Intra

Ordering

1.    If we need consumables/equipment then let’s get it (don’t wait for someone else or just do nothing).

2.    Check on Inventor Manager to see if it's available within IFS already: https://im.massey.ac.nz/Login.aspx

3.    Check suppliers’ websites and with chem stores to get best deal possible. Use these companies and liaise with ChemStores if you need other options or additional information:

        Aldrich: https://www.sigmaaldrich.com/chemistry/chemical-synthesis.html

        Alfa: https://www.alfa.com/en/

        Boron Molecular: http://www.boronmolecular.com/

        Acros: https://www.acros.com/Welcome.aspx

4.    Access to the ordering website can be found in this way:

    • Go to the Massey Homepage
    • Click on ‘staff’ towards the bottom of the page (at the bottom of the ‘white’ segment), slightly to the right of centre
    • Click on  the ‘OneMassey’ option
    • In the banner at the top of the page slightly to the right, click on ‘teams’
    • Choose IFS-Administration from the alphabetical list. Scroll down the page, it's on the left hand side.
    • From the list on the left, click on ‘Goods & Services requests’

Other members of the group have a link directly to the 'Goods & Services requests' website. This may produce an 'oh snap!' error page. If you get this error, try the long way around. It may take several attempts at different times of the day - try using a different browser type. It may cue you for your login information when it's working.  

5. Once you're in the system, here is how the Accounts section functions: 

  • One of the first prompts after entering the group and lab info will be a drop down box where you can enter your code type - this will usually be GL or RM. 
  • The top section will have a bunch of X's next to your GL or RM code. These will change as you enter the information - make sure there aren't any outstanding X's once you're done.
  • Use account GL121211222STELF unless otherwise notified (see Exceptions). This is entered as: 
    • GL 
    • Account number:  12121
    • Item code: 1222
    • Analysis code: STELF
  • For RM codes, it's a little bit different.
    • RM
    • Account number: <account number here>
    • Item code: 1222 (for chemicals)
    • Analysis code: LEAVE THIS BLANK FOR RM NUMBERS

  • Exceptions: Daniel to use RM18007 for those items specifically related to his project. John to use RM20412.

6. Any purchase over $250 needs to be OK’d by Shane.

7. Have you checked if the chemical is available in Stores?

  • If the item is available in Chem Stores, then put the Est. Cost ($) as "1" and write “Available in Chem Stores” in the notes section. Also list the catalogue price in the notes section, if you have it to hand.
  • If it is not available in Chem Stores, then enter the exact price into the Est. Cost field. Also Write the exact price, the supplier name and catalogue number in the notes section when you make the request. This is very important.
  • When ordering chemicals from external suppliers, be sure to check the shipping costs and currencies of the quotes too.

Record Keeping

  • Recording all experiments that you perform is a legal requirement and allows yourself, and others, to track and repeat what you have done. Lab notebooks are legal documents owned by the University and should be treated as such e.g. they should not be taken home.

  • Lab notes should be numbered, date stamped, clearly outline the risks associated with the experiment, and should constantly be kept up-to-date. These notes will be essential for both theses and publications. 

  • Your experiments and samples should be labelled appropriately. Below are some general rules:

    • Number both lab books and experiments within each book sequentially i.e. lab book 1 should contain experiments 101−199, lab book 2 should contain 201−299 etc.
    • Each experiment receives a new number.  If you are doing a series of similar experiments at the same time (e.g. adding several different metals to the same ligand or doing a series of crystallisations) then label each sub-section 101a, 101b, 101c, 101d…..etc
    • Solids should be labelled st101s1, st101s2….etc.  Fractions from a column should be labelled st102f1, st102f2…etc
    • Samples should be clearly labelled with your experiment code, the date, and what it is. If you have a lot of the same type of samples, it is ok to label the tray or other secondary containment. 
    • Use your initials in front of lab book entries when taking NMR spectra, labelling products etc.
    • Make sure any printed spectra are labelled with the relevant lab book code

  • Make sure all important data is regularly backed up to the cloud, the group drive, or to a portable hard disk. It is inevitable that your computer will fail at some point, so be ready.

Group Shared Network Drive

  1. Open windows explorer.  Choose Tools > Map Network Drive
  2. Choose an unused drive (e.g. T: ), type  \\massey\disk\shares\telfergroup into the ‘folder’ box
  3. Select ‘reconnect at logon’ and this drive should appear in “My Computer” every time you log on
  • Printing can be acheived by putting the following address into the explorer bar: \\tur-followme1\followme
    • You will be prompted to enter your username and password. Enter "Massey\username"
    • If this printer address fails, try: \\tur-followme2\followme

Experimental Data Required for Theses and Publication

  • A new compound doesn't exist until you have characterised it by:
    • 1H NMR
    • 13C NMR
    • Mass Spectrometry
    • % Yield

  • It is far easier to collect all these spectra ‘as you go’ rather than having to repeat experiments (or worst-case, re-synthesise) at the end of your project. If you are uncertain as to how some of these experiments are performed and interpreted, be sure to ask a more experienced person. Only perform 2D NMR experiments where necessary.

  • A clear and detailed experimental protocol should be given in your thesis for each compound, including yields - so remember to weigh your flasks/vials!  Relevant characterisation data should be entered in text form (use the formatting in JACS as a guideline). Like the collection of spectra, do these write-ups ‘as you go’.

  • When drawing the structures of your new compounds, set ChemDraw to ACS settings: File-Apply Document Settings From-ACS Document 1996
    • Check the bond angles in the structures you draw. Getting the shape of simple molecules (e.g. acetone) wrong is unacceptable and should be avoided where possible. 
       

Safety

  • Lab safety is everyone's responsibility and is not an individual endeavour. Maintaining lab safety is an ongoing process and the lab itself should be an environment where everyone can comfortably go about their experiments in safety. This means that if you are new to a procedure or are uncertain about performing it, talk to others first (e.g. Shane, Dave L, John..), and take the relevant training when necessary. 

  • If see something unsafe or something that concerns you in the lab, talk to others about it. Report any incidents that occur to Natisha Magan as soon as it is safe to do so.

  • Before handling any chemicals and starting an experiment, you must do the following:
    1. Consider the MSDS of all compounds involved.
    2. Consider the relevant risks associated with each reaction and procedure you are doing e.g. reflux, distillation, recrystallisation, centrifuging, column chromotography etc. Consider safety manuals, where possible.
    3. At this point it is also useful to consider the quantities of each reagent or solvent, and where you are going to dispose of the waste. Generally speaking, larger quantities of solvent (~5L) carry increased risks of handling.
    4. Decide what level of personal protective equipment (PPE) you need. At a bare minimum, this includes: 
      • Enclosed, non-porous shoes. Ideally leather. Jandals, heels, Ugg boots, open toed shoes, and other forms of open shoes are unacceptable 
      • A lab coat
      • Lab glasses
             5. If the experiment you are doing requires gloves, check which gloves are appropriate. Different glove types have varying permeability to certain chemicals so make sure the ones you are wearing are appropriate.
                 Gloves should not be worn when handling common things and should be changed regularly. Gloves should never be worn in the office.

  • Never work with flammable reagents or on a large scale when you’re alone in the lab.

  • Try to avoid doing any form of lab work alone - coordinate with other group members if you're planning on coming in during the weekend.

  • All reactions and samples must be labelled. You may know what they are, but other people may not, which can cause problems if there's an incident.


Lab Etiquette and Procedures

  1. Washing glassware
    • Glassware should be washed thoroughly immediately after use.  Products should not be stored in reaction flasks.
    • Use acetone and/or methanol to clean most glassware – avoid using H2O unless you’ve been using it as a solvent.  Concentrated acid or base sometimes helps to clean really dirty glassware.
    • Never clean chromatography columns, syringes, needles, or measuring cylinders with H2O – they won’t dry out properly and you risk contamination.  Just use acetone to rinse.
    • Put glassware away as soon as it is dry.  Check that it is clean at this point: if not, clean it properly (do not put dirty glassware away)

  2. Balances and Microscopes
    • Clean up after you use the balances and microscopes. Don’t leave any chemicals or other mess on the balance (use the brush to clean off any spills) on the balance table or around the microscopes. Others may not know what you've spilt, the hazards, nor the best way to clean it up.

  3. Rotovaps
    • Empty the collection flask on the rotovap every time you use it and rinse the splashguard (the glass adapter which connects you flask to the rotovap) with acetone.  Don’t forget to turn the pumps cooling water off when not in use.

  4. Broken Glassware
    • If you break any important/expensive glassware then we can send it away repaired by the glassblower (Grant Franklin, Grant.Franklin@vuw.ac.nz, www.glassblowing.co.nz). If it’s irreparable then we’ll re-order it. Broken beakers, RB flasks, conical flasks etc. should be thrown away (buying new ones is cheaper than repairing them). 

  5. Syringes
    • Non-disposable syringes and needles should be rinsed with solvent immediately after use, left to dry, then put away. Make sure the needles are rinsed well, because reagents can crash out within them and block it.
    • Disposable syringes should be rinsed and put in the rubbish bin, needles should be put in the special yellow container marked “sharps”

  6. Chemicals
    • Always keep an eye on chemicals that you are using regularly – re-order when supplies are getting low (esp. NMR solvents). Do not wait until it runs out – deliveries can take months! If you don't know how to order something, ask.
    • Recycle chemical wherever possible. Deuterated DSMO is collected and distilled for re-use.

  7. Solvents
    • Don’t store large solvent vessels on benchtops – put them away in the designated cabinets.
    • Use 1 L Schott bottles for benchtop solvent storage – they are much easier to handle. Be sure to label the Schott bottle with the name of the solvent, and the hazards associate with it e.g. flammable.

  8. Lab Equipment
    • Lab equipment is expensive so be as careful as possible and treat it well.
    • If you need anything, ask around the lab to see if anyone has it. If not, consult SGT and order it in.


Vacuum pumps

1.    The turbo pumps on the gas sorption instrument need particularly careful use. They are super expensive and delicate (not a good combination). Absolutely no solvent should be allowed to pass through them beyond             whatever is trapped in MOF pores. The Quantachrome software protocol is useless for this, so we need to use manual mode. You’ll need special training for this.

2.    For all oil pumps and turbo pumps (e.g. gas sorption instrument): 

  • No solvent should pass through them. 
  • If your sample contains solvent that is visible by eye then these pumps must be protected with a liquid nitrogen Dewar. 
  • The liquid nitrogen dewar must be topped up regularly to ensure that the liquid nitrogen does not evaporate and thus the solvent does not vaporize and pass through the turbo/oil. This generally means that samples with solvent shouldn't be left to evacuate overnight as the liquid nitrogen will evaporate. Pre-dry these samples appropriately first.

3.    Cold traps used in these Dewars must be dried (use a compressed air gun) after use.

4.    Diaphragm pumps are more tolerant of small amounts of solvent. But, try and minimize the amount of solvent that passes through them by using a cold trap if necessary (in your fume hood) or ensuring the pressure is not set too low (rotovap).

5.    Diaphragm pumps can be cleaned by passing a few mL of MeOH through the inlet and collecting it at the outlet while the pump is running.

6.    All pumps should be maintained regularly. This is simple: just ask Olaf. He will measure the vacuum and change the oil or diaphragm, if required.

Approach and characteristics (from the In the Pipeline blog)

There are several characteristics common to good scientists in general – paraphrasing, we have: 

(1) Intellectual curiosity 

(2) Ability to focus on the problem at hand

(3) Pragmatic approach to problem-solving 

(4) Respect for data

(5) Attention to detail

(6) Sense of urgency

(7) Awareness of other work in the field

(8) Openness to new technologies (once they’ve proved their utility!)

(9) Willingness to challenge assumptions and ditch old ones

(10) Enjoyment of their work

(11) Awareness of the limits of their knowledge

(12) Resiliency

(13) Effective at communication

(14) Working well with team members 

(15) Not constantly seeking credit, and 

(16) Looking for mentors early on, and serving as one later.

Chemistry Literature

  • You should have a solid knowledge of the literature relevant to your research project. Relevant past literature can be found using Scifinder and/or by finding one or two key review articles. You should keep up with relevant current literature by subscribing to the email table of contents alerts from the following journals (most important for PhD/MSc students):

    -          Nature Chemistry

    -          Journal of the American Chemical Society

    -          Inorganic Chemistry

    -          Angewandte Chemie (International Edition)

    -          Chemical Communications

    -          Dalton Transactions

  • To access journal articles on campus, the fastest way is to go directly to the journal homepage. Bookmark these!

  • To access SciFinder and other databases when you’re off-campus, head to this library webpage:
    • http://www.massey.ac.nz/massey/research/library/find-information/subject-guides/chemistry/databases.cfm
  • If you want to access a journal for off campus, the simplest way is to go to the journal webpage, then insert “ezproxy.massey.ac.nz” in the appropriate section of the URL. 

  • For example, for JACS http://pubs.acs.org/toc/jacsat/current becomes http://pubs.acs.org.ezproxy.massey.ac.nz/toc/jacsat/current

  • It is sometimes helpful to add researchers in your field on ResearchGate. That way, when the authors upload new papers, you can sometimes catch them before they are published online with the journal. ResearchGate can also recommend papers to you too.
  • Google Scholar is a very useful tool for searching for papers and citations to those papers.

PXRD

  • When predicting PXRD patterns in Mercury, use an X-ray wavelength of 1.54178 A. There are actually two closely-spaced wavelengths produced by the source (Cu-alpha-1 at 1.54056 A and Cu-alpha-2 at 1.54439 A) that have an intensity ratio of 2:1. There is an option to use both wavelengths in the paid version of Mercury but not the free version. The best solution is to use a hybrid of the two numbers (1.54178 A), as used in cif files for SCXRD structures, to predict your PXRD patterns. You’ll get a better match with experimental data this way.

Synthesis of Common Ligands

Truxene (Subo, 2018)

Acetic acid (20 mL) and conc. HCl (10 mL) were introduced to 1-indanone (5.0 g, 37.8 mmol), and the mixture was stirred at 100 °C for 16 h. The mixture was poured onto ice and stirred for 30 mins, then the solid precipitate was filtered and washed with water, acetone and CH2Cl2 to give a light yellow powder (3.48 g, 80 % yield). 

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