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Styles Bitchly Chem430 F16

2017-02-11T20:24:35Z

Mohannadfa: Blanked the page

Mohanad Ahmad Chem430 S17

2017-02-11T20:24:12Z

Mohannadfa: Created page with "Chemistry Research 430 :Spring 2017 :Mohanad Ahmad :Senior Chemistry Major ==Research Times== T/W 2-6 pm : section 02 = 0.50 credit = 8 hours per week. ==Proposed Research P..."

Styles Bitchly Chem430 F16

2017-02-11T20:22:50Z

Mohannadfa:

Chemistry Research 430
:Spring 2017
:Mohanad Ahmad
:Senior Chemistry Major

==Research Times==
T/W 2-6 pm
: section 02 = 0.50 credit = 8 hours per week.

==Proposed Research Project==
===Attachment of DNA to cAMP transcription factor: Atomic Force Microscopy study===

===General Information===
:Advisor: Dr. Laura Moore
:Other research student collaborators: Khdr Eskander

===Proposal===
The goal of this project is to introduce of a strand of DNA that carries a specific mutation into E.coli bacteria in order to over express the bacteria to synthesize the mutated c-AMP receptor protein (CRP), a transcription factor that regulates DNA to mRNA transcription. The intended mutation will expose a cysteine amino acid on the surface of the protein that will, as a result, bind to a gold surface through a thiol bond (R-S-H) in order to obtain images using Atomic Force Microscopy (AFM). Moreover, images of DNA-CRP complex will be taken using AFM, where the DNA will be attached to the tip of the AFM at one end and to the protein at the other end.

===Instruments to be used===
Atomic Force Microscopy

===References===
Ditzler, Lindsay R., Arundhuti Sen, Michael J. Gannon, Amnon Kohen, Alexei V. Tivanski. "Self-Assembled Enzymatic Monolayer Directly Bound to a Gold Surface: Activity and Molecular Recognition Force Spectroscopy Studies." ''J. Am. Chem. Soc'', 2011, 133 (34), pp 13284–13287.

===Research pledge===
I, Mohanad Ahmad, have read the Chem/Bioc 430 course syllabus and understand the general structure and expectations of the research program. The above material was prepared after consultation, and in conjunction with my research advisor.

==Written Report==

...from the course syllabus...

[https://www.acs.org/content/dam/acsorg/about/governance/committees/training/acsapproved/degreeprogram/preparing-a-research-report.pdf ACS Guide to Research Reports]

:''Research students are expected to write a report and submit it to the research coordinator by the last day of regular semester classes. These reports are intended to summarize the data collected over the course of the semester. Since this research course requires you to enroll in at least two semesters of research, two reports will be generated. The first semester report should be considered a work in progress, where as the final report should be a more comprehensive summary of your research project. These reports are necessary since several researchers may work on each project. The report will be organized so that it is clear what material is new and what material is review. When available, research students will be provided with an electronic copy of the latest report on their project. The research student is expected to update and improve the introduction, background, and literature sections with each report. Results that challenge earlier conclusions will be justified in a discussion section. Reports will be submitted in both electronic and hard copy to the Faculty Research Advisor AND Research Coordinator.''

===1. Descriptive information===
A project title, the names of the researcher (past and current), faculty research advisor, and other relevant student researchers and/or collaborators, the name and page numbers of the lab notebook(s) where the research is described, the dates when the work was done, and the names of the document file and its immediate precursor.

Example:

'''Detection of Radical Intermediate generated from the MAO enzymatic system.'''

Styles Bitchly*, Donald Hump, Penn Mickey, and Bradley E. Sturgeon#

*lead author, #research advisor

Research work documented in lab notebooks, SB_01 pages 1-25.

===2. Introduction===
State of the motivation for the project of interest in terms of current literature. When we make reference to current literature, this is where you provide specific reference(s) to this work. This section can be largely copied from an earlier report(s), if they exist, but it is expected that this section is edited to include newly found background information. Note: if the author of previous report(s) is included as a contributor to the project, you may cut and paste text; this is not plagiarism, it is collaboration.

===3. Background from earlier reports===
This section will summarize the work reported in earlier reports. If significant results were presented in the most recent report, these results will be summarized and in most cases can be added to that reports background section. This section is included mainly to confirm the current students overall understanding of the project.

===4. Experimental===
This section describes experiments done during the period covered by the report. Usually, this work will be similar or identical to that described in the prior report, if they exists. Any new experiments will be written up and added to the experimental section. Any experiments preformed under identical conditions need only reference previous reports.

:''Example:''

::'''Reagents''': ''List reagents used by product number and the source''.

::'''Enzyme Reactions''': All enzyme reactions were done using a totlal volume of 5.0 mL. Substrate concentration ranged between 1-12 mM. Reactions were initiated be the addition of enzyme.

::'''HPLC''': HPLC data was collected using the Waters Breeze HPLC with a C18 column (insert specs here). Specific HPLC conditions are given in the figure captions.

::'''UV-Vis''': UV-Vis data was collected using the HP 5832 UV-Vis spectrometer using a quartz cuvette. Sample concentrations were adjusted so as to not exceed 1.0 absorbance unit. Significant data was exported in the ".CSV" format and then worked up in Igor.

===5. Results===
This section documents the results of the experiments done during the period covered by the report. Tabulation of data is encouraged; representative spectra presented.

===6. Discussion===
In this section, the student will discuss the results of their work in context of the literature and the results of earlier reports. Questions that have been raised in earlier reports may be addressed here.

===7. Conclusions===
Restate the findings of this period of research. The statement “No conclusions have been reached,” is an acceptable statement.

===8. Future Directions===
In this section, the student will discuss possible experiments intended to address unanswered questions or technical problems on the project.

===9. Literature references===
Literature referenced in the report will be cited. This will be copied from the earlier report, and the student is expected to contribute to the accumulation of relevant literature. Remember that all cited literature must be read.

===10. Signature===
Two copies of the report will be signed and dated and turned in to the Faculty Research Advisor and archived by the Research Coordinator.

3,3′-Diethylthiacyanine iodide

2017-02-11T19:55:28Z

Mohannadfa:

By: Mohanad Ahmad

This experiment, a particle in a box, intends to measure the maximum UV absorbance, λmax, which will allow us to estimate the size of the box, the molecular frame, in which the compound 3,3′-Diethylthiacyanine iodide can exist. A small amount of 3,3′-Diethylthiacyanine iodide dye was dissolved in methanol and its absorbance was measured using a UV/Vis spectrometer. The structure of these dyes is complex in that the carbon backbone may contain several double bonds, i.e. pi bonds, that will introduce conjugation into the system. Conjugation affects the λmax of these dyes because it will cause a blue shift in their spectra. When two double bonds are conjugated, four pi-molecular orbitals are formed, two occupying the HOMO orbital and two occupying the LUMO orbital. Increased conjugation brings the HOMO and LUMO orbitals closer, reducing the energy gap between them. Therefore π to π* excitation will require less energy to occur. As a result, this shifts the spectra of the dye towards higher wavelengths. Figure 1 shows the structure of 3,3′-Diethylthiacyanine iodide, and figure 2 shows the respective UV spectrum. λmax of this dye was at 424 nm which was smaller compared to the other dyes tested in this experiment. This was accounted for by the fact that this dye has only one double bond in its carbon backbone and it's not a part of a conjugated system. Therefore, no blue hsifts occurred for this dye.

[[Image:3,3′-Diethylthiacyanine_iodide.jpg|250px|thumb|left|text|Figure. 1]]

[[Image:Graph0.jpg|250px|thumb|left|text|Figure. 2]]

3,3′-Diethylthiacyanine iodide

2017-02-11T19:54:53Z

Mohannadfa:

This experiment, a particle in a box, intends to measure the maximum UV absorbance, λmax, which will allow us to estimate the size of the box, the molecular frame, in which the compound 3,3′-Diethylthiacyanine iodide can exist. A small amount of 3,3′-Diethylthiacyanine iodide dye was dissolved in methanol and its absorbance was measured using a UV/Vis spectrometer. The structure of these dyes is complex in that the carbon backbone may contain several double bonds, i.e. pi bonds, that will introduce conjugation into the system. Conjugation affects the λmax of these dyes because it will cause a blue shift in their spectra. When two double bonds are conjugated, four pi-molecular orbitals are formed, two occupying the HOMO orbital and two occupying the LUMO orbital. Increased conjugation brings the HOMO and LUMO orbitals closer, reducing the energy gap between them. Therefore π to π* excitation will require less energy to occur. As a result, this shifts the spectra of the dye towards higher wavelengths. Figure 1 shows the structure of 3,3′-Diethylthiacyanine iodide, and figure 2 shows the respective UV spectrum. λmax of this dye was at 424 nm which was smaller compared to the other dyes tested in this experiment. This was accounted for by the fact that this dye has only one double bond in its carbon backbone and it's not a part of a conjugated system. Therefore, no blue hsifts occurred for this dye.

[[Image:3,3′-Diethylthiacyanine_iodide.jpg|250px|thumb|left|text|Figure. 1]]

[[Image:Graph0.jpg|250px|thumb|left|text|Figure. 2]]

3,3′-Diethylthiacyanine iodide

2017-02-11T19:54:29Z

Mohannadfa:

This experiment, a particle in a box, intends to measure the maximum UV absorbance, λmax, which will allow us to estimate the size of the box, the molecular frame, in which the compound 3,3′-Diethylthiacyanine iodide can exist. A small amount of 3,3′-Diethylthiacyanine iodide dye was dissolved in methanol and its absorbance was measured using a UV/Vis spectrometer. The structure of these dyes is complex in that the carbon backbone may contain several double bonds, i.e. pi bonds, that will introduce conjugation into the system. Conjugation affects the λmax of these dyes because it will cause a blue shift in their spectra. When two double bonds are conjugated, four pi-molecular orbitals are formed, two occupying the HOMO orbital and two occupying the LUMO orbital. Increased conjugation brings the HOMO and LUMO orbitals closer, reducing the energy gap between them. Therefore π to π* excitation will require less energy to occur. As a result, this shifts the spectra of the dye towards higher wavelengths. Figure 1 shows the structure of 3,3′-Diethylthiacyanine iodide, and figure 2 shows the respective UV spectrum. λmax of this dye was at 424 nm which was smaller compared to the other dyes tested in this experiment. This was accounted for by the fact that this dye has only one double bond in its carbon backbone and it's not a part of a conjugated system. Therefore, no blue hsifts occurred for this dye.

[[Image:3,3′-Diethylthiacyanine_iodide.jpg|300px|thumb|left|text|Figure. 1]]

[[Image:Graph0.jpg|300px|thumb|left|text|Figure. 2]]

3,3′-Diethylthiacyanine iodide

2017-02-11T19:54:06Z

Mohannadfa:

File:Graph0.jpg

2017-02-11T19:52:19Z

Mohannadfa: Mohannadfa uploaded a new version of File:Graph0.jpg

3,3′-Diethylthiacyanine iodide

2017-02-11T19:50:29Z

Mohannadfa:

3,3′-Diethylthiacyanine iodide

2017-02-11T19:49:32Z

Mohannadfa:

3,3′-Diethylthiacyanine iodide

2017-02-11T19:47:34Z

Mohannadfa: Created page with "This experiment, a particle in a box, intends to measure the maximum UV absorbance, λmax, which will allow us to estimate the size of the box, the molecular frame, in which t..."

File:3,3′-Diethylthiacyanine iodide.jpg

2017-02-11T19:34:02Z

Mohannadfa: Fig. 1

Fig. 1

Emission intensity of mercury lamp

2017-01-26T23:45:16Z

Mohannadfa:

The emission intensity of mercury lamp was investigated using a photo diode detector. The effect of covering the lamp with glass was also experimented since glass is well known for its ability to block UV light. To start off, the mercury lamp was heated for 5 minutes with a glass test tube covering it. The intensity of the emitted light was measured. Then the glass test tube was removed and the intensity was measured again. Figures 1 shows the variation in the intensity when the glass test tube is on and off. The yellow trace always has greater intensities. e.g. at wavelengths 430 nm and 550 nm, where the later belongs to the green region of the visible spectrum, compared to the red trace. Moreover, there is a yellow peak at around 250 which falls in the UV region of the spectrum. This makes sense because the glass test tube was not placed on the lamp and so UV light was not blocked. Figure two represents the two conditions as in figure 1, but in this case, a pair of eyeglasses were added to measure the difference in intensities. The same trend was shown as in figure 1 but the intensities were decreased because the lenses of the eye glasses added a layer of barrier that decreased the intensity of light detected. A small red peak is shown at 250 nm when the test tube was off the lamp, representing the detection of UV light.

[[File:No cap.jpg|500px|thumb|left|Figure.1]]

[[File:Cap_on.jpg|500px|thumb|left|Figure.2]]

Emission intensity of mercury lamp

2017-01-26T23:44:54Z

Mohannadfa:

The emission intensity of mercury lamp was investigated using a photo diode detector. The effect of covering the lamp with glass was also experimented since glass is well known for its ability to block UV light. To start off, the mercury lamp was heated for 5 minutes with a glass test tube covering it. The intensity of the emitted light was measured. Then the glass test tube was removed and the intensity was measured again. Figures 1 shows the variation in the intensity when the glass test tube is on and off. The yellow trace always has greater intensities. e.g. at wavelengths 430 nm and 550 nm, where the later belongs to the green region of the visible spectrum, compared to the red trace. Moreover, there is a yellow peak at around 250 which falls in the UV region of the spectrum. This makes sense because the glass test tube was not placed on the lamp and so UV light was not blocked. Figure two represents the two conditions as in figure 1, but in this case, a pair of eyeglasses were added to measure the difference in intensities. The same trend was shown as in figure 1 but the intensities were decreased because the lenses of the eye glasses added a layer of barrier that decreased the intensity of light detected. A small red peak is shown at 250 nm when the test tube was off the lamp, representing the detection of UV light.

[[File:Cap_on.jpg|500px|thumb|left|Figure.2]]

[[File:No cap.jpg|500px|thumb|left|Figure.1]]

File:No cap.jpg

2017-01-26T23:43:57Z

Mohannadfa: Figure. 1

Figure. 1

Emission intensity of mercury lamp

2017-01-26T23:43:14Z

Mohannadfa: Created page with "The emission intensity of mercury lamp was investigated using a photo diode detector. The effect of covering the lamp with glass was also experimented since glass is well know..."

File:Cap on.jpg

2017-01-26T23:41:30Z

Mohannadfa: Figure. 2

Figure. 2

File:Derek before.png

2016-09-22T22:19:31Z

Mohannadfa: Mohannadfa uploaded a new version of File:Derek before.png

File:Derek before.png

2016-09-22T22:18:56Z

Mohannadfa: Mohannadfa uploaded a new version of File:Derek before.png

Hot body

2016-09-22T22:17:35Z

Mohannadfa:

This experiment studies the effect of sun heat on body temperature. First, a thermal image of a body was taken inside a building (room temperature), and later, the person went out under the sun for five minutes. Another picture was taken after being outside. As shown, there is a significant increase in body temperature before and after being exposed to the sun. The head of the body was the point of maximum temperature, so this point was compared in the two stages to illustrate the change in body temperature. This point increased in temperature from about 30 degrees Celsius to 33 degrees Celsius.

[[File:Derek before.png]]
[[File:Derek before.png]]

File:Derek before.png

2016-09-22T22:17:12Z

Mohannadfa: Mohannadfa uploaded a new version of File:Derek before.png

Hot body

2016-09-22T22:15:41Z

Mohannadfa:

Hot body

2016-09-22T22:15:27Z

Mohannadfa:

File:Derek before.png

2016-09-22T22:12:07Z

Mohannadfa:

Hot body

2016-09-22T22:06:10Z

Mohannadfa: Created page with "This experiment studies the effect of sun heat on body temperature. First, a thermal image of a body was taken inside a building (room temperature), and later, the person went..."

File:Thermal image.bmp

2016-09-22T22:03:58Z

Mohannadfa: