In Silico Study of Nanoparticle Clusters (LDH) and Different Intercalates: NO3

- and DNA Strands

P. Tran, S. Smith

Centre for Computational Molecular Science and ARC Center for Functional Nanomaterials

Outline

2

• Introduction– Hydrotalcites– Layered Double Hydroxides

• Background– Scientific Relevance– General Mechanism– Problematic

• Computer Simulations– Models– Forcefields– MD Simulation Results

• Conclusion

Introduction

3

Hydrotalcites

• Hydrotalcites Discovered in the 19th Century by Manasse• Permanent Positive Layer Charges• Significant Anion-Exchange Capacities• Large Surface Area

» Catalysis

» Medicine

» Oil-Field Technology

Manasse, E. Atti della Accademia Nazionale dei Lincei, Classe di Scienze Fisiche, Matematiche e Naturali, Rendiconti 1915, 24, 285-289

Introduction

4

LDH Crystal

• Anionic Clay = Hydrotalcites-like structure:

• Layered Double Hydroxides

• Space-Group: • Cell Length (Ǻ): a=b=3.148; c=4.779• Cell Angle: α=β=90; γ=120• Symmetry: Hexagonal

1 2 / 2[ ( ) ] [ ]II III x n

x x x nM M OH A mH O

2 26 2 16 3 2[ ( ) ] 4Mg Al OH CO H O

3 1P m

Introduction

5

LDH Crystal

3D-Polygone Representation

Background Scientific Relevance

As-myc-LDH HL-60+4 days

LDH HL-60+4 days

HL-60

Choy, J.-H.; Park, J.-S.; Kwak, S.-Y.; Jeong, Y.-J.; Han, Y.-S. Molecular Crystals and Liquid Crystals Science and Technology, Section A: Molecular Crystals and Liquid Crystals 2000, 341, 425-429

Background

7

General Mechanism

Choy, J.-H.; Park, J.-S.; Kwak, S.-Y.; Jeong, Y.-J.; Han, Y.-S. Molecular Crystals and Liquid Crystals Science and Technology, Section A: Molecular Crystals and Liquid Crystals 2000, 341, 425-429

+ + + +

+ + + +

+ + + +

+ + + +

Nanohybridization

LDH Bio-LDH Nanohybrid

Endocytosis

Nucleus

Cytoplasm

Endocytosis

8.7 Ǻ 23.9 Ǻ

Computer Simulations

8

Problematic

Choy, J.-H.; Park, J.-S.; Kwak, S.-Y.; Jeong, Y.-J.; Han, Y.-S. Molecular Crystals and Liquid Crystals Science and Technology, Section A: Molecular Crystals and Liquid Crystals 2000, 341, 425-429

19.1 Å

DNA length: 12 base-pairsContraction of double helical DNA strands upon insertion

Computer Simulations

9

Models

LDH

DNA

H2O

Computer Simulations

10

Methodology

ABC

XYZ

FORCEFIELD

MD CONDITIONS

XYZ

FORCEFIELD

MD CONDITIONS

EVOLUTION PARAMETERS

OUTPUT Files

Material StudioNucgen

Xleap

Sander

TOPOLOGYINPUTS

PDB Files

Analysis

Computer Simulations Forcefield

11

  DO,i(kcal/mol) RO,I(Å) qi(e)

Mg 9.03E-07 5.91 1.36

Al 1.33E-06 4.79 1.5752

O 0.1554 3.55 -1.0069

H - - 0.425

, ,

, , , ,

12 6

, ,,

, 0

( );

2

24

O i O j

O ij O ij O i O j

i j O ij O ijO ij

i j ij ij ij

R RR D D D

q q R RU D

r r r

Computer Simulations Forcefield

12

2 2 np 2 0 θ 0 0

b θ Φ

12 6* *i j ij ij

12 10ij ij ij ij

VE = K (b - b ) + H (θ - θ ) + 1+ cos(nΦ - Φ ) +

2

qq C Dr r ε - 2 + + -

r r ε r r r

N

C

N

CT

CT

C

O

H

OH1

CT

HC

HCHC

-0.48

0.52

-0.58

0.37

-0.58

0.77

-0.3

-0.01

0.16

-0.41

0.12

backbone

0.07

Cornell, W. D.; Cieplak, P.; Bayly, C. I.; Gould, I. R.; Merz, K. M., Jr.; Ferguson, D. M.; Spellmeyer, D. C.; Fox, T.; Caldwell, J. W.; Kollman, P. A. Journal of the American Chemical Society, 1996; 118, 2309

Computer Simulations

13

MD Conditions

Periodic Boundary Conditions:

Parallelepiped MD Cell

• Conditions for MD Simulations• NPT ensemble• T=300 K• P=1 bar• δt=0.001 ps, Steps=100 000• Cutoff=8 Å, PME

Systems:

LDH-DNA

12 base-pairs

MG-Al surface: 45*45 Å (450 Atoms)

VdW box=66*94*64 Å

Atoms: 8505 Atoms

Computer Simulations Simulation

14

Computer Simulations

15

Early Results

LDH-GC

Short 200 ps runDisorganised Ionic metal plane

Computer Simulations Early Results16

LDH-GC

Short 200 ps runDisorganised Ionic metal plane

Computer Simulations Current Work

17

Acknowledgments

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• CCMS– Prof. Sean Smith– Dr. Aijun Du

• ARC Centre for Functional Nanomaterials– Prof. G. Q. Lu– Dr. Z. P. Xu