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Summer 2007

Terrill Research Group

San Jose State University Chemistry

Summer Students: 

Arthur Cheng,

Katie Campbell (REU),

Serkan Kabak,

Chris Lee (MS)

Research Projects: Terrill Lab and Collaborations with Dan Straus (SJSU) Shaowei Chen  (UCSC) Andrew Ichimura (SFSU) Cattien Nguyen (NASA) Wendy Fan (NASA)

Initiatives for Monday, June 26, 2006

Roger: 

We are ready to write a manuscript based on the mercaptoundecanoate and mercaptopropionate self assembly:

      To do this we need to do the following:

      Assemble the total shift data – thanks for working toward this Arthur!

      The math that goes along with this involves integrating the Poisson-Boltzmann equation calculation to compute the energy required to bring molecules up the electric field that exists due to the carboxylates at the interface.  This is interesting and tricky, because as the adsorption progresses, the repulsive field will increase, and the work will increase, and the free energy of adsorption will become less favorable as the assembly progresses.  There appears to be overshoot in this process – this kind of physical manifestation, alongside oscillation, is predicted when second-order differential equations govern the processes.  We just have to do the math to see if combining Langmuir or Frumkin adsorption thermodynamics with Poisson-Boltzmann gives this result!  To compare this with theory we need to assemble the kinetic comparisons.  This means comparing the average shapes of the self-assembly curves over the various ionic strengths.  If there is a consistent shape or quality, or trend in shape or quality, then we need to document this.

To do:

Call Mike Stephens to help me to borrow the PAR 163A system from 413. 

We also need water for the Schlenck line.

I need to:  order USB4000, sodium sulfide, more centrifuge vials, some terpyridine, tubing for  peri-pump, FEP tubing, micro-reference for May.

I Found methyl iodide!  This is used to ‘terminate’ silicon hydride surfaces.  We need to vacuum distill it.

Still needs to call Ocean Optics!  We need either a. a driver for the Red Tide or b. a loaner S4000!!!

Good News!  OO has agreed to loan us a USB4000 for a month to get our project going!

Still needs to order or find hydrofluoric acid (note: Paul Wood says there is more in 513…)

Arthur:

OK – So let’s try iodide and bromide at pH = 7.  These may make more easily desorbed ‘competitors’ for the Au surface.

Actually, this is pretty exciting, but weird! – MHA and NaHS have about the same shift! (ca. 7 nm!)

This is so exciting!  We are ready to start the competitive assembly A^-2 and HS^- !!!

Let’s try to keep good records – this will be your second paper!

I need you to put the printouts into a binder that I can use to refer to when writing the paper.

Let’s just document what we found from the TBAP experiments.  This has been difficult, but, we ought to at least have a decent record of the results.

What is going on with these experiments?  It seems that ethanol is ‘unfriendly’ in the presence of thiols.  It seems to promote a great deal of drift in the SPR response.

Can you get the data together for me and Paul to look at?

We also need to integrate the data sets from MUA and MPA in phosphate buffer, plot all the valid net shift data, and see if the story is consistent.

We also need to prepare graphs comparing the shapes of the assembly curves – do different ionic strengths consistently produce different shapes (e.g. bends or peaks) in the assembly curve?  See below for examples…

May:

We need to make some ‘fresh’ Au films for electrochemistry and we need some ferrocene as a non-aqueous standard.

The basic experimental design is:

      Inject analyte.

      Do scan rate series: (10, 20, 50, 100, 200 mV/s) [r010, r020 … r200]

      Scan once per minute over the course of an hour: (100 mV/s – file names ending ts01.txt, ts02.txt … ts60.txt)

      Exchange analyte for blank solution.

      Do scan rate series.

      Scan once per minute over the course of an hour (stability test) [s].

We will do the above on

Fe(tpy)₂Cl₂ in buffer. [tp] [b]

Fe(tpy)MeSRPO₃H in buffer (the free phosphonic acid ligand) [ta]

Fe(tpy)MeSRPO₃Et in buffer (the ester). [te]

Then we will repeat the above in CH₃CN / 0.1M TBAP. [a]

It occurs to me that we need to be able to conveniently exchange the solvents into and out of the electrochemical cell.  This is simply a matter of connecting the tubes properly so that one goes all the way down to the bottom, and the other just comes in the top.  This way we can fill it from the top without introducing bubbles and then suck almost all of the liquid out of the same tube.  We can rinse and refill a couple of times to exchange out solution when we want to change. 

Let’s get you a corner of the lab set up where we can work.  It’s on my list to have Mike Stephens bring the other 263A down for us to use.

OK – now I’m a bit befuddled.  – we need to find some examples of Fe-tpy electrochemistry to see what the heck is going on!

Ended up using Dr. Pak’s 1M pH 7 K2HPO4 buffer as an aqueous electrolyte J.

The ITO sample that we looked at discolored when we ran Fe(phen)₃²⁺ voltammetry – what’s going on with that?

Also, the Fe-phen voltammetry looked pretty slow on Au as well – the Au may have been dirty, or coated with thiols.

OK -

Do a cyclic voltammetry experiment with 1-5 mM Fe(phenanthroline)3Cl₂ in above buffer.

Microsccale prepare Fe(tpy)₂Cl₂ and do the same experiment as above.

Contingent on above results, do the same experiment with a 1mM solution of the phosphonic acid ester.

      Cycle periodically for several hours.

      Exchange out the ester-containing solution, and replace with clean buffer.

      Cycle and examine for evidence of bound complex.

      Continue cycling periodically to evaluate stability of bound complex.

Repeat above, but with dry acetonitrile / 0.1M tetrabutylammonium perchlorate electrolyte (made by Serkan, see below).

Serkan:

I talked to DAS re- the distillation.  He loaned us a 14-20 distillation head.

Contact DAS re-distillation of octadecene – we may need to heat more strongly.

Dry-distill some acetonitrile – same procedure as 1-octene!  Transfer to Kontes container.

Recrystallize and dry under vacuum several grams of tetrabutylammonium perchlorate.

Make 100 mL of dry acetonitrile / 0.1M tetrabutylammonium perchlorate electrolyte solution.

Make a 1mM solution of ferrocene / dry acetonitrile / 0.1M tetrabutylammonium perchlorate electrolyte.

Katie:

Ocean is going to lend us an S4000 – great, but for only a month.  We can hold it hostage until the software comes out!  This week we can work with the SpectraSuite and analyze files one-at-a-time.

Congrats on the recent computational success.  It seems like everything is working well.

We can test you system with water ethanol mixtures:

      0, 5,10,15,20% for starters – this amounts to a pretty small change in RI, but one that should be easily resolved by a decent pSi film.

Perhaps we can integrate the peristaltic pump into this – not crucial, but it might be good.

Momentarily the forces of light appear to have overcome the forces of darkness!   We have learned to loop in LabView 7.0!!!

I think a reasonable goal for today is the accurate identification of the peak in the Fourier transformed spectrum.

      a. A center of mass calculation may be in order.  You simply make a weighted average of the x-values (units of cm) in the region of the peak – the weights in the average are the amplitudes!

      b. You can ‘clone’ the polynomial peak find from the SPR program called ‘rscan.vi’ in the LabView 5.1 area.

      c. You can look at fitting a more appropriate function like a Gaussian or Lorenzian – but I’ve never done this, and the fit is most certainly nonlinear, so we may have some trouble.

I called Ocean Optics yesterday, but they didn’t call me back.  I’m going to try again today.

Congratulations on the loop!!! Divide and conquer ‘interpolation’ VI à we need to work with it starting with functioning examples, and go from there.

Let’s write down, i.e. document, how these were made… Calculate array of ‘F’ values, apply them to the interpolation problem.

Work on cell:

      I found a peristaltic pump in DH 510 – let’s install it on your system and see how it works.

      Clean it up (soap, DI water, alcohol rinse)

      Install Teflon tubing.

      Test with syringe.

      Collect spectra however you can!

1.      Interface Engineering with Surface Plasmon Measurements: Nanoelectromechanical Systems based on ‘loopback electrosorption’. 

To make these types of structures will require that we prepare SAMs with plenty of free surface and headgroup that electrochemically or electrostatically adsorbs

1.1.   electrostatically limited self assembly

1.2.  

1.3.  

1.4.   Arthur Cheng – mercaptopropanoic acid studies pending – hypothesis: impact of u-ion on MPA will be larger … observation – after more experiments, it appears to be very similar in magnitude!  This implies that the headgroup electrostatics and sulfur-gold bond strongly predominate in setting the surface density of the molecules.  Conversely, hydrophobic effects are but minor contributors!

1.5.   OK – the picture looks fairly clear – MPA has a similar magnitude effect.

1.6.   Also interesting – MPA seems kinetically similar in all ionic strength settings:

The following figure is for 3-mercaptopropionate adsorption at pH = 7 from phosphate buffer with log[PO₄^-] = 0,-1,-2,-3,-4

This is not the case for 11-MUA – this longer-chain molecule exhibits a much more striking kinetic dependence on ionic strength:

But wait!  At pH = 2, the MPA has kinetic ‘rebound’ as well (and repeatably…).

This is slightly shy of ‘reproducibly’, but very interesting nonetheless.

1.6.1.   Arthur and Paul Repeated these experiments at pH 2, from 1M down to 0.01M total ionic strength.

1.6.1.1.        Consistent with the screening hypothesis, the dependence on m-ion was not observed for these protonated, neutral molecules.

1.6.1.2.        The layers that formed were thicker, according to the SPR shift, and hence if we make the assumption that they are closely-packed we have a reference point for  calculating the electrostatic contributions to the total layer thickness, and the free energy of binding.

1.6.1.3.        Roger needs to figure out how to do approximate calculations of the free energy cost of bringing like-charged carboxylates together in different ionic strength electrolytes.  Hopefully he can work through the integrals!

1.7.   Next steps: Electrochemical probes of the loosely bound layers.  This effect is evidently real, hence it should, to some extent, affect the desorption potential or layer permeability in a cathodic stripping context.

1.7.1.      A possible question is: Is there a structural difference between low and high ionic strength layers?  Could there be a complicated head-tail type of configuration in the SAM for MPA that defeats the ionic strength effects?

1.7.1.1.            Cathodic stripping experiments may help to resolve this.  In this experiment, the formed SAM is subjected to a cathodic (-) potential sweep in a strong base electrolyte.  The SAM desorption is accompanied by a 1 electron reduction of the S-atoms.  The desorption appears as a peak, that when integrated, tells the number of S-atoms that were chemisorbed.  In this experiment, we can adsorb the SAM under a given set of conditions, and then desorb it in strong base.  Note – the Upchurch selection valve is not compatible with strong base.

1.8.   Carboxylic acid electrosorption on Au

1.8.1.      from base – SPR experiments have been done that show that heptanoic acid anion adsorbs to Au from strong base at open circuit – about -0.1 V vs Ag/AgCl.  According to SPR results heptanoate also desorbs at positive potentials above about 0.5V (onset of Au-oxide).  No clear evidence of this could be seen in the electrochemistry, e.g. in the form of a desorptive peak, or a capacitive feature.  FTIR measurements of the adsorption of heptanoate have not been successful – a signal to noise ratio problem! 

1.8.1.1.            contact angle measurements may be helpful here to try to determine if the alkanoate layers may be alternating head-tail in the open-circuit case

1.8.1.2.            QCM measurements may be made as well… this can be done at UCSC with Shaowei Chen.

1.8.2.      from acid! – other groups have shown that carboxylic acids adsorb from 0.1M acid.  A re-run of experiments as above, but in 0.1M perchloric acid may reveal whether this is a better pH range to explore for possible loopback type chemistry.

1.9. A NEW INITIATIVE from Shaowei.  Layer dilution with HS-.  Hydrogen sulfide, as HS^- and S^-2 chemisorbs like alkanethiols.  We want to know if we can make mixed monolayers of MHA and HS^- , and then, possibly, selectively desorb the HS- monolayers.  Or it may be the case that electrostatic headgroup adsorption may occur for the HS- coated layers!

1.9.1.   Make pH 9 solutions of varying mole-fraction HS- and MHA such that the total molarity is 10^-3. 

1.9.1.1.        0.0     0.2     0.4     0.6     0.8     1.0

1.9.1.2.        100% HS-       à          100% MHA

1.9.1.3.        Perform assembly experiments from the above solutions.

1.9.2.   The pKa is about 7 for the first proton, hence pH = 9 should be used for these studies. 

1.10.                    dynamic contact angle measurements

1.11.                    layer-building

2.     Porous Silicon Modification for Sensing and Molecular Electronics.- Katie, Chris and Serkan

2.1. flow-cell interferometer development: Katie

2.1.1.   Install LabView 7

2.1.2.   Write a program to:

2.1.2.1.        Read in an interferogram

2.1.2.2.        interpolate data onto evenly spaced, 2ⁿ point cm^-1 x-axis

2.1.2.3.        n should = 14 – this will make the FFT have more points

2.1.2.4.        perform a FFT on it

2.1.2.5.        implement a ‘center-of-mass’ (or polynomial J) peak-finding routine

2.1.2.6.        return the ‘k-value’ of the peak in the FFT

2.1.3.   Bug me to call Ocean Optics and bug them about the LabView drivers for the Red Tide spectrometer!

2.1.4.   Bug me to explain to you how we transform k into optical thickness (This way I’ll remember how we did it!  Hopefully Chris has notes… otherwise we can re-invent the wheel here).

2.1.5.   Eventually we will get the OOI-LVD and we can start doing the assembly.

2.1.6.   Lee, our machinist, is working hard to get the cell done – we can do some calibration experiments with the thick-O-ring cell in the meantime.

2.1.7.   The calibration experiments will consist of measuring the interfeorgram of both as-prepared and alkylated (e.g. hydrosilated) samples.

2.2.   study hydrosilation by FTIR / vis interferometry and electrochemistry

2.2.1.      prepare ‘fresh’ porous silicon

2.2.1.1.            cleave ½” or slightly larger squares from existing p++ wafer

2.2.1.2.            etch new samples using literature protocol to prepare samples with modest pore depth – prejudice against very long etch times or high current densities that may create anisotropy

2.2.1.3.            PAR 273 à etch Si to make pSi (3:1 EtOH:HF) – make new samples with smaller etch cell to conserve Si – BE EXTREMELY CAREFUL WITH HF! IT WILL SCAR YOU AND CAN HAVE SEVERE SHORT TERM TOXICITY! – WEAR GLOVES AND EYE PROTECTION AND LAB COAT!

2.2.1.4.            give each sample a code name and clearly record this along with the sample etch conditions in your notebook and on a note-paper stored along with samples – samples can be stored in little home-made envelopes, made from kim-wipe and tape in dessicator

2.2.1.5.            store in vacuum dessicator with clean, dust-free dessicant or  no dissicant – good vacuum needed, not just reduced pressure from ‘house’ system

2.2.1.6.            these samples will be examined with SEM later, so take good care of them!

2.2.2.      measure visible interference pattern in dry He (or N₂) and dry isopropanol ethanol for pore volume fraction calculation – avoid water that may break down Si-H – keep track of file names – keep data on diskette or similar

2.2.3.      measure transmission FTIR spectra of each one vs. the same clean Si –  4 cm^-1 resolution, 32 scans should suffice – Serkan can do this if necessary – keep track of file names in notebook and instrument log

2.2.3.1.            spectra of neat 1-octene and terpyridine acquired 6.12.2006 SK

2.2.4.      expose to olefin (e.g. vinyl terpyridine) with PtCl₆ or AIBN catalyst – note new PtCl₆ catalyst requirements from Sundanini Velapula thesis

2.2.5.      rinse very well with clean, dry solvent to remove any material that is not covalently bound

2.2.6.      measure visible interference pattern as above

2.2.7.      measure FTIR spectrum, same conditions as above

2.2.8.      for vinyl tpy, expose to FeCl₂ solution – e.g. 100 mM, 20 min

2.2.9.      rinse

2.2.10.  measure vis interference and FTIR as above

2.2.11.  expose to terpyridine

2.2.12.  measure vis interference and FTIR as above

2.3.   hydrosilation chemistry – see existing work for conditions

2.4.   radical initiation is also a possibility: see Katie’s database for concentrations

2.5.   measure electrochemistry or

2.6.   measure sensitivity to gasses such as H2O, EtOH, toluene w/ vis

2.7.   measure SEM

2.8.   tasks

2.8.1.      distill octene / octadecene

2.8.2.      order methyl iodide

2.8.3.      finish cell plans – give to Lee

2.8.4.      work with small etch cell

2.8.5.      look into electrochemistry on pSi

3.      Phosphonic acid (ester) coupling to indium-tin oxide: rate and stability studies.

We are investigating molecules that can bind to an interesting mixed oxide semiconductor film: InO2/SnO2 - a transparent conductor also known as ITO, or indium-tin oxide.  Along with Dan Straus and Wendy Fan (NASA) we have done a few experiments that show that this system 'works' - but we have a few more to go before we can publish the study.

The molecules that Dan and Wendy prepared are redox-active iron complexes - modified iron bis terpyridines.  The terpyridine complex is 'modified' by an alkyl phosphonic acid or phosphonic acid ester.  The alkyl (thioether) linker is tethered to the periphery of the complex and serves to bind the iron complex to the ITO surface.  Because it is bound there, if you put the ITO into an electrolyte solution you can reversibly oxidize and reduce the Fe complex by biasing the ITO. 

These molecules have been investigated in a very interesting ZnO 'nanowire' system recently - a collaboration between a UCSB group, Wendy and Dan.  They showed that the Fe centers can store charge in such a way that the nanowires behave like memory units.  The experiments that we are doing are not as device-oriented, but rather seek to characterize the kinetics, strentgh and stability of the binding.

We will use electrochemistry to examine the binding, cycling and retention of the complex on ITO in both aqueous and non-aqueous settings.

A broad overeview:

0. Prepare some non-aqueous solutions and

1. Prepare some aqueous solutions of the Fe-tpy-PO3 / ester.

2. Do some electrochemistry on ITO with blank electrolyte solutions.

3. Do some electrochemistry on ITO periodically while the molecules are binding.

4. Look at the electrochemistry of the molecules after they have bound.

5. See for how long they remain on the surface.

Very 'doable' very likely lead to a quick publication.

Deposition solutions:

0.1 mM complex (depending on the amount we have) in either dry CH3CN /or aqueous electrolytes.  0.1 M tetrabutylammonium perchlorate, recrystallized from ethanol  will be the electrolyte for the CH3CN, and 0.1M pH7 phosphate buffer water will be the electrolytes for the aqueous echem.  (Note: ITO dissolves in HCl and some other acids - we'll stay away from chloride and other halides and strong acid.)

3.1.   Electrochemistry project – molecules already synthesized – Serkan can prepare Fe(tpy)₂Cl₂ for control experiments.

3.2.   miscellaneous tasks / methods

3.2.1.      do basic elecrochem tutorial with ferri/ferrocyanide (scanned doc for that)

3.2.2.      understand how to use M270 software as well as possible.

3.2.3.      get the o-ring cell functioning properly with ferrocyanide

3.2.4.      clean ITO slides (wash with soap, rinse with ethanol and acetone, soak in ammonia solution with about 1-5% H2O2, don’t leave soaking in ammonia/peroxide for more than a few hours, never treat with HCl or other strong acids)

3.2.5.   Locate additional ITO slides, clean and store them in sealed container of very pure water.  Perhaps weighing bottles or vials will work well for this.

3.2.6.   Prepare, get from service center, or buy a small amount of Fe(tpy)₂²⁺ and measure electrochemistry on ITO – does it adsorb?

3.2.6.1.        A sweep-rate series experiment will serve well here: Do CV experiments generously spanning the redox wave (e.g. E^o±250 mV if possible).  Sequential experiments should be done from 10 mV/s to 1000 mV/s.

3.2.7.   Set up o-ring echem-cell to accommodate injections of analyte.

3.2.8.      Prepare pH 7.0 phosphate buffer.

3.2.9.      Dry CH3CN solvent by distillation from CaH₂ under Schlenck conditions (like 1-octene, use a transfer arm and cool the receiving flask with dry ice (3-25-15) or liquid N₂.

3.2.10.  order tetrabutylammonium perchlorate (TBAP) or

3.2.11.  recrystallize existing TBAP

3.2.11.1.        dissolve a lot of TBAP in hot ethanol to nearly saturate – precise amount is not important

3.2.11.2.        add cold pure water to cause crystallization

3.2.11.3.        promptly vacuum filter wet crystals

3.2.11.4.        dry under vacuum to reasonably constant weight (overnight?)

3.2.12.  prepare electrolytes

3.2.12.1.        0.1M TBAP, dry / CH3CN, dry

3.2.12.2.        1M pH 7 phosphate buffer (potassium or sodium) – boil and seal to prevent bacteria/mold growth

3.2.13.  measure sample echem in target electrolyte

3.2.14.  do sweep rate series to establish mass transfer

3.2.15.  measure, by cyclic Voltammetry, blank electrolyte, with clean ITO to confirm absence of redox activity in above

3.3.   optical (vis) spectroscopy also possible – estimate needed of epsilon for Fe(tpy)

3.4.   binding rate

3.5.   stability of bound complex in organic electrolyte, and aqueous basic and neutral conditions

3.6.   metal assembly on surface

3.7.   visible spectroelectrochemistry

3.8.   quantitative coverage evaluation

4.      Pyrene-modified redox moieties for carbon nanotube sensor applications

4.1.   assist in synthesis of pyrene-ferrocene

4.2.   construct electrochemical cell

4.3.   perform electrochemistry experiments

4.4.   couple to carbon nanotubes and measure properties (conductivity etc.) w/ Cattien Nguen at NASA

5.      ‘Tripod’ SAM analysis by electrochemistry and SPR (a collaboration with Andrew Ichimura from San Francisco State University) – limited scope at present

5.1.   electrochemistry of layers prepared at SFSU

5.1.1.      evaluate blocking of tripods to redox moieties

5.1.2.      evaluate electrochemical desorption characteristics of ‘tripods’

5.2.   possibly preparation of new layers at SJSU

6.      Vitamin-D receptor Binding Studies for Dr. Elaine Collins:

6.1.   basic study of protein adsorption using glutaraldehyde coupling

6.2.   as above but with vitamin-D receptor / vitamin-D and analogues

Resources:

SPR / reflectometer with flow system  DH 4A – main system for SPR, complete

Par 263A potentiostat w/cell stand – used for standalone and SPR-Echem

PE-2000 FTIR with ATR flow system – good for pSi studies, but lacks sensitivity for monolayer analyses at present.

New VIS reflectometer for pSi work, light source etc.

Par 263A potentiostat #2 (to be stolen from 55 lab) DH4A or 3A w/cell stand etc.

BAS 100B DH 3A w/cell stand – can be used for phosphonic acid ester molecules as well as pyrene and modified pSi. 

Cary 50 Bio with reflectometer capability DH 3A – needs improved flow cell or similar for flow analyses

Mattson FTIR instruments: DH-020 and DH-D006 – both good for pSi studies.

SPREETA instruments – w/o flow cell capability at present, need to be developed, good for SPR.

Needs:

Temperature controlled enclosure for pSi interferometry.

Peristaltic pump or similar for pSi interferometry.

Win2K PC

Cell (design under construction)

Borrow 263A from 4^th floor – ask Maria, Joe Pesek