biomolecule-material interface at the nanoscale: atomic structure, electronic properties, and energy...
TRANSCRIPT
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Biomolecule-Material Interface at the Nanoscale:atomic structure, electronic properties, and energy applications
Sheng Meng
Department of Physics and School of Engineering and Applied Sciences,
Harvard University
Colloquium Department of Physics and Astronomy, University of Mississippi
Jan. 31, 2008
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Biology is naturally nanoscale
Spinach aquaporin
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We need tools to manipulate …
• Substrates for investigating biomolecules• Biosensor for recognition and diagnosis • Implants for medical operation & recovery• Drug delivery• Building up bio-chips• Bio-nanotechnology
A hybrid bio-nano machine?
Schwegler, LLNL
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Bring Materials to Life
In Contact With a Cell
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A closer look: BIO|materials interfaceat nanoscale
Kasemo, Surf. Sci. (2002).
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Microscopic Understanding of BIO|materials Interface
OUTLINE
1. Water-surface interaction and a molecular view of hydrophilicity
2. DNA-carbon nanotube interaction and identification
3. Melanin structure and implications in phototechnology
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I. Water at surfaces
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Our strategy for water/surface
BondingH2O/Pt(111)Structure: monomer→multilayer
Vibration
H2O/metal
H2O/non-metal
Structure→Properties
Properties→Structure
Superhydrophilic
Wetting
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Density functional theory (DFT)
)...,,,( 21 Nrrr
Many-electron Schrödinger equation Single-particle Kohn-Sham equation2
21 )...,,,( Nrrr
)()(]['
)(')(
22
2
rErVrr
rdrrV
m iiixcexternal
Theorem II.
Theorem I.
)...,,,( 21 Nrrr
)(r
Calculation details:
• Plane-waves
• Pseudopotential(USPP,PAW)+GGA(PBE)
• Ab initio molecular dynamics (MD)
• Nudged Elastic Band for reaction barriers W. KohnNobel prize, 1998
•Advantages: 1. First-principles (=“parameter free”) Input: atomic numbers
2. Practicality. N ~ 1000, accuracy ~ 0.01 eV.
•Drawback: Unknown Vxc? Approximations: LDA
GGA
))(()( rVrV xcxc
))(),(()( rrVrV xcxc
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Time-dependent DFT (TDDFT) for electron dynamics
Our implementation:
• Real time
• Local bases: numeric atomic orbitals
• Parallelizable
• Order (N)
Biomolecules, nanomaterials
)(),,(ˆ)(),0(Given tttrH
t
ti
TDDFT:
Applications:
• Optical absorption (linear response)
• Excited state dynamics
• Chemical reactions
• Atom collision
• Quantum control (strong laser field)
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Multiscale modelling
Time: 10-18 10-15 10-12 10-9 10-6 10-3 100 s
Length: 0.1 1 10 100 1000 109 nmThe scale we are working on:
Adapted from
DOE (2006)
TDDFTAb initio MD
Classic MDNon-atomistic models
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Results
• Nearly atop, flat (14º), free rotation• dOH (0.98Å) elongated, HOH (105.
6º) broadened• Electron transfer (O→Pt) 0.02e• Diffusion barrier: 0.13 eV
Metal surfaces:
1.Simple structure.
2.Wide applications.
Single water adsorption
A Model System: H2O/Pt(111)
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304 meV/H2O
Water clusters
433
359
520
H-bond energy in dimer: >260 meV > 240 meV (free).
H-bonds enhanced upon adsorption.
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2D bilayers to 3D multilayers
H-up H-down 2 BL
• H-up: 512 meV
• H-down: 524 meV
• Half-dissociated: 291 meV No dissociation on Pt(111).
bottomup
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Nature of water-Pt bonds
H-up H-down
Singlemolecule Dimer
• Chemical bonding
• Lone pair-surface d states
• Localized at bottom layer
d-orbital
lone-pair
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Vibrational recognition
0 100 200 300 400 5000.00
0.02
0.04 H-down bilayer
438424
384
202196
91
6957
3416
6
In
tensi
ty (
arb
. un
its)
Vibrational Energy (meV)
0.00
0.04
0.08
53
H-up bilayer
467432
388
198
8769
32184
Meng et al., Phys. Rev. Lett. (2002).
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Summary of water/Pt
• Top sites, nearly flatly, various structures• Water doesn’t dissociate
• Local lone pair-dz2,dxz chemical bonds • H-bonds strengthened
• OH stretches for vibration recognition • Two types of H-bonds
Structure
Bonding
Vibration
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General trends: water-surface distance
Meng et al., Phys. Rev. B (2004); Phys. Rev. Lett (2003).
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cHydrophili
cHydrophobi
E
E
ads
HB
1
1
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Wetting order
Wetting order: RuRh Pd Pt Au
0
1
2
3
AuPtPdRhRu
EH
B/E
a
d7s1 d8s1 d9s1 d10s1
ω
hydrophobic
hydrophilic
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Ice tessellation on silica
Yang, Meng et al., Phys. Rev. Lett. (2004).
Water/-cristobalite (100)
2.82 Ǻ
3.16 Ǻ
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Inverse Design: Properties →Structure
Meng, Zhang, Kaxiras, Phys. Rev. Lett.(2006).
Why diamond?• Lattice match: 2% • Carbon only—biocompatible• Affinity to proteins/DNA: better than Si, Au• Additional merits: hardness, low friction etc• Low cost: Nanocrystalline
Na/K H/F
Applications• Self-cleaning• Scratch and fouling resistant• Heat transfer
A superhydrophilic biocompatible surfaceA superhydrophilic diamond surface
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Wettability before and after surface modification
1 2 3 4 5 6 7 8 90.1
1
10
Water Coverage (BL)
1ML H 1/3ML K+2/3ML H 1/3ML Na+2/3ML H 1/3ML Na+2/3ML F
Eb=0.674 eV
>Eice=0.670 eV
hydrophobic
hydrophilic
superhydrophilic
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Water/surface: Summary
BondingH2O/Pt(111)Structure: monomer→multilayer
Vibration
H2O/metal
H2O/non-metal
Structure→Properties
Properties→Structure
Superhydrophilic
Wetting
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II. DNA nucleoside interaction and identification with carbon nanotubes
Nano Letters 7, 45 (2007).Nano Letters 7, 663 (2007).
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Why DNA-carbon nanotube (CNT)?
Similarities:• Prototypical one-dimensional• Conducting properties: metal, semiconductor, or
insulator?
Differences: (single-stranded) DNA: CNT:• extremely flexible stiff• strongly hydrophilic hydrophobic• central in biology central in nanotechnology
Combine!
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d(GT)30/CNT
Poly(T)/CNT(10,0)Zheng et al., Science (2003); Nature Materials (2003).
It is also possible to wrap CNT using long genomic ssDNA (>>100 bases).Gigliotti et al., Nano Lett. (2006).
Structure of the single-strand DNA wrapped CNT
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Label-free DNA detection by electronic signals
Jeng et al., Nano Lett. (2006).
Ultimate goal:
Ultrafast DNA sequencing
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What’s missing?• The nature of DNA-CNT interaction• Its dependence on nucleoside identity
Our objective
• Single nucleoside/CNT interaction• Discriminate nucleosides based on electronic
features
MethodologyConfiguration space search: Force FieldsElectronic features: Density Functional
TheoryNucleoside identification: Artificial Neural
Network
DNA detection by electronic means:Is that possible at single-base resolution?
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DNA/CNT molecular dynamics
DNA wraps around CNT in a short time ~ 2 ns.
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Proposed experimental setup
Meng, Maragakis, Papaloukas, Kaxiras, Nano Letters 7, 45 (2007).
i) Orientationii) Electronic featureiii) STM image
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Most stable configurations
28.4% 27.6% 10.1%
~1000 configurations (local minima)
25.2% 6.8%
4.3% 3.2%
• Interaction through base plane
• van der Waals interaction: 0.7~0.8 eV (LDA~0.4 eV)
• Electric field further stabilizes adsorption
A/CNT
C/CNT
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Reduced noises: favorable base orientations
Experiment Hughes et al. (Harvard)
On CNTFree
Our Theory: through very delicate simulations of electron dynamics (TDDFT), all features are reproduced if we align nanotube axis as indicated.
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“Measured” vs. calculated orientation
•Red line: “measured” CNT axis
•Atomic models: Calculated
Meng et al., Nano Letters 7, 663 (2007).
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• Mutual polarization
• Slight electron transfer from base to CNT
Electronic interaction: charge density
Red: electron depletionBlue: electron accumulation
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Electronic features: density of states
Six featuresF1: HOMO
F2: LUMO
F3: Band-gap
F4: Number of occupied peaks
F5: Highest occupied peak
F6: Integral
100% accuracyH
OM
O LUM
O
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Identification made easy: STM images
Ultrafast sequencing: currently availabe: 30, 000 bases/day (454 LifeSciences)
20 images/s: 1,728,000 bases/day!
Simulation Voltage: +1.4 V
Odom et al., Nature (1998).
Experiment: CNT
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III. Melanin structure, flavonoids, and renewable energy applications
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Melanin is a ubiquitous pigment
Existence• Human: skin, hair, eye, ear, brain• Animals• Plant• Microorganism
Functions • Photoprotection• Camouflage• Vitamin D synthesis• Antioxidation• Hearing• Parkinson’s disease
Meng & Kaxiras, Biophys. J. (2008).
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Molecular structure unknown
300 400 500 600 700 800
Abs
orba
nce
(arb
. uni
ts)
Wavelength (nm)
UV-vis spectra
Monomer units
Chen et al., Pigment Cell Res. (1994).Meredith & Sarna, Pigment Cell Res. (2006).
?
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Our model: a porphyrin-like 2nd structure
Kaxiras, Tsolakidis, Zonios, Meng, Phys. Rev. Lett. 97, 128102 (2006).
X-ray
UV-vis
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Hybrid melanin/solid structure for photo-technology
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“Just for flavor”: Flavonoids as one of natural pigments
Flavonoids Chlorophyll Carotene
TiO2 Dye-sensitized TiO2
Melanin
? A
B
C
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Attach the pigment to TiO2 semiconductor
Band structure wavefunction
HOMO
LUMO
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Optical absorption
experiment
dye
dye/TiO2
Wongcharee et al. (2007).
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Charge injection dynamics
T=350 Kδt=0.02419 fs
excited electron
HOMO
LUMO
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Pigment/semiconductor antenna system for solar cells
e
e
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ConclusionsConclusions
• Design biocompatible, superphilic surface
• DNA/CNT at different levels -Experimental determination of base orientation -Electronic characteristics in spectroscopy and images: ultrafast sequencing
• Renewable energy applications -Porphorin-like melanin structure -light harvest
BIO|materials contact very promising.
water/surface
pigment/TiO2DNA/CNT
Basics:
Sensor: Energy:
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AcknowledgmentAcknowledgmentTheoretical:Prof. E.G. Wang (IoP,CAS)Dr. Jianjun Yang (IoP,CAS)Dr. Yong Yang (IoP,CAS)
Prof. Efthimios KaxirasDr. Weili WangDr. Maria FytaDr. Yina MoDr. P. Maragakis (DE Shaw Co.)Dr. C. Papaloukas (Ioannina U)
Experimental:Prof. Jene A. GolovchenkoProf. Daniel BrantonMary HughesProf. Michael Aziz
Funded by:Prof. Shiwu Gao (GU/Chalmers)Prof. B. I. Lundqvist (Chalmers)
Prof. Zhenyu Zhang (ORNL/UT)Dr. Wenguang Zhu (UT)Yang Lei (U. London)
Prof. Bengt Kasemo (Chalmers)Prof. D. V. Chakarov (Chalmers)
Prof. Martin Wolf (Freie U, Berlin)Dr. Ch. Frischkorn (Freie U, Berlin)
Prof. P. Meredith (U. Queensland)Jennifer Riesz (U. Queensland)
Prof. Z.X. Guo (U. London)
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l
alalvv vtvmtC )0()()(
)()())(2/(1)(exp
)()()(
2/1
2/1
kakakRkitki
kikeNmtv
jjjlj
kjj
jaal
kjjB
kjjjjvv
tkiTkV
knktkiV
tC
)(exp)2(
)2/1)()(()(exp)2(
)(
3
3
kj
j kg
))(()( Fourier transformation
Molecular dynamics (MD) simulation
Vibrational spectrum
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Basics about waterflexible Water structure according to BFP rule
Ice Liquid water
~0.24 eV
even more flexible
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Connection with macroscopic
= – Eads
Werder et al., J. Phys. Chem. B (2003).
θ ∝ -Eabs= -EHB/ ω
Assume EHB =constant, θ ∝ -1/ ω (ω> ω0 )θ = 180° – 108° / ω
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Water/Pt vs Water/Au
Meng et al., J. Chem. Phys. (2003).
ω
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(III) Hydrogen generation and storage•H2 from water splitting
-thermal precious metal (Pt)/O2 separation
-electrolysis electricity?
-photolysis solar cell?
-biophotolysis hydrogenases (cyanobacteria) ?
Ti
CNT
H2/TiB2 nanotube: 5.5 wt%, 0.2-0.6 eV
Meng, Kaxiras, Zhang, Nano Lett. (2007).