Notes-DH

STM Main Page
=Notes= //Piece my progress in what I have been learning//

//- The difference between ://

 * **approach /advance** || **scan** ||
 * this function is an easy mecahnical way for the tip to be at a distance that is close enough to get the current but not crash the tip || this function triggers the actual scna of the sample and then provides you with the data ||

//- The piezo tube://


The Piezo Electric Tube is made of ceramic that expands and contacts as voltage is applied.
 * **x range** || controls left or right slope of your tip scanning ; controls the slope of the tip on regards of the x-axis ||
 * **y range** || controls up or down of your tip scanning ; controls the slope of the tip on regards of the y-axis ||
 * **z range** || control the height of the piezo tube as to obtain more or less current; controls how far your tip is from the sample ||

//This ranges are controled by applying bias, whici most of the time are automatically put in by the software//.

- The different functions for improving the image by editing

 * **xoffset** || takes the average of the heights that are showned as lines as to give a more one level image ||
 * **mask** || defines areas flater ||
 * **filtering** || smooth out streaks ||

- Octathentiol VS Benzene

 * **Octanethiol** || pert of the alkylene group, [[image:http://www.cheric.org/research/kdb/hcprop/molimg/1841.gif]] || Diamond shape alignment || media type="custom" key="409307" ||
 * **Benzene** || an organic chemical compound with the formula C6H6; sometimes abbreviated Ph-H || Z alignment || [[image:http://upload.wikimedia.org/wikipedia/commons/6/67/Benzene_structure.png]] ||


 * **Oct** || **ane** || thiol ||
 * eigth || single bonded Carbons || a Sulfur atom atttached ||
 * [[image:octanethiol_sam.png width="175" height="158" align="center" caption="octanethiol sample"]] ||


 * Shape that Gold forms ---> hexagonal ||
 * media type="custom" key="409331" ||
 * __- Running the soft ware__**
 * 1) Start the software by turning it on and clicking on the computer icon.
 * 2) Click approach
 * 3) Arrange your x-slope as it to be a straight line.
 * 4) Change your rotation to 90° and arrange your y-slope to be a straight line.
 * 5) After you can play around with
 * optimize ---> make the image look better
 * line/time --> speed up/down the scan
 * z-range --> get more detail as you get to a smaller area

__**Samples matter?**__

__//Factors that influence the choice of a sample to scan//__



 * 1) oxidation || [[image:http://tbn0.google.com/images?q=tbn:vf1T4eKfUgBfkM:http://www1.istockphoto.com/file_thumbview_approve/3568255/2/istockphoto_3568255_original_right_arrow.jpg width="34" height="35" link="http://www1.istockphoto.com/file_thumbview_approve/3568255/2/istockphoto_3568255_original_right_arrow.jpg"]] || in many cases oxides might be created || [[image:http://tbn0.google.com/images?q=tbn:hbPOD4ut4fEg4M:http://www.co.beaufort.sc.us/bftlib/Pointing%2520hand%2520R.gif width="44" height="34" link="http://images.google.com/imgres?imgurl=http://www.co.beaufort.sc.us/bftlib/Pointing%2520hand%2520R.gif&imgrefurl=http://www.co.beaufort.sc.us/bftlib/friendsletter2.htm&h=277&w=466&sz=49&hl=en&start=14&sig2=CHdaUJprHmrrIgfJuDcxXw&tbnid=hbPOD4ut4fEg4M:&tbnh=76&tbnw=128&ei=YsGHR5-yKZLIhgLt2cXhDQ&prev=/images%3Fq%3Dpointing%2Bto%2Bthe%2Bright%26gbv%3D2%26ndsp%3D18%26svnum%3D10%26hl%3Den%26safe%3Dactive%26sa%3DN"]] || the oxygen atoms attached to teh surface will not allow you to see the raw of the compound/substance ||
 * 2) the purpose of the scan || [[image:http://tbn0.google.com/images?q=tbn:vf1T4eKfUgBfkM:http://www1.istockphoto.com/file_thumbview_approve/3568255/2/istockphoto_3568255_original_right_arrow.jpg width="34" height="42" link="http://www1.istockphoto.com/file_thumbview_approve/3568255/2/istockphoto_3568255_original_right_arrow.jpg"]] || trying to see patern || [[image:http://tbn0.google.com/images?q=tbn:hbPOD4ut4fEg4M:http://www.co.beaufort.sc.us/bftlib/Pointing%2520hand%2520R.gif width="45" height="35" link="http://images.google.com/imgres?imgurl=http://www.co.beaufort.sc.us/bftlib/Pointing%2520hand%2520R.gif&imgrefurl=http://www.co.beaufort.sc.us/bftlib/friendsletter2.htm&h=277&w=466&sz=49&hl=en&start=14&sig2=CHdaUJprHmrrIgfJuDcxXw&tbnid=hbPOD4ut4fEg4M:&tbnh=76&tbnw=128&ei=YsGHR5-yKZLIhgLt2cXhDQ&prev=/images%3Fq%3Dpointing%2Bto%2Bthe%2Bright%26gbv%3D2%26ndsp%3D18%26svnum%3D10%26hl%3Den%26safe%3Dactive%26sa%3DN"]] || then the particles should be compatible ||
 * 3) volatility || [[image:http://tbn0.google.com/images?q=tbn:vf1T4eKfUgBfkM:http://www1.istockphoto.com/file_thumbview_approve/3568255/2/istockphoto_3568255_original_right_arrow.jpg width="32" height="36" link="http://www1.istockphoto.com/file_thumbview_approve/3568255/2/istockphoto_3568255_original_right_arrow.jpg"]] || the ability to react to room conditions || [[image:http://tbn0.google.com/images?q=tbn:hbPOD4ut4fEg4M:http://www.co.beaufort.sc.us/bftlib/Pointing%2520hand%2520R.gif width="43" height="41" link="http://images.google.com/imgres?imgurl=http://www.co.beaufort.sc.us/bftlib/Pointing%2520hand%2520R.gif&imgrefurl=http://www.co.beaufort.sc.us/bftlib/friendsletter2.htm&h=277&w=466&sz=49&hl=en&start=14&sig2=CHdaUJprHmrrIgfJuDcxXw&tbnid=hbPOD4ut4fEg4M:&tbnh=76&tbnw=128&ei=YsGHR5-yKZLIhgLt2cXhDQ&prev=/images%3Fq%3Dpointing%2Bto%2Bthe%2Bright%26gbv%3D2%26ndsp%3D18%26svnum%3D10%26hl%3Den%26safe%3Dactive%26sa%3DN"]] || the room temperature, and pressure must be control ||
 * 4) electronegativity || [[image:http://tbn0.google.com/images?q=tbn:vf1T4eKfUgBfkM:http://www1.istockphoto.com/file_thumbview_approve/3568255/2/istockphoto_3568255_original_right_arrow.jpg width="34" height="39" link="http://www1.istockphoto.com/file_thumbview_approve/3568255/2/istockphoto_3568255_original_right_arrow.jpg"]] || tunneling || [[image:http://tbn0.google.com/images?q=tbn:hbPOD4ut4fEg4M:http://www.co.beaufort.sc.us/bftlib/Pointing%2520hand%2520R.gif width="43" height="41" link="http://images.google.com/imgres?imgurl=http://www.co.beaufort.sc.us/bftlib/Pointing%2520hand%2520R.gif&imgrefurl=http://www.co.beaufort.sc.us/bftlib/friendsletter2.htm&h=277&w=466&sz=49&hl=en&start=14&sig2=CHdaUJprHmrrIgfJuDcxXw&tbnid=hbPOD4ut4fEg4M:&tbnh=76&tbnw=128&ei=YsGHR5-yKZLIhgLt2cXhDQ&prev=/images%3Fq%3Dpointing%2Bto%2Bthe%2Bright%26gbv%3D2%26ndsp%3D18%26svnum%3D10%26hl%3Den%26safe%3Dactive%26sa%3DN"]] || ability of electrons to transfer ||
 * 5) resources || [[image:http://tbn0.google.com/images?q=tbn:vf1T4eKfUgBfkM:http://www1.istockphoto.com/file_thumbview_approve/3568255/2/istockphoto_3568255_original_right_arrow.jpg width="32" height="38" link="http://www1.istockphoto.com/file_thumbview_approve/3568255/2/istockphoto_3568255_original_right_arrow.jpg"]] || limitations || [[image:http://tbn0.google.com/images?q=tbn:hbPOD4ut4fEg4M:http://www.co.beaufort.sc.us/bftlib/Pointing%2520hand%2520R.gif width="49" height="37" link="http://images.google.com/imgres?imgurl=http://www.co.beaufort.sc.us/bftlib/Pointing%2520hand%2520R.gif&imgrefurl=http://www.co.beaufort.sc.us/bftlib/friendsletter2.htm&h=277&w=466&sz=49&hl=en&start=14&sig2=CHdaUJprHmrrIgfJuDcxXw&tbnid=hbPOD4ut4fEg4M:&tbnh=76&tbnw=128&ei=YsGHR5-yKZLIhgLt2cXhDQ&prev=/images%3Fq%3Dpointing%2Bto%2Bthe%2Bright%26gbv%3D2%26ndsp%3D18%26svnum%3D10%26hl%3Den%26safe%3Dactive%26sa%3DN"]] || options available ||

Macrocycles containing a rubicene moiety could be interesting fluorescing units to be used in the synthesis of [n]catenanes. On the other hand, crown ethers bearing a rubicene unit could be used as selective cation sensitive fluorescence indicators. ||
 * __Rubicene -__**polycyclic aromatic hydrocarbon
 * The formula is: C26H14 ||
 * Mass: 326.39716 ||
 * Exact mass: 326.10955 ||
 * Elemental analysis of C26H14: ||~ Element ||~ Number ||~ Percentage ||
 * C || 26 || 95.67669 ||
 * H || 14 || 4.32331 ||  ||
 * [[image:http://www.steve.gb.com/images/molecules/arenes/rubicene.png width="95" height="93" link="http://www.steve.gb.com/images/molecules/arenes/rubicene.png"]] ||
 * [|Melting Point: 305°C] ||
 * ===highly fluorescing and photostable=== ||
 * Rubicene application in systems have great potential as supramolecular building blocks, namely macrocycles and crown ethers.


 * [|Pre-lab precaution information] ||

http://www.chemexper.com/cheminfo/servlet/org.chemcalc.ChemCalc?isograph=on&mformula=C26H14 http://www.mdpi.org/molecules/papers/50300620.pdf


 * __Truxene__** - polycyclic aromatic hydrocarbons


 * __polycyclic aromatic hydrocarbons__**
 * organic molecules made up of only carbon and hydrogen ||  ||
 * flat ||
 * standard product of combustion ||
 * very stable ||
 * highly carcinogenic but very common ||

ultraviolet light from solar radiation || http://en.wikipedia.org/wiki/Polycyclic_aromatic_hydrocarbon [|http://web99.arc.nasa.gov/~astrochm/PAHs.html] http://www.euro.who.int/document/aiq/5_9pah.pdf
 * consist of fused aromatic rings ||
 * PAHs can undergo photodecomposition when exposed to
 * media type="custom" key="472551" ||  ||
 * [|Human Health Hazards] ||

__Getting confortable with the scope__

 * Practice //(January 28, 2008)//**

media type="custom" key="472559" Would it be scratches (hills) ? //Answer// - peel and try again //Prediction// - becasue by peeling the top graphite will be removed and a new smooth surface will be left. media type="custom" key="472541"
 * 1) Set up the scope
 * sample --> graphite
 * cut the tip
 * start easy scan
 * load default STM
 * 1) Trial 1
 * approach --> 397 steps
 * crashed
 * 1) Trial 2
 * withdraw
 * re-approach --> 296 steps
 * scan
 * obtain images
 * analyze results
 * 1) Conclusion
 * Sample moves quickly i the direction up and left
 * Sample is scratched = many dislevels due to graphite being in contact with other objects and snce is to smooth any sharp tip would scratch it
 * The Theory**
 * Follow up the theory (//January 28, 2008)//**
 * 1) Double peel
 * 2) Change tip
 * 3) Crashed tip!
 * 4) Change Tip Again
 * 5) crashed tip
 * 6) Change Tip once more
 * 7) Scan succesfully
 * 8) Conclusion
 * smoother surfaces and less unlevelness --> the peeling did like a cutting action leaving a uniform layer

//This info might helpyou get better images//
 * Different ways to get display an sample being scanned**
 * 1) 3-D --> image that allows you to see what exatly is going
 * 2) Shade View ---> 2-D image that shows shades to differentiate levels (hills)
 * 3) Line View ---> graph of the x slope
 * 4) Dual Line View ---> graph of the x and y slope
 * 5) Forward Scan Top View > most used and shows the 2-D image of the sample
 * Helpful Info**
 * //**X**//**- OFFSET** --> //help you move scanning area to a different horizontal area --->// positive = right & negative = left ||
 * **Y-OFFSET** --> //help you move scacing area vertically// --> Positive = up & negative = down ||
 * **Set point** --> .021 nA
 * Gap / Voltage** --> 0.5 nA ||
 * **Z-range** --> smaller = more detail & larger = general view ||
 * **View panel** -->
 * Front Scan
 * Z-Output
 * Average
 * Top View ||
 * General and common ways to deposit a substance on a substrate**
 * 1) Vapor deposit --> in a sealed vial with parafilm you put a tube with the a solution of the desired substance and your substrate.( //Make sure you substrate has the sample up and not the mica)// You put in in the oven (//temperature and time depends on substances)//. The solution with evaporate; to later condense on the substrate.
 * 2) Dip casting --> In a solution of the desired substance, you dip the substrate. And then let it dry.
 * 3) Drop Casting --> With a dropper, drop some solution of the desired substance onto the substrate and let it dry


 * Truxene and Octanethiol onto a gold (Au 111) substrate.** --> //How I make my samples?//
 * 1) get a gold substrate on mica
 * 2) cut it in four --> the cutting will create the corners of the substrate to somewhat peel off the corners so tossed the worst out
 * 3) Anneal with Hydrogen flame ( Y//ou have a hose connected to a tank with H2 gas and striker. You make a torch out of the hydrogen gas that is coming out the tube lighting it with the striker.//) Anneal for 5 min to remove water vapor and other contaminants from the surface, any longer the mica will bubble and you will not get a flat surface.
 * 4) Drop cast a solution of truxene and toluene or methylene chloride and toluene
 * 5) Let it dry
 * 6) Vapor deposit octanethiol. ( //oven should be about 70 C and the sample should rest in there for 15-24 hrs)//