oxygen atoms. 2. There is precisely one hydrogen between each pair of oxygen atoms. 17/36
  29. Introduction Ice between graphene layers Interested in the behaviour of

    water when confined by graphene layers 18/36
  30. Introduction Ice between graphene layers Interested in the behaviour of

    water when confined by graphene layers ... Why? 18/36
  31. Square ice in graphene nanocapillaries Experiment Square ice in graphene

    nanocapillaries: Experiment Setup 1. Graphene-water-graphene sandwich 2. Dry overnight 3. Water bubbles remain trapped between the two hydrophobic layers 21/36
  32. Square ice in graphene nanocapillaries Experiment Square ice in graphene

    nanocapillaries: Experiment 5 nm Setup 1. Graphene-water-graphene sandwich 2. Dry overnight 3. Water bubbles remain trapped between the two hydrophobic layers TEM experiment Square lattice with rOO = 2.83 ± 0.03˚ A No alignment with the graphene lattice Few monolayers thick 21/36
  33. Square ice in graphene nanocapillaries Experiment Square ice in graphene

    nanocapillaries: Analysis Analysis Comparison between experimental and simulated TEM images 22/36
  34. Square ice in graphene nanocapillaries Experiment Square ice in graphene

    nanocapillaries: Analysis Analysis Comparison between experimental and simulated TEM images The Claim Cubic crystal lattice corresponding with 90◦ hydrogen bonding both within and between layers 22/36
  35. Square ice in graphene nanocapillaries Remarks Bernal-Fowler Ice-rules 1. Each

    oxygen is covalently bonded to two hydrogen atoms and forms two hydrogen bonds between other oxygen atoms. 2. There is precisely one hydrogen between each pair of oxygen atoms. 23/36
  36. Square ice in graphene nanocapillaries Remarks Bernal-Fowler Ice-rules 1. Each

    oxygen is covalently bonded to two hydrogen atoms and forms two hydrogen bonds between other oxygen atoms. 2. There is precisely one hydrogen between each pair of oxygen atoms. 23/36
  37. Square ice in graphene nanocapillaries Remarks Bernal-Fowler Ice-rules 1. Each

    oxygen is covalently bonded to two hydrogen atoms and forms two hydrogen bonds between other oxygen atoms. 2. There is precisely one hydrogen between each pair of oxygen atoms. Bond angle between hydrogen atoms is 90◦ 23/36
  38. Square ice in graphene nanocapillaries Remarks Bernal-Fowler Ice-rules 1. Each

    oxygen is covalently bonded to two hydrogen atoms and forms two hydrogen bonds between other oxygen atoms. 2. There is precisely one hydrogen between each pair of oxygen atoms. Bond angle between hydrogen atoms is 90◦ Requires ≈ 3 eV per water molecule 23/36
  39. Square ice in graphene nanocapillaries Remarks Bernal-Fowler Ice-rules 1. Each

    oxygen is covalently bonded to two hydrogen atoms and forms two hydrogen bonds between other oxygen atoms. 2. There is precisely one hydrogen between each pair of oxygen atoms. Bond angle between hydrogen atoms is 90◦ Requires ≈ 3 eV per water molecule Bond dissociation energy is ≈ 4.5 eV 23/36
  40. Molecular dynamics Initial Configuration (r, v) Calculate Forces Predict subsequent

    (r, v) Sample Apply External Conditions Measure physical quantities of interest More time-steps needed? Stop - Numerical Integration - Energy - Temperature - Stresses - Thermostat - Pressure control - Boundary Conditions MD Loop 25/36
  41. Molecular dynamics ReaxFF Model: ReaxFF Simulate chemical reaction pathways in

    a classical simulation box 1. Continuous bond formation/breaking 26/36
  42. Molecular dynamics ReaxFF Model: ReaxFF Simulate chemical reaction pathways in

    a classical simulation box 1. Continuous bond formation/breaking Bond-order parameter 26/36
  43. Molecular dynamics ReaxFF Model: ReaxFF ReaxFF DFT Simulate chemical reaction

    pathways in a classical simulation box 1. Continuous bond formation/breaking Bond-order parameter 2. Charge relaxation 26/36
  44. Molecular dynamics ReaxFF Model: ReaxFF ReaxFF DFT Simulate chemical reaction

    pathways in a classical simulation box 1. Continuous bond formation/breaking Bond-order parameter 2. Charge relaxation 3. Long range, partially bonded configurations 26/36
  45. Molecular dynamics ReaxFF Model: ReaxFF ReaxFF DFT Simulate chemical reaction

    pathways in a classical simulation box 1. Continuous bond formation/breaking Bond-order parameter 2. Charge relaxation 3. Long range, partially bonded configurations 4. Molecular geometry: bond lengths, bond angles and torsional angles Bond stretching Angle bending Bond rotation (torsion) Non-bonded in- teractions 26/36
  46. Molecular dynamics ReaxFF MD excels in making an abstraction of

    the physical world. Hydrogen bond energy between molecules: 27/36
  47. Molecular dynamics ReaxFF MD excels in making an abstraction of

    the physical world. Hydrogen bond energy between molecules: 27/36
  48. Molecular dynamics ReaxFF MD excels in making an abstraction of

    the physical world. Hydrogen bond energy between molecules: EHbond = phb,1 [1 − exp (phb,2 · BOXH )] exp phb,3 rhb 0 rHZ + rHZ rhb 0 − 2 sin4 ΘXHZ 2 27/36
  49. Square ice? Methodology Methodology Replication study of the experiment using

    MD Two graphene layers encapsulate n water layers Interlayer distance 6.5 + 2.5(n − 1) ˚ A 34848 carbon atoms 5700n water molecules 28/36
  50. Square ice? Ice monolayer Experiment h [˚ A] 6.5 roo

    [˚ A] 2.83 ± 0.03  h d d = 0.53Å 29/36
  51. Square ice? Ice monolayer Experiment α-phase h [˚ A] 6.5

    6.5 roo [˚ A] 2.83 ± 0.03 2.84 ± 0.01   h d d = 0.53Å 29/36
  52. Square ice? Ice bilayer Experiment h [˚ A] 9 roo

    [˚ A] 2.83 ± 0.03 c [˚ A] 2.83 ± 0.03 d [˚ A] 3.11 ± 0.01  30/36
  53. Square ice? Ice bilayer Experiment h [˚ A] 9 roo

    [˚ A] 2.83 ± 0.03 c [˚ A] 2.83 ± 0.03 d [˚ A] 3.11 ± 0.01  30/36
  54. Square ice? Ice bilayer Experiment Bilayer h [˚ A] 9

    9 roo [˚ A] 2.83 ± 0.03 2.88 ± 0.01 c [˚ A] 2.83 ± 0.03 3.24 ± 0.01 d [˚ A] 3.11 ± 0.01 2.88 ± 0.01   30/36
  55. Square ice? Multi-layered ice Cubic crystal lattice corresponding with 90◦

    hydrogen bonding both within and between layers 33/36
  56. Square ice? Multi-layered ice Cubic crystal lattice corresponding with 90◦

    hydrogen bonding both within and between layers Layered structure of flat ice where all H-bonds lie in the same plane. 33/36
  57. Square ice? Multi-layered ice Cubic crystal lattice corresponding with 90◦

    hydrogen bonding both within and between layers Layered structure of flat ice where all H-bonds lie in the same plane. Bernal-Fowler rules are conserved 33/36
  58. Square ice? Multi-layered ice Cubic crystal lattice corresponding with 90◦

    hydrogen bonding both within and between layers Layered structure of flat ice where all H-bonds lie in the same plane. Bernal-Fowler rules are conserved Hydrogen bond angle remains unaltered 33/36
  59. Square ice? Multi-layered ice Cubic crystal lattice corresponding with 90◦

    hydrogen bonding both within and between layers Layered structure of flat ice where all H-bonds lie in the same plane. Bernal-Fowler rules are conserved Hydrogen bond angle remains unaltered 33/36
  60. Concluding remarks Molecular dynamics simulations of confined anisotropic particles Ice

    between graphene layers Similar to the experiment: 34/36
  61. Concluding remarks Molecular dynamics simulations of confined anisotropic particles Ice

    between graphene layers Similar to the experiment: 1. Flat layers, parallel to the graphene sheets 34/36
  62. Concluding remarks Molecular dynamics simulations of confined anisotropic particles Ice

    between graphene layers Similar to the experiment: 1. Flat layers, parallel to the graphene sheets In contrast with the experiment: 34/36
  63. Concluding remarks Molecular dynamics simulations of confined anisotropic particles Ice

    between graphene layers Similar to the experiment: 1. Flat layers, parallel to the graphene sheets In contrast with the experiment: 1. Hydrogen bonds between neighbouring molecules within each layer 34/36
  64. Concluding remarks Molecular dynamics simulations of confined anisotropic particles Ice

    between graphene layers Similar to the experiment: 1. Flat layers, parallel to the graphene sheets In contrast with the experiment: 1. Hydrogen bonds between neighbouring molecules within each layer 2. Interlayer configuration between AA and AB stacked 34/36
  65. Concluding remarks Molecular dynamics simulations of confined anisotropic particles Ice

    between graphene layers Similar to the experiment: 1. Flat layers, parallel to the graphene sheets In contrast with the experiment: 1. Hydrogen bonds between neighbouring molecules within each layer 2. Interlayer configuration between AA and AB stacked What about water permeation? 34/36
  66. Concluding remarks Molecular dynamics simulations of confined anisotropic particles Ice

    between graphene layers Similar to the experiment: 1. Flat layers, parallel to the graphene sheets In contrast with the experiment: 1. Hydrogen bonds between neighbouring molecules within each layer 2. Interlayer configuration between AA and AB stacked What about water permeation? Only important that confined water forms a layered structure 34/36
  67. Concluding remarks Molecular dynamics simulations of confined anisotropic particles Ice

    between graphene layers Similar to the experiment: 1. Flat layers, parallel to the graphene sheets In contrast with the experiment: 1. Hydrogen bonds between neighbouring molecules within each layer 2. Interlayer configuration between AA and AB stacked What about water permeation? Only important that confined water forms a layered structure For desalination purposes, pore sizes must be < 9 ˚ A 34/36
  68. Concluding remarks Molecular dynamics simulations of confined anisotropic particles Ice

    between graphene layers Similar to the experiment: 1. Flat layers, parallel to the graphene sheets In contrast with the experiment: 1. Hydrogen bonds between neighbouring molecules within each layer 2. Interlayer configuration between AA and AB stacked What about water permeation? Only important that confined water forms a layered structure For desalination purposes, pore sizes must be < 9 ˚ A ”Just for a laugh, we sealed a bottle of vodka with our membrane and found that the distilled solution became stronger and stronger with time” 34/36
  69. References References 1. S. C. Glotzer and M. J. Solomon,

    Anisotropy of building blocks and their assembly into complex structures, Nature Materials, vol. 6, no. 8, pp. 55762, (2007). 2. R. M. Erb,, N. J. Jenness, R. L. Clark, and B. B. Yellen, Towards Holonomic Control of Janus Particles in Optomagnetic Traps. Adv. Mater., 21: 48254829 (2009). 3. T. Nisisako, T. Torii, T. Takahashi, and Y. Takizawa, Synthesis of monodisperse bicolored janus particles with electrical anisotropy using a microfluidic co-flow system, Advanced Materials, vol. 18, no. 9, pp. 11521156, (2006). 4. L. Y. Wu, B. M. Ross, S. Hong, and L. P. Lee, Bioinspired nanocorals with decoupled cellular targeting and sensing functionality, Small, vol. 6, no. 4, pp. 503507, (2010). 5. Q. Chen, S. C. Bae, and S. Granick, Directed self-assembly of a colloidal kagome lattice, Nature, vol. 469, pp. 381384, (2011). 6. F. Sciortino, A. Giacometti, and G. Pastore, Phase diagram of janus particles, Phys. Rev. Lett., vol. 103, p. 237801, (2009). 7. R. Munroe, Water phase diagram http://xkcd.com/1561/ 8. M. Hao, Theoretical calculation of hydrogen-bonding strength for drug molecules, J. Chem. Theory Computat., vol. 2, p. 863-872, (2006). 9. G. Algara-Siller, O. Lehtinen, F. C. Wang, R. R. Nair, U. Kaiser, H. A. Wu, A. K. Geim, and I. V. Grigorieva, Square ice in graphene nanocapillaries, Nature, vol. 519, no. 24, pp. 443445, (2015). 35/36