Department of Chemistry

SOPs

Dept. data last updated on :21/03/2024

Standard Operating Procedures (SOPs) for Management of Departmental Resources

1. Laboratory and Chemical Safety

Labs:

· Each lab (UG and PG practical labs, research, and instrumental labs) will have a safety manual and the students are required to use personal protective equipment before entering the labs.

· Labs will have local exhaust and hoods for proper ventilation and all chemical containers must be properly labeled and arranged alphabetically.

· Potentially hazardous chemical processes or procedures will be carried out by following their specific SOPs, and must not be left unattended by the lab technician.

· Storing food in the lab refrigerator is strictly prohibited.

Chemicals:

· Chemicals, particularly hazardous and high risk must be safely used according to the laboratory-specific SOPs and chemical safety guideline.

· Students must be encouraged to use online resources such as ‘’Laboratory Chemical Safety Summaries (LCSS)’’ published on PubChem and ‘’Prudent Practices in the Laboratory’’ published by the National Research Council for handling and management of chemical hazards.

Equipment:

· Sophisticated instruments and equipment that involve high hazard operations (EPR, PXRD, UV-Vis spectrometry, FTIR, AAS, ITC, and GCMS) must be handled with their special handling procedures for their safe and proper use and be regularly monitored by engineers to maintain their quality.

2. Storage of Chemicals

· Chemicals must be stocked in separate chemical storerooms.

· Each chemical will be kept in defined storage place alphabetically, and toxic and hazardous chemicals will be separately stored in a well-identified area.

· Photosensitive chemicals will be kept in a dark place.

· Chemical and stationary inventory will be updated regularly and accurately.

3. Seminar Library

· The library will purchase the latest books, e-books, journals, e-journals, and newspapers to improve the knowledge and critical thinking of the students, researchers, and teachers.

· Faculty and students after their appointment or enrolment will fill library form with their details to become the member of the library and submit it to library in-charge, and only then library cards will be issued.

· The library will use its own guideline for the borrowing of books and journals.

· All member will follow the general guidelines and instructions issued by the library in-charge for the proper functioning of the library.

SOP For Cell Culture Lab

1. Access to the laboratory is limited to facility users only.

2. Remove all reagents and supplies from the Biosafety Cabinet upon completion of the experiment, or if there is a long delay in time between experimental steps.

3. Users MUST follow all safety and cleanliness guidelines:

a. Label all reagents and samples stored in common areas (not-labeled samples will be thrown away during weekly lab clean-up)

b. Clean the internal surface of the Biosafety Cabinet with 70% Ethanol/water solution. Bottles with the mixed solutions are available. Please refill bottles (ethanol and distilled water are available in the lab) upon usage.

c. All waist must be properly placed into the biosafety waste container (containers are provided and will be cleaned weekly).

d. If User generates a lot of waste and fills out the container, User should remove the full plastic back from the container, seal it and place a new bag into the waste container. Bags are located at the bottom of the waste container.

4. Persons must wash their hands after working with potentially hazardous materials and before leaving the laboratory.

5. Sharps, such as needles, scalpels, pipettes, and broken glassware must be placed in the appropriate designated containers.

6. Decontaminate work surfaces after completion of work and after any spill or splash of potentially infectious material with appropriate disinfectant.

7. Decontaminate all cultures, stocks, and other potentially infectious materials before disposal with bleach or autoclaving.

8. All procedures involving the manipulation of cells, tissues or other potentially infectious materials will be performed in a certified biological safety cabinet and in a manner that minimizes splashing, spraying or aerosolization.

9. Before leaving the laboratory, all personal protective equipment shall be removed and placed in an appropriately designated place for storage, washing, decontamination or disposal.

10. Used needles and other contaminated sharps must be discarded immediately after use into a sharps disposal container. Needles and other sharps shall not be sheared, bent, broken, recapped or re-sheathed unless required by a specific procedure and it can be demonstrated that there is no other feasible alternative.

11. Eating, drinking, smoking, applying cosmetics or lip balm or handling contact lenses is prohibited in laboratories.

12. Food and Drink shall not be eaten or stored in the Laboratory.

13. Mechanical devices are used for all pipetting and suctioning procedures (no mouth pipetting).

14. Gloves made from nitrile or another appropriate material will be worn when working with cell and tissue cultures and other potentially infectious materials.

15. Never touch your eyes, nose, mouth or your face while wearing gloves.

16. To prevent the spread of contamination gloves must be removed before touching “clean” surfaces such as door knobs, computer keyboards, books, telephones/cell phones, etc. Similarly, gloves used for other laboratory activities should be removed and new clean pair put on before beginning work with cell and tissue cultures.

17. Do not wash or reuse disposable gloves.

18. Before starting work in the BSC, review all procedures that will be used; identify the necessary equipment and materials that will be needed and develop a plan for safe and efficient work.

19. If the cabinet is not running, turn on the blower and fluorescent lights and turn off the UV light if it is on.

20. Verify that the BSC is operating correctly:

a. Check the instrument display/gauges for operational status.

b. Check the intake and exhaust grills for obstructions.

c. Check that the sash is in the appropriate position.

d. Check for the inward flow of air at the face of the BSC by holding a tissue near the bottom edge of the sash

21. Wipe down the interior surfaces of the cabinet with an appropriate disinfectant such as 70% ethanol

22. Load the cabinet with materials that will be needed for the procedure, wiping their surfaces with 70% ethanol to minimize the introduction of contaminants into the BSC. Position the materials near the back of the hood and organize them in a manner that will allow for the separation of clean and contaminated items during your work in the hood. Only materials needed for immediate work should be place in the cabinet. Extra supplies (gloves, culture flasks/plates should be stored outside the cabinet).

23. Before beginning your work, allow the hood to run for a minimum of 5 minutes to purge any airborne contaminates from the work area.

24. Avoid rapid, sweeping movements of the arms into or out of the cabinet. Move items into our out of the cabinet slowly and perpendicular to the face of the cabinet to minimize disturbance to the protective curtain of air.

25. Discard all waste materials generated by your work into appropriate containers inside the BSC. Close or cover all open containers.

26. Allow the cabinet to run for 3 to 5 minutes with no activity.

27. Disinfect the surfaces of all materials, equipment and containers that will be removed from the BSC, to minimize subsequent contamination in the laboratory.

28. Remove contaminated gloves and dispose of them appropriately

29. After putting on a clean pair of gloves, remove all materials for the BSC.

30. Wipe down all interior surfaces of the BSC with an appropriate disinfectant.

31. If the BSC is not scheduled for subsequent use, turn off the fluorescent light and cabinet blower. BSCs are designed for 24 hour operation, but in the interest of energy conservation it should be shut down when it will not be used for an extended period of time.

32. Work surfaces and equipment shall be cleaned and decontaminated on a regular basis with a freshly made solution of household bleach diluted between 1:10 to 1:100 or another suitable cleaner/disinfectant.

a. After completion of procedures involving potentially infectious materials.

b. Immediately after a spill of potentially infectious material and/or when surfaces or equipment become overtly contaminated

Perkin Elmer Lamda 25

UV/VIS Spectrometer SOP

The usage of the machine is NOT allowed without a proper training by the operator of the facility.

Ø Handling the instrument

ü START UP

1. Open the sample compartment cover.

2. Make sure that beam paths are free,i.e no objects project into beam paths, no samples are in the sample compartment.

3. Close the sample compartment cover.

4. Switch on the power switch.

5. Wait for approximately 3 minutes until all initialization is complete.

6. Ensure that PC is correctly connected.

7. Start UV WinLab.

ü ANALYSIS OF DATA

1. Oncetheinstrument ison,thecomputer maybepluggedinandturnedon.

2. Allowtheinstrument towarmupforat least 20 minutesbeforeuse.

3. On the desktop screen the PerkinElmer UV WinLab shortcut has to be double clicked to begin.

4. When software is openedinstrument, method has to be selected.

After selecting the instrument scan method, DataCollection” has to be clicked under the folder list on the left-hand side of the screen. This screenallows the user to note and change several data collection parameters such as the data interval andwavelength range as well as wavelengths at which there is a lamp or detector change.

5. Click on the sample info icon. This is where the user will input the number of samples wish need to be run.

6. When ready to continue, select the Auto zero button at the top of the screen. The user will beprompted to remove samples to perform a 100%T or 0A correction. Remove any samples fromtheinstrument, close the lidand press OK

7. Once complete the user will be prompted to insert the samples. The Lambda spectrometer is a double pass instrument and has a cuvette holder for both a blank and a sample. Place the blank in the holder nearest to the center of the instrument and the sample in the holder nearest to the front of the instrument. Close lid and hit OK to acquire a scan.When all samples have been run results can be saved.

ü SHUT DOWN

1. Close down UV Win Lab

2. Open the sample compartment cover and remove samples and cells from the sample compartment.

3. Close the sample compartment cover and switch off the spectrometer.

Ø MAINTENANCE

1. The instrument is constructed with high quality components and requires little maintenance other than to keep it clean and free of dust. To protect the optical system from dust and fumes the sample compartment should be kept closed when not in use.

2. Cells should only be held by non- optical surfaces

3. Cells should be protected from scratches and should never be rubbed against each other or any hard surfaces.

4. Avoid abrasive, corrosive or stain-producing cleaning agents, and make certain that the exposed surfaces of cells are optically clean.

5. Always wipe the optical surfaces of cells dry and free of fingermarks, using a soft cloth or cleaning tissue, just before placing them in the cell holder.

6. A constant temperature between 15 ºC and 35 ºC and constant humidity between 20% and 80% relative humidity need to be maintained for proper maintenance of the instrument.

7. Keep out of direct sunlight.

8. Illumination with diffuse lighting is ideal.

9. A suitable source of electrical power should be located in the vicinity of the instrument.

10. Electrical power must be available at a proper earth-grounded 3-wire electrical outlet

Perkin Elmer Lamda 45

UV/VIS Spectrometer SOP

The usage of the machine is NOT allowed without a proper training by the operator of the facility.

Ø Handling the instrument

ü START UP

1. Open the sample compartment cover.

2. Make sure that beam paths are free,i.e no objects project into beam paths, no samples are in the sample compartment.

3. Close the sample compartment cover.

4. Switch on the power switch.

5. Wait for approximately 3 minutes until all initialization is complete.

6. Ensure that PC is correctly connected.

7. Start UV WinLab.

ü ANALYSIS OF DATA

1. Oncetheinstrument ison,thecomputer maybepluggedinandturnedon.

2. Allowtheinstrument towarmupforat least 20 minutesbeforeuse.

3. On the desktop screen the PerkinElmer UV WinLab shortcut has to be double clicked to begin.

4. When software is openedinstrument, method has to be selected.

After selecting the instrument scan method , Data Collection” has to be clicked under the folder list on the left hand side of the screen. This screenallows the user to note and change several data collection parameters such as the data interval andwavelength range as well as wavelengths at which there is a lamp or detector change.

5. Click on the sample info icon . This is where the user will input the number of samples wish need to be run.

ü SHUT DOWN

1. Close down UV Win Lab

2. Open the sample compartment cover and remove samples and cells from the sample compartment.

3. Close the sample compartment cover and switch off the spectrometer.

Ø MAINTENANCE

2. Cells should only be held by non- optical surfaces

3. Cells should be protected from scratches and should never be rubbed against each other or any hard surfaces.

4. Avoid abrasive, corrosive or stain-producing cleaning agents, and make certain that the exposed surfaces of cells are optically clean.

5. Always wipe the optical surfaces of cells dry and free of fingermarks, using a soft cloth or cleaning tissue, just before placing them in the cell holder.

6. A constant temperature between 15 ºC and 35 ºC and constant humidity between 20% and 80% relative humidity need to be maintained for proper maintenance of the instrument.

7. Keep out of direct sunlight.

8. Illumination with diffuse lighting is ideal.

9. A suitable source of electrical power should be located in the vicinity of the instrument.

10. Electrical power must be available at a proper earth-grounded 3-wire electrical outlet

Perkin Elmer Lamda 365 UV/VIS Spectrometer SOP

1. The usage of the machine is NOT allowed without a proper training by the operator of the facility.

Ø Handling the instrument

ü START UP

8. Turn on power switch and allow instrument to warm up for at least 20 minutes.

9. Check LED light which is the lower left hand in front of the system

Power: blue > Power on

Ready: white > The communication of between PC and system

System: white > during the checking of system status

Caution: Do not execute UV Winlab before finishing the initialization of grating

10. Double click UV Winlab software.

ü ANALYSIS OF DATA

8. After opening UV Winlab , execute Scan mode icon in UVWin lab. The following message box will be displayed

Please confirm there is empty in the cell holder and close the sample compartment cover firmly before the initialization.

Empty the cell holder and close the lid firmly.Click O.K.

9. Start system Self Test. Check all parameters has pass click .

10. After selecting the instrument scan method the sample info screen will be opened. This is where the user will input the number of samples wish need to be run.

11. After this “Data Collection” has to be clicked under the folder list on the left hand side of the screen. This screenallows the user to note and change several data collection parameters such as the data interval andwavelength range as well as wavelengths at which there is a lamp or detector change.

12. When ready to continue, select the Auto zero button at the top of the screen. The user will beprompted to remove samples to perform a 100%T or 0A correction. Remove any samples fromtheinstrument, close the lidand press OK

13. Once complete the user will be prompted to insert the samples. The Lambda spectrometer is a double pass instrument and has a cuvette holder for both a blank and a sample. Place the blank in the holder nearest to the center of the instrument and the sample in the holder nearest to the front of the instrument. Close lid and hit OK to acquire a scan.When all samples have been run results can be saved .

ü SHUT DOWN

4. Close down UV Win Lab

5. Open the sample compartment cover and remove samples and cells from the sample compartment.

6. Close the sample compartment cover and switch off the spectrometer.

Ø MAINTENANCE

11. The instrument is constructed with high quality components and requires little maintenance other than to keep it clean and free of dust. To protect the optical system from dust and fumes the sample compartment should be kept closed when not in use.

12. Cells should only be held by non- optical surfaces

13. Cells should be protected from scratches and should never be rubbed against each other or any hard surfaces.

14. Avoid abrasive, corrosive or stain-producing cleaning agents, and make certain that the exposed surfaces of cells are optically clean.

15. Always wipe the optical surfaces of cells dry and free of fingermarks, using a soft cloth or cleaning tissue, just before placing them in the cell holder.

16. A constant temperature between 15 ºC and 35 ºC and constant humidity between 20% and 80% relative humidity need to be maintained for proper maintenance of the instrument.

17. Keep out of direct sunlight.

18. Illumination with diffuse lighting is ideal.

19. A suitable source of electrical power should be located in the vicinity of the instrument.

20. Electrical power must be available at a proper earth-grounded 3-wire electrical outlet

PERKIN Elmer frontier FTIR Protocol/SOP

The usage of the machine is NOT allowed without a proper training by the operator of the facility.

v HANDLING OF INSTRUMENT

· Switch on the power to the instrument using the switch on the rear of the instrument. The instrument will initialize, which will take approximately 2 minutes.

· On the computer desktop screen double click on Perkin Elmer icon to open the software to collect data.

· In the set up instrument Basic tab of the software set Start and End points of the required scan range and the accumulatios required either as number of scans or as a length of time. Resolution in cm^-1 can also be set here.

· In the instrument Advance tab CO₂and H₂O correction tab is left on and acquisition is set to medium.

· Scan speed is adjusted to change signal to noise collection time. Slower speed results in better signal to noise but longer collection time and faster speed results in worse signal to noise but shorter collection time.

· If the results obtained are coming strange than click on restore defaults.

· To set up instrument data collection in auto save option save location, select your own folder.

· Before collecting the data., beam path needs to be cleared for that sample chamber is opened and it is assured that mojo is basic transmission mojo, than the lid is closed and it is made sure that it latches. Now instrument is ready to do background correction.

· To collect background, click on background icon in the software window.

· After background collection is done sample can be mounted.

· To mount a sample open the chamber place sample using double sided tape close the lid make sure it latches.

· Sample name is typed in sample ID box in the software window and than scan icon is clicked to obtain the data.

· After obtaining all the required data the software is closed and computer is shut down.

v MAINTENANCE

· Clean the outside of the instrument using damp cloth. If necessary a mild detergent may be used.

· Avoid spilling liquids into the instrument.

· Do not touch or attempt to clean any optical surface in the instrument because this will impair its performance and may easily damage the component.

· Before moving the spectrometer, switch off the power supply wait 60 seconds and disconnect the power cable.

· When all three sectors of dessicant indicator are pink than dessicant must be changed. The instrument optics may be fogged . Do not switch the instrument either ON or OFF until all sectors are blue.

· Don not use flammable gas to purge the instrument. The spectrometer contains a hot source, and a fire and explosion will result. Only use clean dry oil free nitrogen or air to purge the instrument.

Perkin Elmer Lamda 850

UV/VIS Spectrometer SOP

The usage of the machine is NOT allowed without a proper training by the operator of the facility.

Ø Handling the instrument

ü START UP

11. . Switch on the power switch.

12. Wait for approximately 5 minutes until all initialization is complete.

13. Ensure that PC is correctly connected.

14. Place solid sample in the universal reflectance accessory.

15. Start UV WinLab.

ü ANALYSIS OF DATA

14. Oncetheinstrument ison,thecomputer maybepluggedinandturnedon.

15. Allowtheinstrument towarmupforat least 20 minutesbeforeuse.

16. On the desktop screen the PerkinElmer UV WinLab shortcut has to be double clicked to begin.

17. When software is openedinstrument method has to be selected .

18. Click on the sample info icon . This is where the user will input the number of samples wish need to be run.

19. When ready to continue, select the Auto zero button at the top of the screen. The user will beprompted to remove samples to perform a 100%T or 0A correction. Remove any samples fromtheinstrument, close the lidand press OK

20. Once complete the user will be prompted to insert the samples. The Lambda spectrometer is a double pass instrument and has a cuvette holder for both a blank and a sample. Place the blank in the holder nearest to the center of the instrument and the sample in the holder nearest to the front of the instrument. Close lid and hit OK to acquire a scan.When all samples have been run results can be saved .

ü SHUT DOWN

7. Close down UV Win Lab

8. Open the sample compartment cover and remove samples and cells from the sample compartment.

9. Close the sample compartment cover and switch off the spectrometer.

Ø MAINTENANCE

21. The instrument is constructed with high quality components and requires little maintenance other than to keep it clean and free of dust. To protect the optical system from dust and fumes the sample compartment should be kept closed when not in use.

22. Cells should only be held by non- optical surfaces

23. Cells should be protected from scratches and should never be rubbed against each other or any hard surfaces.

24. Avoid abrasive, corrosive or stain-producing cleaning agents, and make certain that the exposed surfaces of cells are optically clean.

25. Always wipe the optical surfaces of cells dry and free of fingermarks, using a soft cloth or cleaning tissue, just before placing them in the cell holder.

26. A constant temperature between 15 ºC and 35 ºC and constant humidity between 20% and 80% relative humidity need to be maintained for proper maintenance of the instrument.

27. Keep out of direct sunlight.

28. Illumination with diffuse lighting is ideal.

29. A suitable source of electrical power should be located in the vicinity of the instrument.

30. Electrical power must be available at a proper earth-grounded 3-wire electrical outlet

EPR Protocol/SOP

The usage of the machine is NOT allowed without a proper training by the operator of the facility.

Handling the Instrument:

Startup

(a) Turn the spectrometer power switch on.

(b) Turn the host computer on.

(d) Enter ID = xxx, Password =xxx and Double click on the ESR icon.

(e) The spectrometer control program is automatically started.

(f) Verify the indicators

(i) Water

(ii) Magnet

(iii) Gunn

(g) ESR standby

1) Measurement of the sample

(a) Start the instrument

(b) The SPECTROMETER window is diplayed.

(d) The Q-DIP and SHF parameters windows is displayed.

(e) Insert the sample in the cavity resonator.

(f) Set the dial of the manganese marrker, if you will use the ESR marker

(g) Select the operation method, and adjust the microwave parameters.

(i) Manual operation

(ii) Automatic tuning

(iii)Semi-automatic tuing

(h) Perform measurement

(i) Create a file and save it.

(j) Start the data processing program, if you want to analyze data.

(k) Shut down the instrument

Precautions

· When you walk around the instrument, be aware of the cables, hoses or protruding objects to prevent tripping, damaging or disturbing the instrument.

· Do not step on the frame or table of the instrument during daily operations or maintenance. Use a steady footstool to prevent falling or damaging the instrument.

· Be sure to wear protective gloves when handling a sample tube containing a poisonous sample to avoid contact with the sample.

· Do not pack a sample which might explode or ignite by temperature, impact or pressure into the sample tube to prevent the risk of injury receiving from the shattered fragments of the sample tube..

· Beware of water leak i.e. after turning on the cooling water system, make sure that there is no water leak.

· Be careful no to exceed the specified pressure and flow rate of cooling water, otherwise, the cooling water tube might burst with pressure.

· Do not bring any iron objects near the electromagnetic field during the operation.

· If you wear a medical device such as cardiac pacemaker, stay out of areas where the magnetic field is strong enough to affect it.

· Do not bring a magnetic tape or floppy disk near the magnet.

· While working in the EPR Laboratory, researchers are always required to wear Personal Protective Equipment (PPE). The appropriate PPE include safety glasses, long pants/skirt covering the legs completely, and closed-toe shoes.

· Food and beverages cannot enter the lab. Never eat or drink inside the lab.

· Samples should be prepared in the user’s chemistry lab. The outside of sample tubes should be cleaned with an appropriate solvent in the user’s lab.

GC-MS Protocol/SOP

The usage of the machine is NOT allowed without a proper training by the operator of the facility.

Handling of Instrument

· Make sure that carrier gas (Helium or Nitrogen gas) cylinder is open and flowing at 7.0 bar.

· Turn on the main power switch of the GC, MS, PC and printer.

· Double Click 'GCMS' Real time analysis' icon from the main screen.

· Click 'Instrument from the main menu and select 'vacuum control".

· Click "Auto startup' in the 'vacuum Control window and wait until the function is completed.

· Open the Method file' required for the analysis and click download initial parameters from 'Acquisition' in the main Manu.

· It display in green signal as 'GC Ready & MS Ready.

· Open Peak View monitor screen from assistant bar.

· Click Start Auto Tuning' from the Assistant bar, once tuning finished save the Tuning file from 'save as with today date then click 'Auto tuning Report.

· Click 'sample login from Assistant Bar, and then enter the sample name, datafile, analysis details etc. and current Tuning File' then click OK.

· Click 'Stand by' from the Assistant bar and wait till GC & MS Ready display on the screen.

· Inject 1 μl sample and press Start button from GC control panel.

Note: (a) The pressure value should reach upto 2.5 x 10^-5.

(b) Sample must be volatile.

(d) After analysis the temperature should go down to fix 100.

2. Analysis of Data

· After completion of analysis. Click GCMS post run analysis' in Desktop.

· Go to File' in the main menu and open the Data required for the report preparation and do the integration.

· Click peak table in the side menu and click Select all and register in the Edit menu,

· Tab to the next window and click Similarity search.

· Click Save from the main menu and close peak table.

3. Shutdown:

· Click "Instrument' from main menu and select "Vacuum control" icon.

· Click 'Auto shutdown' in the window, wait till Auto shutdown 'completed appear on the screen.

· Close 'GCMS Real Time Analysis' window and shutdown the PC.

· Turn off the MS, GC, PC and printer

· Close the 'Cylinder' tightly.

4. Precautions:

· Temperature should be maintained between 15°C and 27°C respectively.

· Humidity should be maintained between 40 % and 60 %.

· Purity of helium or nitrogen used for analysis should be A grade.

· Change the vacuum pump oil for every 4-6 months.

· Replace the injection septa for minimum of 100 injections.

· Keep the split/spit less liners clean and free from deposition.

· Cleaning is recommended when the deposition is high and reduced response, peak tailing/mounting/fronting is observed.

· Monitor the leak parameters for air and water every day.

· Food and beverages cannot enter the lab. Never eat or drink inside the lab.

· Samples should be prepared in the user’s chemistry lab. The outside of sample tubes should be cleaned with an appropriate solvent in the user’s lab.

· Be sure to wear protective gloves when handling a sample tube containing a poisonous sample to avoid contact with the sample.

Powder X-ray Diffraction Protocol/SOP

1. The usage of the machine is NOT allowed without a proper training by the manager of the

facility.

2. General introduction

a) Figure 1 shows the XRD main unit. The X-ray warning lamp (#4) will light if the equipment is energized. To open the door, press the door-lock button, wait for 5 seconds, then slide the door open. Click the button again when the door is closed.

b) There is an indication light on the X-ray tube as shown in Figure 2. When it is on, it means the shutter is open and that an experiment is in progress. Please refer to the online scheduler in order to reserve a time to use the XRD.

3. Starting the XRD

(You may skip step a. c. d if the system and X-ray is already on. When the X-ray light on top the system is lit, it means the X-ray was left on, you don’t need to turn it on again.)

a)To turn on the Main unit, press the “|” ON button from the main panel as shown in Figure 1. Then the OPERATE light should light up in green.

Figure. Main panel

b) The computer on the desk to the right of the XRD controls the SmartLab software. This computer should always be left on.

c) Turn on the Haskris water chiller located to the left of the XRD unit by flipping the ON/Off button. Wait for at least 30 minutes before turning on X-ray Tube. THIS IS VERY IMPORTANT! DO NOT FORGET THIS STEP!

d) The X-ray tube may be turned on after the 30 minutes wait. From the flow chart section of the software as indicated in Figure 5, click “Startup”. In the new window that appears (see Figure 7b) click “execute” to start the X-ray tube. There is no need to change any parameters in this window. This process may take 5 minutes

4. General Procedure:

Switch on the UPS.
Open the chiller and wait until the operating temperature (21oC) is reached
Adjust the water pressure at46psi.
Turn on the computer.
Turn on the XRD instrument by switching on the MCB.
Prepare the sample slide for analysis.
Insert the USB in computer and run the software.
Wait for 15 minutes until the instrument is ready for analysis.
Place the slide between the X-ray beams and analyze the sample..

5. Precautions:

Follow the SOP strictly to keep the instrument in good condition. No explorations allowed on software unless permitted by lab operator.
Never use your own USB drive on the XPS computer.
Never surf the web on the XPS computer to minimize the risk of the computer being hacked.
Only trained personnel are permitted to operate XRD unit.
Be aware of the xray beam path and never lace any part of the body in the direct beam path.
Food and beverages cannot enter the lab. Never eat or drink inside the lab.
Samples should be cleaned with an appropriate solvent in the lab.
Be sure to wear protective gloves when handling a sample tube containing a poisonous sample to avoid contact with the sample
To insure your safety, do not attempt any unauthorized repair of x-ray unit. ··
Be sure the beam is off and shutter is closed prior to sample changing or other activity. Check all warning lights prior to placing hands near the beam line. Use a GM radiation survey instrument to confirm “beam off” conditions. · Use the shielding and interlocks provided. Do not bypass interlocks.
Users should acknowledge Department of Chemistry in their publications.

SOP FOR CIRCULAR DICHROISM

I. Start up

1. Turn on Nitrogen gas flow.

2. Turn on the computer and open the program “Spectra Manager”

3. Turn the power switch on the CD to “ON” position (note: this will not turn the lamp on)

4. Start the “Spectra Manager Program” and double click on “Spectrum Measurement”.

II. Data Acquisition

1. On the drop-down menu bar, select the “Parameters” tab. The following are only a guideline for peptide/protein solutions.

(i) Bandwidth = 1 nm.

(ii) Response = 4 sec (1 sec)

(iii) Sensitivity = Standard.

(iv) Measurement Range = 250 – 190 nm.

(v) Data Pitch = 0.1 nm.

(vi) Scanning Mode = Continuous.

(vii) Scanning Speed = 100 nm/min.

(viii) Accumulation = 5

2. At the “Data Mode” tab, ensure the settings are appropriate for your experiment: For CD experiments:

Channel #1 = CD

Channel #2 = HT

3. Click “OK” to apply the parameters and close the dialog box.

4. Click “Start” to begin data acquisition.

5. Once a scan is complete, it will automatically open up in “Spectra Analysis”. This software can be used to perform background subtraction and peak fitting.

III. USING the Peltier temperature controller

1. Turn on the water bath and make sure that the temperature is set to 20°C.

2. Turn the power switch on the Peltier controller (located between the PC and CD) to “On” position.

3. Press the “Start” button on the Peltier controller.

4. In “Spectrum Measurement”, go to the menu Measurement→ Accessory

5. Choose “Temperature” and change the option to “JASCO Peltier Type (Single, RTE On)”

6. You can now use Control → Accessory menu in the “Spectrum Measurement” software to set the temperature.

7. When you are done power down the Peltier controller and the water bath.

IV. Shut down

1. Leave the Nitrogen gas ON.

2. In the “Spectrum Measurement” software go to the menu Control → Light Source. Uncheck “Lamp On” box and click OK. This will turn the lamp off.

3. Quit the software and turn off the main green power switch.

4. Now, turn the Nitrogen gas off.

# Always Remember:

1. Do not use the CD without training!

2. Do not change settings on the regulator or the gauge itself.

3. Always leave the nitrogen stream on when the instrument (specifically the instrument lamp) is on! Once the instrument is fully shut down, wait a few minutes and only then turn the nitrogen off.

4. The lamps should never have > 1000 hours of use.

5. If case of Peltier controller, Do not allow water to circulate when the lamp is not lit!

Fluorescence Spectrophotometer SOP

I. Start up

5. Turn on the spectrophotometer and the computer.

6. Double-click the “FL Solutions” program icon. A window will appear which displays all tool bars.

II. Parameters settings

1. From the R.H.S tool bar, select the “Method” command then follow the steps:

(a) General> Measurement> Wavelength scan

(b) Instrument> Scan mode> Emission

(d) Set excitation and emission wavelengths, Slit widths, PMT voltage and scan speed values and then click “OK” to apply the parameters.

2. Select Sample> Select the specified folder (already created in the D: file)> write the sample name for each run>OK.

3. Select Monitor> Put Y-axis max and min values > Ok

III. Sample run

1. Clean the cuvette properly and fill it with blank solution.

2. Keep the cuvette in the chamber and click the “auto zero” button.

3. Now fill the cuvette with sample solution and click “measure” button for each run. The instrument records the spectra within the specified wavelength range.

4. The spectra and data will be saved in the specified folder.

5. Open the data processing window after data acquisition via File > Open. A spectrum alone can be displayed or both spectrum and peak table can be displayed.

IV. Shut down

After completion of measurement, shut down the instrument in the following procedure

5. Select File > Exit command.

6. A window will appear from where choose the second option.

(i) Close the monitor window but keep the lamp operating?

(ii) Close the lamp and then close the monitor window?

7. Click Yes, and the FL Solutions program will then be terminated.

8. Allow the light source to cool for approximately five minutes.

9. Confirm that the sample chamber is empty and then Turn off the power switch of the spectrophotometer main unit.

10. Then Turn off power to the personal computer.

# Always Remember:

6. Do not use the fluorescence spectrophotometer without proper training!

7. Keep the lamp off when you are not using spectrophotometer.

8. Check the usage period of the Xenon lamp. It should not exceed 500 hours of use.

9. Do not smoke or hold a flame near the fluorescence spectrophotometer.

ISOTHERMAL TITRATION CALORIMETRY (ITC) SOP

I. Start up

7. Turn on the computer

8. Turn on the ITC instrument (there are 2 power switches, one at the back)

9. Then open the MicroCal iTC₂₀₀ software. Verify that the red light at the front of the instrument is on.

II. Cleaning of cell & syringe

1. Make sure you have wash station bottles and filled to at least 50% with the appropriate solutions i.e with distilled water and methanol respectively.

2. Select the Instrument Controls tab and click the Cell and Syringe Wash button in the Washing Module panel to clean the cell and syringe.

3. Follow the step-by-step screen instructions and then click OK to start the washing procedure of cell as well as syringe.

4. While the syringe washing procedure is running, rinse the sample cell manually with blank solution a number of times.

5. Repeat these cleaning steps after completion of experiment/titration.

III. Cell and syringe filling

1. Fill the sample cell and reference cell carefully with water and sample solution, respectively by the Hamilton syringe. Be careful not to introduce air when doing this.
2. Click on the Syringe Fill button in the Washing module panel and follow the step-by-step instructions on screen to load the syringe with ligand solution.

3. Insert the pipette into the cell port. Apply light pressure on the top to make sure it is correctly seated. Click OK.

IV. Experimental set up

1. Click on the “Advanced Experimental Design” tab.

2. Set the Experimental Parameters as follows and set the Feedback Mode/Gain to High.

3. Set the Edit Mode to All Same and enter the following injection parameters

4. Enter a file name for the results (e.g. Training.itc) in the Data File Name field.

5. After filling cell and syringe, click Start button to begin the titration. The run time will be approximately 1 hour.

6. Click on the Real Time Plot tab to view the raw data.

V. Data analysis

1. Double click on the MicroCal Analysis Launcher icon on the desktop.

2. Click on iTC200. This will open the analysis software for Microcal iTC200.

3. Click on Read Data. To open your titration experiment data file Training.itc, click on the data file, click on Add File(s) and then on OK.

4. Click the model fitting to fit the data. This will open a dialogue box showing the initial fitting and values for stoichiometry (N), association equilibrium constant (K) and enthalpy change (H).

5. The N, K_a, ΔH and ΔS values based on the fitting will be displayed next to the plot.

6. Select File>Save Project As to save the fitted results. Enter a name and click Save.

VI. Shut down

1. Close the software.

2. Shutdown Personal Computer.

3. Turn off 2 switches of ITC.

Always Remember:

1.Do not work with the device unless you have proper knowledge of handling.

2.The system should be cleaned after each run using the Cell and Syringe Wash command.

3.Replace the distilled water in the reference cell every week.

4.There should be NO air bubbles inside the cell during the experiment run.

5.do not invert the Hamilton syringe.

ATOMIC ABSORPTION SPECTROMETER, GBC-932-PLUS, AUSTRALIA

Objective

This document outlines the procedure for the operation of the Atomic Absorption Spectrophotometer from GBC Company (Model 932-Plus), Australia.

Scope
Atomic absorption spectrometry (AAS) is a technique in which free gaseous atoms absorb electromagnetic radiation at a specific wavelength to produce a measurable signal. it is an important sensitive method that is suitable for the determination of selected elements at the trace and partly at the ultra-trace level.

Operating procedure

Ø Turn on the instrument (Power switch at the right hand of the instrument is only turned on when we wish to use furnace), computer and verify ventilation.

Ø Double click on the “GBC Avanta” program located on the desktop.

Ø From the drop-down menu select the “online” item and press OK. The program will proceed through a checking process. Please wait until finishing the checking process. This usually takes a few minutes.

Ø An element selection window will appear. Select the working lamp and click on finish.

Ø GBC Avanta” software will open. Open the “instrument” menu and select the “measure method” item. The “set measurement method” dialog box opens. Select the method you wish to use then click on Execute. Wait for the system to locate the selected atomizer in the path of light. This usually takes a few minutes. After finishing this procedure, close the “set measurement method” dialog box

Ø Optimize atomizer position using instrument” menu-Burner parameters. The position of the atomizer should be adjusted carefully so that the whole energy of the hollow cathode lamp reaches the detector. The path of light can be checked by a piece of white paper.

Ø After adjusting the position of the atomizer, click on “Lamp” icon and then click Next. Press “search peak” button. The “wavelength scanning/peak searching” dialog box opens.

Ø Click “search peak” button and wait. This usually takes a few minutes. After appearing the spectrum, close the “wavelength scanning/peak searching” dialog box.

Ø Click on “Energy” icon. The “Energy” dialog box opens. Click on “Auto-balance”. Energy of the lamp should be about 100 %.

Ø Click on “Sample” icon and enter calibration and sample information.

Ø Prepare standard solution (dilute) for calibration. Blank should be prepared for adjusting zero (0)

Ø Run the prepared sample.

Do’s and Don’t

Ø Do not leave without closing the acetylene tank when not in use. Acetylene is explosive and quite dangerous.

Ø To shut off the flame in an emergency- push the red button on the right-front of the instrument.

Ø The pressure of the acetylene gas cylinder must never fall below 4 bar.

Ø When the flame is ignited, to protect the furnace, insert the steel plate which separates the furnace from the flame.

Ø Water trap should be filled with water, so that excess amounts of water overflow into the waste container.

THERMOGRAVIMETRIC ANALYSIS/DIFFERENTIAL SCANNING CALORIMETRY, SHIMADZU, JAPAN

Purpose and Scope:

This document describes the procedures and for using the TG/DTA-60 (SHIMADZU C30574300134)/DSC-60 (SHIMADZU C30454400547) series Instruments TGA/DSC. The scope of this document is to establish user procedures. TGA stands for ‘Thermogravimetric Analysis’. A very versatile and sensitive instrument to measure the change in weight as a function of temperature. From TGA/DSC we can determine the number of dynamic properties. DSC stands f6r differential scanning calorimeter used to study various endothermic and exothermic reactions in the sample as well as thermal transitions.

Ø Thermal stability of materials

Ø Oxidative stability of materials

Ø Estimated lifetime of a product

Ø Decomposition kinetics of materials

Ø The effect of reactive or corrosive atmospheres on materials

Ø Moisture and volatiles content of materials.

Ø Thermal transition

Ø Exothermic and endothermic reaction

These properties can be determined from either weight gain or weight loss. It is also important to remember that this is a kinetic measurement so rates and masses should be carefully chosen and they should be included in any reporting of data.

Features and Specifications of the Instruments DTG-60 (SHIMADZU C30574300134):

Ø RT-1000 C

Ø N2 and/or dry air purge

Ø Mass accuracy: +/- 0.5%

Ø Mass precision: +/- 0/01%

Ø Sensitivity: 0.1 ug

Do’s and Don’t

Ø Please do not eat or drink while operating this instrument.

Ø Never touch the hang-down wire or thermocouple.

Ø Never attempt to operate the instrument without nitrogen flow.

Ø Do not change any of the user preferences or instrument preferences.

Ø Notify the staff member of any issues; do not attempt to ‘fix a problem.

Ø Once a measurement is running it is very important not to bump or disturb the instrument or the table it’s sitting on, it is very sensitive to vibrations and can cause erroneous or anomalous behaviour.

Ø Before starting, please verify that there is plenty of N₂ in the cylinder and that the flow rate is at 10/90 mL/min for the furnace.

Procedure steps

Ø Turn on the stabilizer and computer

Ø Switch on the instrument, and wait for 10 mins.

Ø Calibrate the detector to a zero (0) position

Ø Left the instrument on for about 20 mins. After calibration.

Ø Again, calibrate the detector to zero (0) position by placing alumina pan on it.

Ø Place the sample (4-8 mg) in the right alumina pan.

Ø Adjust the operating temperature, suggested by the scholar

Ø Set the parameter

Ø Make a folder by name of supervisor and scholar

Ø Code the sample

Ø Run the instruments for the analysis

Ø Use the nitrogen gas for purging during the analysis

ELECTROCHEMICAL ANALYSIS SYSTEM, VersaSTAT 3, AMETEK SCIENTIFIC, USA

Cyclic Voltammetry is a versatile method for scientific investigation and innovation due to the fact that most processes involve electron transfer, which makes them be able to be monitored by this technique.

Beginning Experiments:

Ø Turn on the VersaSTAT 3 Instrument Electrochemical Workstation. The switch is a button on the front, facing the small box, and the button will be green when it’s on. Make sure to turn it off at the end of use.

Ø Open the VersaStudio software located on the desktop of the computer.

Ø Click Setup and Techniques to choose your method of electrochemistry, e.g. cyclic voltammetry (CV)/Chronoamprometery/Chronopotentiometry/LSV etc.

Ø Click Parameters to set up your method, and save the change.

· For CV, set initial and final E (usually 0.00V), and high and low E will be determined by the desired potential window for your experiment. Scan polarization will depend on which direction you want to scan first, negative or positive. The scan rate is usually set as 0.1V/s, and you can change this to the desired scan rate based on your needs. Set the sensitivity to be the value bigger than what you think the current will be. It can stay as default, 10^-6, or you can change it to a lower sensitivity setting, preferably 10^-5. See the VersaSTAT 3 point-person for questions. Sweep segments are usually set as 5. Sample interval and quiet time will stay asdefault.

Ø Once the parameters are set, click the Play button to start the measurement. You
can Pause and Stop a run.

Ø When the measurement is done, make sure to save the data. It will say Run
Unsaved at right if you haven’t saved.

Ø Data save as a VersaSTAT 3 Instruments file, you can download the software if you have aPC and analyze data with their program or you can convert the data to text.

Ø If the data is very noisy, smoothing can be performed by the software by clicking
DataProc and smooth.

· The noise of the data can also be due to the fluctuation of the glovebox atmosphere. If this is the case, repeated measurement is recommended.

Do’s and Don’t

Ø Do not touch the electrode during the analysis.

Ø There should be no electricity fluctuations.

Ø Only see a flat line without signals. Check whether your electrodes are connected properly.

Ø Only see noise or weird curves-check whether electrodes are connected properly and are not touching the side or each other, and are submerged down into the solution.

Ø When you open the program you get an error message-shut down the program and turn on VersaSTAT 3workstation first, then open the program.

Ø If you see the signal at first and then it flats out-stop the run and set your sensitivity to a
higher value, or lower value; you are just out of the range of the current you chose.

After Experiments:

Ø Used Pt wire counter electrodes need to be soaked in 1M HNO₃ for at least 1 h.

Ø Used Ag wire reference electrodes with the glass tubes need to be rinsed by the solvent used for Echem data collection at least 3 times and soaked in 1M HCl for about 1 h.

Ø Used working electrodes (Pt or glassy carbon or graphite) need to be rinsed by the solvent used for Echem measurement at least 3 times.

Ø Used Ag/AgCl reference electrode will be soaked in the solvent used for experiments, DMF, and MeOH for 5 mins respectively. After that, rinse the electrode in distilled water and put it back in a vial with fresh 1M KCl solution.

Ø Turn off the VersaSTAT 3 Instrument Electrochemical Workstation after use.

MAGNETIC SUSCEPTIBILITYBALANCES SHERWOOD SCIENTIFIC, UK

Identification of the method

Operation of the Magnetic Susceptibility Meter (SHERWOOD).

Applicable matrix of the method

This instrument can be used for soil/sediment samples.

Scope and Summary of the Method

This standard operating procedure is required to operate the SHERWOOD Magnetic Susceptibility Meter. This method is used to determine the magnetic susceptibility of soil and sediment collected from the field or artificial mixtures of mineral or chemical ingredients.

The SHERWOOD Magnetic Susceptibility System comprises a portable measuring instrument, the SHERWOOD meter, and three sensors controlled by a handheld Trimble Nomad field data logger loaded with Bartsoft control software. A low-frequency AC magnetic field is generated by the SHERWOOD Magnetic Susceptibility System. When a sample is placed in this field, there is a change in the field that is detected by the system. This change is converted into a magnetic susceptibility reading. Use SI units when taking measurements.

Detection Limit

The SHERWOODMagnetic Susceptibility Meter is capable of measuring the magnetic susceptibility System International Units (SI). The maximum resolution is 2x10^-6 SI (vol) depending on the attached sensor and environment. The operating temperature range for this instrument is -40° C to 70° C.

Procedure Steps

Ø Turn on the instrument.

Ø Wait until the instrument is calibrated.

Ø Weigh the empty capillary.

Ø Weigh the capillary with the sample in it more than 1.5 cm.

Ø Run the instrument and note the reading.

Do’s and Don’t

1. Temperature-induced drift - Each sensor compensates to minimize temperature-induced drift that arises from changes in the permeability of free space which affects the calculation for magnetic susceptibility.

2. Wet conditions - Very wet conditions should be avoided, but the instruments are sealed to prevent the entrance of moisture.

3. This instrument should not be operated close to high power radio transmitters or heavy electrical machinery.

4. If measurements fluctuate, the removal of the transit clamp may alter the zero setting of the beam.

5. Should it not be possible to zero the display using the zero knob.

6. The balance should be set up on a flat, stable surface free from vibration, and should be positioned away from the influence of stray magnetic fields.

7. The sample guide is designed such that a glass tube that is broken while using the balance will fall through the base of the unit. Care should be taken not to damage the thin wall of the guide tube when cleaning.

DIGITAL AUTOMATIC POLARIMETER (M-HB-P701) HELIX BIOSCIENCES, NEW DELHI, INDIA

Objective: This SOP gives the procedure of operation and calibration of polarimeter.

Scope: The operation and calibration of Polarimeter instrument to determine the specific optical rotation of given test sample.

Operating Procedure

1. Switch On the electric supply and within 10 minutes, the sodium lamp to glow optimally.

2. Check the polarimeter tube and its cabinet. It should be clean.

3. Position the incoming light source, polarimeter tube and cabinet in a line by rotating the revolving stand of sodium lamp.

4. For clear vision of colour shade, adjust the upper and lower eyepiece to anterior and posterior side.

5. Fill the polarimeter tube with water / blank in which the substance is dissolved and place this in cabinet. (Determine at Temperature 25°C, unless & otherwise specified in the procedure/monograph)

6. Rotate the knob at the anterior right and match the colour shade in both sections by
observing in lower eyepiece.

7. Take the reading in upper eyepiece, it should be about zero. Rotate the vernier scale
at the left anterior head of instrument. Add the reading of main scale and vernier scale,
and find the reading of rotation.

8. Fill the polarimeter tube with the liquid / prescribed solution. Solution / liquid should be clear and free from air-bubble.

9. Rotate the knob for matching the colour shade similarly as step 6

10. Take the reading in + or – in upper eyepiece and note it. (Take three concurrent readings of blank as well as sample and consider the mean value).

Do’s and Don’t

Ø Handle the instrument and polarimeter tube carefully.

Ø Do not keep polar meter’s tube without cleaning after use. It should be clean after each use.

Ø Keep Switch off the instrument when not in use.

Ø The solution should be homogenized.

Ø Specific optical rotation to be measure sample should be clear.

Ø Avoid air bubbles in sample tube, and if any small air bubble observed, then should be adjusted in the middle portion of the tube.

Ø The cell should be placed properly.

Ø Read the scale properly.

Ø The cell should be clean properly.

Ø The polarimeter should be placed in a flat surface.