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2 12/16/2017 PART II    Surfaces; self-assembly; some ways to characterize surfaces (CPD, CA, ellipsometry, IR) Surfaces  Interfaces ; contacts for soft matter molecules as surface / interface modifiers molecules as transport media More solid state electronic measurements, incl. IETS, capacitance-voltage     ·     

3 Ellipsometry When is this important for bio The laser beam gets elliptically polarized after passing a linear polarizer and a quarter-wave plate 

4 Methodology 12/16/2017 Polarized light is reflected at an oblique angle to a surface The change to or from a generally elliptical polarization is measured. From these measurements, the complex index of refraction and/or the thickness of the material can be obtained.

5 IR Spectroscopy Gives information about the vibrational modes of matter. Valuable as fingerprint and for confirming presence of molecules on surfaces. P-polarized: electric vector amplified at surface. S-polarized: electric vector cancels at surface. Ep Ep When is this important for bio? h Es Es * Characterization of linkers commonly used for protein immobilization * Secondary structure determination

6 12/16/2017 PM-IRRAS incoming IR-light polarization is modulated at high frequency,  simultaneous collection of surface specific spectra with one experiment. Spectra are measured simultaneously  environmental effects (O2 and CO2) &instrument drift over time are almost completely removed. PM-IRRAS allows determining molecular orientation of functional groups and of whole molecule. From relative peak ratios of functional groups of known orientation we determine the tilt of the molecules compared to the surface. An effect called “surface image selection rule” that is present in PM-IRRAS performed on good conductors leads to enhancement of perpendicular and cancellation of planar dipoles in the spectra. This can be utilized in determining the molecular orientation by comparing peak intensities, or by calculating from a theoretical spectrum.

7 C=O and a bit C-N N-H and a bit C-C and C-N(a) Representative IRRAS spectrum of the SSA80Fc SAM, (b) simulated IRRAS spectra with various tilt angles of the helix axis from the surface normal, and (c) the calculated dependence of the amide I/II absorbance ratios on the tilt angles. Published in: Yoko Arikuma; Hidenori Nakayama; Tomoyuki Morita; Shunsaku Kimura; Langmuir  2011, 27, DOI: /la103882r Copyright © 2010 American Chemical Society

8 Attenuated Total (internal) Reflection How does ATR work?In IR internal reflection spectroscopy radiation passes through a high refractive index, IR-transmitting, crystal; the IR radiation is reflected ≥ 1 times in the crystal . The evanescent wave of the IR beam penetrates into the sample in contact with the crystal, and is partially absorbed there  spectrum of the sample. In ATR –IR one measures the total reflected IR beam after the beam interacted with the sample. When is this important for bio? 1)ATR captures most of the the mid-infrared region ( inverse cm) The complete mid-infrared region is ( cm-1) DON’T USE The beam is a Class IIIb diode laser--invisible IR captures the vibrational and rotational states of a molecule Vibrational: liquids and solids—broader peaks Vibrational and rotational states result from a dipole moment Interferogram--signal PM-IR-RAS - Suitable for high reflective substrate (metals, usually > 20nm) ATR – Suitable for semiconductors

9 PM-IRRAS This is a diagram of the path of the infrared beam from the IR source, through the crystal and to the detector When the beam is directed from the IR onto an optically dense crystal at a certain angle, the beam is reflected through the crystal. When a sample is placed on the crystal, the infrared radiation interacts with the sample, producing a “transmission-like” spectrum The evanescent waves penetrate 1 to 4 micrometers into the sample at each reflection point. A portion of the wave is absorbed by the sample. The altered (attenuated) beam from each wave exits at the opposite end of the crystal and is directed to the detector. The detector records the attenuated beam as an interferogram signal, which generates an infrared spectrum Because the evanescent waves decay rapidly as they move away from the surface of the ATR crystal, the sample must contact the crystal surface to produce an accurate spectrum There are two types of ATR crystals: multi-bounce and single-bounce Multi-bounce (as shown in the picture) is used when increased sensitivity is desired Single-bounce is for the every day user (Lewis University) DON’T USE materials that are optically dense have a high refractive index

10 ATR vs. Transmission IR spectroscopyIn ATR most samples can be run “neat”, i.e.,“in their natural state” ATR sampling is fast and easy because little or no sample preparation is required IR transmission often requires the sample to be pressed or ground to collect the spectrum 3) These processing steps for transmission analysis take time and can cause structural changes to the sample. In addition, samples that must be diluted for transmission analysis are usually mixed with salts or Nujol, which may have spectral features of their own As a result, ATR analysis is much quicker than transmission analysis Attenuated total reflection (ATR) spectroscopy is a powerful technique for infrared analysis of a wide range of for sample types

11 Two Conductors in Contact12/16/2017 electron flow – + leads to charge separation Contact potential difference Note that the vacuum level shifts for the two materials. This is because the charge that is transferred establishes a potential that produces the shift in all the states of the sample. Fermi level equal throughout electronic equilibrium Dan Thomas, Univ. Guelph, Canada

12 Contact Potential Difference (CPD) ++Kelvin probe Measuring Contact Potential Difference (CPD) ++  ( V CPD + comp )  o d Q = Total C = C = A V V CPD comp light C = . A  o (do + d1 sin t) vibrating grid  d = do + d1 sin t dQ dC . semiconductor sample i(t) = = V CPD dt dt i (t) i (t) = IF compensating voltage V(comp) = -VCPD R • V(comp) [ qVCPD = Ø grid - Ø sample ]

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15 Contact Angle SURFACE TENSION IS A CONTRACTIVE TENDENCY OF SURFACE OF A LIQUID THIS ALLOWS IT TO RESIST AN EXTERNAL FORCE HIGH SURFACE TENSION LIQUID  MINIMUM SURFACE AREA SURFACE TENSION IS CAUSED BECAUSE OF MOLECULAR ATTRACTION FORCES IN GENERAL on a HYDROPHOBIC SURFACE: DISSOLVED CONTAMINATION IN WATER REDUCES SURFACE TENSION  REDUCES CONTACT ANGLE

16 DEPENDENCE OF CONTACT ANGLE ON SURFACE ENERGY AND SURFACE TENSIONQuick and effective method for defining how hydrophobic or hydrophilic is the surface after modification. useful for linkers and proteins as well

17 What do we mean by (Bio)molecular Electronics?Electronics with (Bio)Molecules? A. Vilan

18 Electronics with (Bio)Molecules?substrate: metal , semiconductor idealized cartoon Electronics with (Bio)Molecules? HOW to go about it? single molecule ? monolayer ? multilayer ? bulk material? Great idea, but ………….. HOW can you connect them to outside world ?

19 What Do we Measure? Surface Interface / Junction A Z Top ContactSubstrate (Si) Substrate (Si)

20 Interfaces ≠ surfaces Interfaces Basic Concepts Dipolar effectA. Vilan

21 Types of Contacts Rectifying Ohmic Built-in potential;Asymmetric current-voltage: One bias polarity = “ON” Opposite polarity = “OFF” Flat interface potential; Symmetric current-voltage; High currents. A. Vilan

22 Diode and resistor Current-Voltage plot12/16/2017 Diode and resistor Current-Voltage plot

23 Electronic Contacts to Soft MatterHg electrode Si substrate Back Contact

24 DC & H. Haick

25 Molecular Junctions i In-wire AFM/STM Break junctionsSemic./Molecules/Metal Metal / Molecules/Metal AFM/STM i In-wire DC & Y Selzer

26 Another Approach dimer Au nanoparticles Organic molecules 10 – 50 nmDadosh, Gordin et al.

27 Electrostatic TrappingBezryadin et al., APL 71 (97) V Control parameters – voltage, frequency and time Dadosh, Gordin et al.

28 Preparation of Metal / Monolayer / Substrate Hybrid Devices(1) Molecules in solution Substrate Metal contact (3) Substrate monomolecular film on substrate (2) Pinhole Adsorption of Molecules

29 One can actually “see” a monolayerSi Pb ~1nm Robert Lovrincic Wenjie Li Yu Xi +++

30 How does a single isolated molecule differ from otherwise identical molecules, assembled in a monolayer? ~1 isolated molecule ~ 5000 molecules Y. Selzer et al.

31 Single isolated Monolayer molecule of identical molecules~1 isolated molecule ~ 5000 molecules 0.00 0.02 0.04 0.06 0.08 0.10 0.12 -28 -26 -24 -22 -20 -18 -16 -14 Ln(Current) 1/Temperature (1/K) 0.00 0.02 0.04 0.06 0.08 0.10 0.12 -20 -19 -18 -17 -16 -15 -14 1.0V 0.3V 0.2V 0.1V Ln(Current) 1/Temperature (1/K) Y. Selzer et al.

32 Transition from coherent tunneling to thermally activated transport.. 2 4 6 8 - T h e r m a l y c t i v d o n u Ln (G) 1 / p ( K ) Single molecule ΔE ~ 100meV Temperature effect Ei Ef M1 Molecule M2 Y. Selzer et al.

33 “Zoo” of Electronic Transport Mechanisms through ultra-thin and thin insulators

34 Polaron hopping transportImplicit in band model is assumption that carrier mean free path > several lattice sites, with residence time on each site << relaxation time of the charged molecule. Assumption is not valid anymore if mean free path ~ intermolecular distance, or if transport  short jump between trap sites, where charge spends most of the time. In that case, the carrier polarizes surrounding molecules and forms a polaron. If polarization extends only to nearest neighbor molecules, small polaron At equilibrium position, the polaron stabilization is maximum and any polaron movement reduces this stabilization  charge carriers reside in potential well centered at equilibrium position To move from one site to the next, the polaron must overcome a barrier. Charge carrier motion is a series of hops from one site to the next  hopping transport + - A. Kahn, Princeton

35 Recall the T-1.5 dependence of the mobilityBand transport vs. polaron hopping Recall the T-1.5 dependence of the mobility Pope and Swenberg, in Electronic Processes in Organic Crystals and Polymers, Oxford Science, p. 339 A. Kahn, Princeton

36 Charge carrier transport in molecular filmsProbability of hopping events: product of probability of carrier achieving an energy = ΔG (barrier) and probability of carrier with this energy undergoing transfer to neighboring site. Non adiabatic vs. adiabatic polaron transfer: non-adiabatic: transfer time < reorganization time adiabatic: transfer time > reorganization time This is proportional to with m = 0 or ½. The mobility is given by At low T, the exponential dominates, so μ will decrease sharply with T, in contrast with case of band-conduction semiconductor: transport is thermally activated Configurational coordinates of 2-site small polaron system.  Is reorganization energy (~ few 100 meV) ΔG ~ /4 Pope and Swenberg, in Electronic Processes in Organic Crystals and Polymers, Oxford Science, p. 339 A. Kahn, Princeton

37 Role of traps in transport in organic filmsMolecular and polymer thin films are fraught with electronic states with energy within the normal energy gap of the material. These are due to Impurities (oxygen-related, damaged molecules, etc.) Static and dynamic disorder These electronic states can act as traps (shallow or deeper) and considerably slow down transport LUMO level EF X Trap states Electron injected from neighboring material / electrode Carrier trapping-induced low mobility A. Kahn, Princeton

38 Dipolar Effect Interfaces? Basic Concepts Dipolar effect A. Vilan

39 Molecular Dipole Effectinterface = e·N·µ· sinθ /ε b= metal +interface -sc + – θ N The dipole layer adjusts the electrostatic balance; The width of the potential drop is so narrow (~1nm) that it hardly affects the current (cf. ~100nm thick SCR).

40 In- Situ Characterization12/16/2017 In- Situ Characterization

41 Principle of the inelastic tunneling spectroscopy (IETS)Inelastic channel open when eV =ℏωvib Similar to Raman Spectrum IETS gives vibrational information on the sample Molecular Layer Measurement of IETS Lock-in amplifier V= Vb + Vac cos(ωac t) ∂2I/∂V2 can be directly obtained from lock in amplifier

42 Inelastic Electron Tunneling Spectroscopy (IETS)Probability ~ 10-3 Low temperature 1 meV ~ 8 cm-1 Y. Selzer et al.

43 ∂I/∂V Au-S (∂2I/∂V2)/(∂I/∂V) Current -Voltage Differential ConductanceInelastic Electron Tunneling Spectroscopy Hepta Lys N-H modes

44 IETS of Azurin on suspended nanowireAu-S C-H Amide ? Typtophan? ? Amide ? Typtophan? C-H Au-S

45 Capacitance – Voltage methodCapacitance - Voltage sweep State Why one wants to do this measurement Charging / discharging Contact area Do not confuse with cyclic voltammetry

46 Flat band (VFB) and Doping Density (ND) from C-V @high ωPlot slope ND Intercept with x axis VFB ND (EC – Ef)

47 Summary Measuring flat band potential Measuring excess capacitance 1High frequency, Reverse bias Built-in voltage Measuring excess capacitance Comparing high and low frequency Low current regime Density of interface trap states EC Ef EV