Dr. Grice again! My last blog post was about solvent properties (see here) and I wanted to make another post.
Disclaimer: I recognize it is April Fool’s day, but unfortunately this post does not contain any April Fool’s jokes or pranks. There are some good chemistry-related ones online, like this one.
Ok, on to the topic for today: General Chemistry I, II, and III introduce many key foundational topics that appear again and again in other chemistry courses, in research, and beyond. In our General Chemistry I Lecture, we cover the concepts of Stoichiometry, Limiting Reagent, and Percent Yield. I wanted to highlight these topics because they are used in all areas of chemistry, including in organic chemistry laboratory, other classes, and our research labs.
These topics are particularly important whenever you make (or “synthesize”) a chemical, which is why they show up so much in organic chemistry lab, inorganic chemistry, other labs involving synthesis, and in research.
Stoichiometry is the concept that we can use the “coefficients”, or numbers in front of chemical species in a balanced chemical reaction, to find how many moles of reactants are needed, how many moles of reactants will be consumed, or how many moles of product will be formed in a reaction, given some other information. A balanced chemical equation can be interpreted in terms of molecules reacting with molecules, or moles reacting with moles. So, in this reaction below, you can think of it as 1 molecule of N2 reacting with 3 molecules of H2, or you can think of it as 1 mole of N2 reacting with 3 moles of H2. A mole is a huge number of molecules (6.022 × 1023 things per mole!), and brings the teeny tiny atoms up to the scale of things we can weigh.
We often start with masses of species (in grams or milligrams, g or mg) and obtain products as solids that we can weigh, so we can use molar masses to go from mass to moles of reactant or product, to moles or another reactant or product, to mass of that other reactant or product. You can calculate molar masses by hand from the periodic table, look them up for common chemicals, or use a handy calculator like this one if you know your formula. This is the general idea for using molar masses in stoichiometry:
For example, here’s a simple balanced chemical reaction, an acid-base reaction of triethylamine (sometimes abbreviated TEA) and hydrochloric acid to form triethylammonium chloride. Notice there are no numbers, or coefficients, in the chemical equation… that’s because they are all 1 (we usually just leave off the “1”). It’s 1 mole of triethylamine reacting with 1 mole of HCl to make 1 mole of triethylammonium chloride.
If you want to react 25.0 g of triethylamine, you can use stoichiometry to figure out how many g of HCl you will need. You use the molar masses and the coefficients as conversions in your calculation. Here’s how I would set it up to find how much HCl I need to react with 25.0 g of triethylamine. Start with what you know, the mass of triethylamine. Students often ask “do I mutiply or divide the values?”, and my answer is: “I don’t know, let’s check the units!”. When you arrange a series of conversions, make it so the units cancel out from what units you start with to get to the units you want. Notice how the units cancel on top and bottom (usually diagonally) and you are left in the unit you are trying to find. We call that approach of using units as our guide Dimensional Analysis.
So, to react with 25.0 g of TEA, we would need at least 9.01 g of HCl. Also, you can calculate the mass of product you will obtain from 25.0 g of TEA using stoichiometry in a similar fashion (we would obtain 34.0 g of TEAHCl):
Now, triethylamine is a liquid, so you can use it’s density to figure out the volume you will need to use. Many small organic compounds are liquids, and weighing out a liquid can be annoying, so this approach of using volume and density is common. Densities are often on the bottle of liquid chemicals, or can be found online in places like Wikipedia. Let’s say I wanted to make 75.0 g of triethylammonium chloride, how many milliliters of triethylamine would I need? We can calculate that, again starting with the known info:
Also, we often use reactants or reagents as solutions. For example, pure HCl is a gas, but is most commonly encountered as an aqueous solution, hydrochloric acid (HCl(aq)). It’s often sold as concentrated as possible, which is about 37% by mass (37 g of HCl for every 100 g of solution), which is about 12 M (M is molarity, which is moles of solute per liter of solution).
We often make more diluted solutions to use (using the dilution equation C1V1=C2V2). The HCl could be provided as a 1.00 M solution of HCl. You can always use volume multiplied by concentration to find the amount of solute in the solution (in this case, moles of HCl), and so those can also be used to find out how much 1.00 M HCl solution to use to react with 25.0 g of TEA. Here’s how many mL of 1.00 M HCl you would need to react with 25.0 g TEA. Again, start with your known value, the 25.0 g TEA you have that you want to completely react with the HCl:
So, you can use densities to convert between mass and volume of liquids, and molarity to convert between moles of solute and volume of solution. We can revise the stoichiometry scheme to include those ideas like this, and there are many different paths you could take, depending on if you are working with a solid, a pure liquid, or a solution.
The idea of Limiting Reagent is that in general, when we react things, we don’t measure out things to be perfectly the right values needed for the exact ratio in the balanced chemical reaction. In reality, we usually have one thing that will get used up first (the limiting reagent), and the other reactants or reagents will still be there, so they were “in excess” to begin with. You had more than you needed of those. Using the limiting reagent, you can figure out how much product you expect to form.
My favorite way to deal with limiting reagent calculations is to just take all reactants on to the product you want to form and see how much mass of product is formed. Whichever reactant forms the least product will get used up first and therefore is the limiting reagent. You now also know how much product you expect to form! There’s also a way where you calculate the moles of each reagent and compare ratios of moles with the stoichiometric coefficients, but I like the way I do it, because you get both which species is limiting and also how much product you will form.
Let’s say we react 45.5 mL of triethylamine with 105 mL of 2.00 M HCl, how much NEt3HCl should we get? I’d do both calculations to product:
So, my limiting reactant is HCl the most NEt3HCl I could make would be 28.9 g!
Now, we can talk about Percent Yield. This is the percentage of the expected mass or moles of product that you actually obtain from your reaction. Percent yield is just your actual obtained value (in mass or moles) divided by expected value from your stoichiometry calculations (in the same unit) multiplied by 100. You can never get above 100% yield. If your product weighs more than it should, then it’s impure! For example, if you isolate a product from water by filtration, and get a mass that is 115% yield, maybe there is still water in there, and you need to dry your solid by rinsing the water off with a solvent that has a high vapor pressure, or removing the water with heat or vacuum. This is why it’s so important to use spectroscopy such as NMR spectroscopy to check that your product is what you think it is and is pure. It can happen that you actually form something totally different than you expect, so your %yield calculations would be wrong if your actual product had a different molar mass or different coefficients in the balanced chemical reaction.
Looking back up at our last limiting reagent calculations, let’s say we react 45.5 mL of triethylamine with 105 mL of 2.00 M HCl (which are the values in the calculations above, that showed us we coulld only make 28.9 g TEAHCl), and then isolate our product and when it’s pure and dry, it weighs 17.7 g. We can calculate the percent yield like this:
Ok, so how does this work in research? We do stoichiometry calculations every time we do a reaction! First we do it in planning to see how much we can make, and then use the actual numbers we measured out and obtained to get the percent yield. I often work with metal complexes and we generally make 50-200 mg of a complex to work with. So, I often use mmol in my calculations (you can use the molar mass number as g/mol or as mg/mmol!).
Let’s say I want to do this reaction below to form this cool copper cluster that emits different colors under blacklight when it’s room temperature or liquid nitrogen temperature (we make this cluster and similar ones in Inorganic Chemistry Laboratory!). Note that the stoichiometry requires 4 moles of CuI per 4 moles of pyridine to make 1 mole of cluster. When trying to figure out how much reagent to use, I often pick a round number like 100 mg, and calculate how much of the reactants I would need to make 100 mg of product.
Here’s the calculation for how much CuI I need for 100 mg of product:
Here’s the calculation for how much pyridine I need for 100 mg of product (in microliters, because it’s a liquid! Density in g/mL is also the same value in mg/µL!)
Note that KI and ascorbic acid are additives in the reaction, but not in the balanced chemical equation (they help increase the yield and make sure we get the product we want and not other stuff). If I want to make more than 100 mg, I can just “scale up” the reaction by multiplying everything by the same number. If I want 300 mg, I just triple the amount of each reagent. Also, even if I try to measure the values I calculated, I will add a little more of one reagent so it’s in excess.
Now, let’s say I reacted 625 mg of CuI with 275 µL pyridine and I isolated 584 mg of product, what’s my percent yield? Here’s what I would do: first do the limiting reactant calculation and at the same time find out what my 100% yield would be:
So, CuI was limiting, and I would make 885 mg of the cluster for 100% yield. Since I only obtained 584 mg, here’s my %yield calculation:
Some folks really care about high yields, and try to “optimize” a reaction to give the highest yield possible. For my research, as long as I have enough of the product for what I want to do, and it’s pure, I’m happy. A low yield is just fine. A higher yield is better, but not critical for a project where the main goal is some application of the metal complex.
Whenever you publish a paper about making something, you need to report how you did it in the “Experimental Section” and you need to include masses and moles (or mmoles) of reagents, volumes of solvents, time and temperature, and mass of product, as well as a percent yield! That way, other scientists can reproduce your work and should expect to get a similar percent yield if everything is done right. Maybe writing a good experimental section will be a topic of a future blog post!
I want to talk about something near and dear to my heart in this post – Solvent properties! This information is useful for laboratory classes and also for students doing research projects (Did you know you can do research as a class for your experiential learning LSP requirement if you are a DePaul student?). Solvents are everywhere, and a solvent is just the major component in a mixture, usually the liquid that things are dissolved in, so most of the time when we talk about solvents, we are talking about liquids. Chemists use solvents as reaction media, for analytical methods like spectroscopy and titration, and in purifications such as crystallizations, acid-base extractions, and chromatography. In living systems and in nature, the common solvent is water, but many more solvents exist and their properties vary considerably.
Safety and Physical Properties
When working with solvents, it’s always good to review basic parameters: safety (toxicity/flammability/carcinogenicity/etc.), boiling point, freezing point, density, molar mass, polarity and if it’s miscible with water. That info is available in many places, including Wikipedia. The Safety Data Sheet (SDS) for a chemical also has basic properties and safety info. These can be found on supplier websites and other locations. Learning about the safety and physical properties of a compound is important for any chemical you will be working with, not just solvents. Many solvents have very flammable vapors, so you should not be working with open flames (like a Bunsen burner) at the same time as working with flammable solvents. The boiling point of a solvent is valuable to know because a lower boiling point means a higher vapor pressure (so the solvent will evaporate faster/will be easier to remove on a rotary evaporator for the o-chem folks!). Also, if you do a reaction in a boiling solvent, often called a reflux reaction, the temperature of the reaction will be approximately at the boiling point temperature.
I should note that freezing points of solvents is something we often ignore when thinking about solvent properties because many freezing points are very very low, but there are solvents that freeze close to room temperature. For example, if you have very pure DMSO or DMSO-d6 and your lab space is relatively cold (18 degrees Celsius or colder, which is about 64 degrees Fahrenheit), it can freeze on you because it’s freezing point is 19 degrees Celcius! I’ve had to run my bottles under warm water (tightly closed) or put them on a hot plate to get it to melt before dispensing. Once you make a DMSO solution by dissolving something in the DMSO, it’s freezing point drops, so it’s not as much of an issue. This is due to “colligative properties”, a concept I taught this quarter in Gen Chem II Lecture!
Some solvents are very polar and mix with water (“like dissolves like”) and some do not and will make two layers if you try to mix them with water (like oil and vinegar dressing or oil spills floating on water). Here’s a nice little table showing what solvents are miscible (can mix) or not. I have this posted in my research lab: https://www.precisionlabware.com/content/18-solvent-miscibility
Note that even if solvents are listed as immiscible (meaning they don’t mix and will form two layers if you combine them in a container, with the more dense liquid on the bottom), some small amount may dissolve in the other solvent. For example, when you take a Nuclear Magnetic Resonance (NMR) spectrum of a compound in chloroform-d (CDCl3), there’s always some water there even though chloroform is technically not miscible with water.
However, thinking about solvents doesn’t stop there! There are several other solvent properties/concepts that are important to think about and understand.
Acid-Base Characteristics – The Importance of Protons (or Lack Thereof)
One important aspect of solvents is acid-base chemistry. Remember that the pH scale and pKa values we usually look at are in water…. but as soon as you are doing chemistry in a different solvent, the pH scale and pKa values become different! A pKa tells you how acidic an acid is relative to other acids, and similarly a pKb tells you how basic a base is compared to other bases. Acid-base chemistry is discussed in general chemistry and in organic chemistry and is critical to understand for working with buffers, doing reactions with acids and bases, and in purifications like acid-base extractions.
So, how can you think about acid-base chemistry/pKa values in other solvents besides water? First of all, in any solvent, the strongest acid you can make is protonated solvent, and the strongest base you can make is deprotonated solvent. Anything stronger than those will just form the protonated or deprotonated solvent as soon as it touches it. This is sometimes called “the solvent levelling effect” because the solvent defines the levels of acidity and basicity that you can access. In water, you can’t have an acid stronger than hydronium (H3O+) or a base stronger than hydroxide (OH–). For example, if you try to put n-butyllithium, nBuLi (a compound with an extremely basic anionic carbon), in water, it’s so basic it will just react with water right away to make LiOH and butane (a gas at room temperature and pressure). You have to use aprotic organic solvents (not having any acidic or hydrogen bonding groups like OH or NH) like THF or diethyl ether when working with alkyl-lithium reagents (R-Li) or Grignard reagents (R-Mg-X) because they are so basic that they react nearly instantly with protic or somewhat acidic things like water. Similarly, putting a strong acid in water just makes hydronium, so you can’t make an acid stronger than hydronium in water.
For pKa values of organic compounds outside of water, often the numbers are reported in DMSO solution, and you can use those pKa values as a rough approximation for similar polar aprotic solvents in terms of what is more acidic/basic than what, but not quantitatively. The concept of “pH” doesn’t really work well outside of water, so we generally just consider pKa and pKb values to understand relative acidity and basicity in non-aqueous solutions.
Here are good resources for looking up pKa numbers:
The Evans pKa table is great, it’s a summary of a larger set of data:
For other solvents besides water and DMSO, my go-to has been Dr. Ivo Leito’s work. He’s a chemist in Estonia who has collected great pKa data for a variety molecules in a variety of solvents, including DCM, acetonitrile (one of the polar aprotic solvents I commonly use my catalysis research), and others. Here’s a compilation of his papers relevant to pKa’s in solvents:
DISCLAIMER: Some measurements in the literature can be wrong and mistakes could be made in writing or data processing, so there may be errors in large datasets! Mistakes get made in science because it’s a human endeavor and we make mistakes, it’s normal and inevitable. However, as scientists keep studying things and reproduce previous results, those mistakes eventually get caught and corrected. In this way, you can think of science as being self-correcting. Doing science in a team can also help prevent errors slipping into the literature because more eyes look over the results before they are published. If something can’t be reproduced by other scientists, its probably not real. A single paper or report on something new is exciting and interesting, but more than one paper is needed to build scientific consensus and further verify a result is reproducible and happening as initially described. This is also why it’s so important to share/publish all science, even if it’s not “big news” or “game-changing” for technology and society. News articles and social media posts about science sometimes over-inflate the real findings of a research article to make it sound more exciting, which can damage public understanding of what science is and how science is done. TV shows and movies also usually portray the process of science inaccurately to make things appear quicker and more dramatic than real science.
Ok… what about Polarity? We generally classify solvents as polar or non-polar, but really it’s a spectrum of polarity from low to high and different solvents lie at different values along the spectrum. Also, solvents can be protic (having acidic or hydrogen bonding groups like OH or NH) or aprotic (not having acidic or hydrogen-bonding protons). Methanol, ethanol, acetic acid, and water are polar protic solvents, whereas DCM, DMF, THF, and acetonitrile are polar aprotic solvents. Pentane, hexane, and heptane, etc. would be non-polar (and aprotic). If you have taken organic chemistry, you know that some reactions are more favored in polar protic solvents and others are more favored in polar aprotic solvents, such as SN1 vs. SN2 reactions.
Polarity can be measured or calculated a few different ways. Often a “dielectric constant” is reported for a solvent. These show up commonly on solvent property tables, including the miscibility table in the link I posted above in the “Safety and Solvent Properties” section. The dielectric constant is measured by capacitors, and it is not a dipole moment, which is another common way of thinking of polarity of a molecule. A dipole moment is the sum of the bond dipoles, something we teach in Gen Chem I Lecture. You can calculate overall molecular dipole moments using computational chemistry, and often dipole moments are correlated with dielectric constants. Basically, the higher the dielectric or dipole moment, the more polar the molecule!
But, I like some other ways of measuring polarity. My favorite is the ET(30) scale, which uses a “solvatochromic” dye from Dimroth and Reichardt, which is generally called “Reichardt’s Dye”. The dye changes color in a solvent due to the polarity of the solvent affecting the energy of the ground or excited state of the dye. Light excites a molecule from its ground state to an excited state, and the energy difference between those states is equal to the energy of light absorbed by the molecule, so different energy gaps give different colors of the dye (we see the complementary color to the absorbed color, so if a dye absorbs red, we see green, and vice versa). Many dyes are solvatochromic (change color based on solvent) and many dyes are also often pH-dependent (like phenolphthalein, a common indicator used in titrations… it changes color from colorless to pink when going from acidic to basic conditions!).
There are some limitations to Reichardt’s dye, but it’s pretty good and has been used in 1000’s of research papers! You can even use it to look at polarity of complex solvent mixtures, on surfaces, or in solids like polymers. I’ve got some in my research lab if anyone wants to try using it. Polarity will affect how well polar or non-polar things will dissolve in a solvent (that “like dissolves like” idea), which is valuable to know for reactions, crystallizations, acid-base and other extractions, and chromatography! Sometimes you can design a reaction (or just have it happen by luck) where your reactants are soluble but your product crystallizes/precipitates out of your reaction mixture, making purification a breeze. You just filter the solid off, rinse it, and dry it, and you’ve got your pure product.
Ok… so far, I’ve talked about simple physical properties, acid-base chemistry, and polarity… what else is there to know about solvents?
Hydrogen Bonding and Lewis Acid-Base Characteristics
But wait, there’s more! I want to mention two more topics: solvents as hydrogen bond donors/acceptors and solvents as Lewis Acids/Bases.
Hydrogen bonding kind of relates to polarity, but it’s a separate thing conceptually. Remember that Hydrogen bonding is the strongest intermolecular force (IMF) for pure substances, so it can have an outsized effect on molecular properties compared to dipole-dipole and dispersion IMFs. Protic solvents can do hydrogen bonding. This is why water, which has 2 O-H bonds and 2 lone pairs to accept hydrogen bonding, is a liquid at room temperature and doesn’t boil until 100 Celsius, even though it’s a relatively small molecule. Non-polar molecules of similar sizes (like CH4, methane) are gases at room temperature and can only be made into liquids at extremely low temperatures (-183 Celcius for methane)!
So, how can you tell how good a solvent is at being a hydrogen bond donor or acceptor?
Well, there are parameters for that! One set that I like is the Kamlet-Taft parameters, where one parameter tells you how good a solvent is a being a hydrogen bond donor (it has the H doing the hydrogen bonding) and one parameter tells you how good a solvent is at being a hydrogen bond acceptor (having a long pair to interact with the H from another molecule). For example, pyridine is a liquid that doesn’t have any OH’s or NH’s but it’s a great hydrogen bond acceptor because it has a relatively basic N lone pair.
Another way of thinking about molecules is as them behaving as Lewis Acids (electrophiles) or Lewis Bases (nucleophiles), and this is true of solvents too! I think about this a lot because Lewis Bases make good “ligands” to bind metals (metals can be thought of as Lewis Acids). Water can be a ligand bound to metals, so can methanol, THF, pyridine, acetonitrile, etc.
I love the Gutmann parameters, AN and DN, which are Acceptor Number (how Lewis Acidic is the molecule) and Donor Number (how Lewis Basic is the molecule). You can measure these with calorimetry or spectroscopy, and I’ve had students use 31P NMR spectroscopy of triethylphosphine oxide to measure AN of a solvent mixture. Solvents that have high AN and DN values are good at dissolving ionic solids because the solvent can act as a Lewis Base to the cation of the ionic species and as a Lewis Acid to the anion of the ionic species. This is why many ionic species (like NaCl) are soluble in water but not in other solvents. We sometimes call those interactions “ion-dipole” forces between the solvent and solute, but considering them as Lewis-Acid-Base interactions is a little deeper of an understanding. In fact, when we write “Na+(aq)”, the reality is that the sodium ion is bound to about 6 water molecules, so it would be better described as “[Na(H2O)6]+”.
Green chemistry is another thing you can think about when considering solvents. The 12 principles of Green Chemistry define the various ways you can think about making things more “Green”: 12 Principles of Green Chemistry – American Chemical Society
Fundamentally, Green Chemistry attempts to make chemistry less damaging to the global environment by making less waste, using less energy, and using safer chemicals. Some solvents take more steps and energy to make than others, and so are “less green”. Similarly, a solvent that doesn’t biodegrade well or is significantly damaging to the environment is “less green” than others. It’s good practice to try to find ways of reducing energy consumption and waste in reactions. You can substitute a “Greener” solvent for less green solvents, and there are some good articles and tables out there about this. As with many things, “Greenness” is not a black-and-white decision, it’s a judgement call and there are many aspects of “Greenness” to consider.
There’s also mechanochemistry, where you grind reactants together instead of heating them up in a solvent, and mechanochemistry can be very green because you usually eliminate the need for solvent in the reaction. Not all reactions work via mechanochemistry, but it’s a growing area of modern research with modern instrumentation (such as electronic ball mills or planetary mills and mixers). It’s also a very old area of research because the concept of mechanochemistry has been around since alchemists, the precursors to chemists, reported grinding chemicals together in mortars and pestles over 1000 years ago, and mortars and pestles themselves have been around since the stone age. We have a modern electronic ball mill in the department, and I am happy to show folks how to use it.
One More Important Point About Safety – Peroxide-Forming Solvents
We started with safety on this post, and I think we should end with safety, as we should always think about safety when we do our work. In addition to toxicity, carcinogenicity, and flammability, when working with a solvent, check to see if they are peroxide formers! These solvents slowly get oxidized by the O2 in air over the course of weeks/months/years make peroxides (R-O-O-H), which are potent oxidants that can affect your reactions and are explosive if they get concentrated enough. THF and other ethers (R-O-R) are the most common culprits, so if you have a bottle of THF or diethyl ether that’s been opened for while, it’s important to test it for peroxides. This is because the C-H bond next to the ether group has a weak C-H bond dissociation energy, so can be broken to make a radical that binds O2 to make a peroxide. You can get test strips to test solvents to see if peroxides have formed – you put a drop of solvent on the strip and look for a color change from white to blue. If you see solid crystals at the bottom of an old bottle of an ether solvent… consider it to be a very very very dangerous thing. So much peroxide has formed over time that the peroxide is now crystallizing out because it is so concentrated. Those crystals can be explosive even just from vibrations/scraping/etc., so do not touch the bottle, and contact your departmental safety or EHS representative. For us, that person to contact would be your research advisor or the lab managers.
Many THF bottles and other ethers are sold with BHT or another radical inhibitor in it that slows down that oxidation, but it won’t completely stop it over the course of months/years if it’s exposed to air. It also means that if you use those solvents, the BHT or other inhibitor in there that could affect your chemistry. Another way to prevent the peroxide problem is just store your solvents under N2 or Argon, but that usually can only be done well with smaller containers, not large solvent bottles. Keeping bottles dark/away from sunlight also slows down the oxidation. This is why most solvents are sold and stored in brown bottles! The UV light in sunlight is higher energy than visible light, and can make excited states that can break bonds and make the peroxides form quicker. Similarly, beer/wine/etc is sold in brown bottles to prevent damage that sunlight can cause (“off”/”skunky” odors and flavors). This is how sunburns work too, the UV light damages the molecules in your skin cells
Isopropanol (also called 2-propanol or “rubbing alcohol”) also forms peroxides over time, so an old bottle of isopropanol should be tested for peroxides. If you do a reaction or purification using isopropanol or an etheric solvent that’s been opened for a long time and you get products that are somehow more oxidized than you expected, peroxides could be the culprit!
The test for peroxides is based on the reaction of a peroxide with an iodide salt and starch in the presence of some acid. Peroxides oxidize two iodide (I–) ions into I2, which reacts with another iodide to form I3–, which is very bright blue/purple in the presence of starch. That’s all that’s in those test strips, so in a pinch you could do the test as a solution method with NaI or KI, some acid, and starch in water. Make the solution, add some of your solvent (even if not miscible with water), shake it up and look for a blue color. You could even make a calibration curve for it (using H2O2 or another commercially available peroxide to make standards of known concentration) using Beer’s Law and UV-Visible spectrophotometry, a tool we use in Gen Chem Labs, in other classes, and in research.
Organic peroxides do get used in organic synthesis, and can be used safely if you are using them properly and understand their reactivity. They are great oxidizing agents so can be used to oxidize things by installing an oxygen atom or removing a formal H2 equivalent from a molecule. meta-Chloroperbenzoic acid (mCPBA) is one of the more safe peroxide reagents and is a solid, while other peroxides can be viscous liquids or oils, or sold as solutions.
Ok, that’s enough for now!
Ok. I think that’s enough for now. You can see that thinking about solvents is more than just looking up their safety and basic physical properties! Hopefully this will help you have more appreciation for and understanding of solvents when using them in the future. They’re more than just a liquid you do a reaction in!
I’m hoping to do more of these blog posts about chemistry information and resources in the future, so if there’s any specific topic you want me to post about, shoot me an email. I might do posts about Redox Chemistry, NMR spectroscopy, Green Chemistry, and/or Catalysis in the future. Finally, if anyone has any other useful tables or links to resources about solvents or molecules that they like, I’d love to hear about them!
We have a Department of Chemistry and Biochemistry discord server that DePaul students (any major), faculty, staff, and alumni can join to continue the conversation about chemistry as well. Here’s the invite link: https://discord.gg/gYT8Juk
Sincerely,
Dr. Grice
PS – Many chemists have a favorite solvent or favorite solvents. My favorite polar aprotic solvents are acetonitrile and DMF, and my favorite non-polar solvent is heptane, because it’s less toxic than hexane and can be used to azeotrope/co-evaporate other solvents. I like water and ethanol for polar protic solvents because they are relatively “Green” and safe (although ethanol is flammable).
Universities subscribe to a variety of journal articles and databases that are extremely valuable for research and learning, and DePaul is no different. However, you aren’t always on campus to use them, so how can you access DePaul’s journal subscriptions from home?
It turns out its fairly straightforward to set up for any DePaul student, faculty, or staff!
You should check out the Chemistry Library Website, which has a variety of great information, but we will focus one key tool below:
Google Scholar – This is the premier research tool to find peer-reviewed articles. It’s like google but the output only includes journal articles and similar scholarly documents, and leaves off regular websites. You can use it on campus or from home to get access to articles while off campus! To set it up properly, do the following (this can be done at home too):
In the top left corner, click on the menu dropdown:
In that menu, select “settings”:
4. In the settings menu, select “library links” on the left, and search for “DePaul University”. Then select both options and hit Save. The “full-text” is the most important one:
Ok! You are all set. Now, go back to Google Scholar and search for something. For example, you could search for “Alkyne Reduction” and you would see the page shown below. If you want to access an article off campus, click the “Find full-text @ DePaul” link and enter your campus connect login as needed. It will take you to the article’s page, with full access to the article! Remember you can save pdfs to your computer to look at the later.
What can you do if DePaul doesn’t have access and that link doesn’t show up??? One option is to see if the pdf is at academia.edu or researchgate.net, two websites where people sometimes post articles. Those links also show up on a Google Scholar Search:
If it is nowhere online, you can request it through the library, and they will look for it and send you a pdf within a few days. Here’s how to do that from Google Scholar. Click the “>>” symbol beneath the abstract:
Then select “DePaul Library Holdings“. It will send you to this page:
Under “Check availability”, select “Request via Illiad” and follow the directions to request a copy. If the library can find it through their library partners, they will send it to you.
So there you have it! We highly recommend using this approach, and also becoming familiar with Google Scholar, Endnote, and SciFinder. We’ll cover more on of these tools future blog posts, like how to use Endnote and Google scholar to easily cite articles and make bibliographies. In addition you should definitely check out the SciFinder setup pages at the Chemistry Library Website and get setup with that tool as well!
Part of doing science is communicating your results in both written and oral form. Towards this end, DePaul faculty travel to conferences to present the work they’ve done with students here in the department of chemistry and biochemistry.
Both Dr. Grice and Dr. Vadola will be presenting, and a poster by one of Dr. Griffin’s Collaborators is also being presented.
Dr. Grice is giving a talk on carbon dioxide reduction research performed with DePaul undergraduates.Here’s the abstract.
Dr. Vadola is giving a talk on gold-catalyzed C-C coupling reaction research he has been performing with DePaul undergraduates. Here’s the abstract.
Here’s the abstractto the poster by Dr. Griffin’s collaborators. Dr. Grice’s collaborator at RFUMS is also giving a poster based on the DePaul-RFUMS collaborative work, see here.
If you want to hear about what happens at the ACS meeting, you can follow the hashtag #ACSNOLA on twitter.
Also, if you are a student researcher and want to go to a conference, you should definitely find a way to do so! They are great experiences for learning about science, practicing science communication, networking with peers, and learning about potential career information. Talk to your research advisor well in advance and you might be able to find a way to fund the trip. The ACS Great Lakes Regional Meeting 2019 will be in Lisle, IL, and will be much cheaper than a ACS National meeting, so it should be fairly easy to attend. There are also many other options out there, so keep your eyes out and talk to your research advisor!
We will have a research lab open house next Thursday (Jan 12th) from 11am to 1pm.
We have 14 research-active chemistry faculty here at Lincoln Park, and their research labs are on the 3rd floor of McGowan South, as well as one lab on the 4th floor of McGowan South.
The research lab open house is a great opportunity to come and see what faculty do for research and also find out how to get involved in research in the chemistry department!
Each summer, the Department of Chemistry holds a weekly meeting of a “Journal Club” in which faculty and students gather to discuss a recent paper from the chemical literature in a relaxed and collegial atmosphere. Typically, a student from a research group will select and present a paper, after which they will respond to questions. The paper is sent out over email several days before the presentation so that everyone has a chance to read it and be prepared to discuss it. Each of the different research groups participating usually give at least one presentation, so the topics cover a wide variety of chemistry research. The goal is to help everyone learn more about chemistry literature and current research methods that may be relevant to our work here at DePaul.
Every other week lunch is provided by the Department of Chemistry. All DePaul students and faculty interested in attending are welcome. Meeting times and location for this coming summer have yet to be determined, but we will most likely meet in one of the classrooms on the first floor of McGowan South around noon. Please email Dr. Southern if you would like to receive more information about the journal club and/or be placed on the contact list.
Spring quarter is more than halfway done and you might be curious what goes on over the summer here in the Chemistry Department. One of the things that takes place every summer is research. The Chemistry Department at DePaul University hosts a diverse collection of research programs, and much of this research activity occurs during the summer months. Below is a summary of just a few of the projects that will be active in the coming summer.
…has a team of students working in collaboration with Rosalind Franklin University of Medicine and Science researchers Dr. Raúl J. Gazmuri, Dr. Jeejabai Radhakrishnan and Dr. Eric Walters, as well as DePaul Biology Professor Dr. Talitha Rajah. These researchers will investigate the role of cyclophilin-D (Cyp-D) in mitochondrial transcription initiation in terms of whether it acts through simple binding with mitochondrial transcription factors (mTFs) or via its peptidylprolyl cis/trans isomerase (PPIase) activity. Dr. Jin’s team will focus on determining the enzyme kinetics of Cyp-D with mitochondrial transcription factors (mTFs) TFB2M with and without Cyp-D inhibitors or to determine the thermodynamic binding parameters using isothermal titration calorimetry (ITC).
Dr. Jin, Dr. Caitlin Karver, and Dr. Kyle Grice…
…are directing a team of students studying the interaction of small molecule ligands with transition metal ions including Cu2+, Ni2+ and Co2+. They plan to identify metalloenzyme active sites metal structural mimetics and will then use the mimetics to study their interactions with metalloenzyme competitive inhibitors. These inhibitors are drug molecules targeting diseases such as cancer.
Sophia Robinson graduated from DePaul in 2015 with a BS/MS in Chemistry. Here she reflects back on her academic career at DePaul University’s Department of Chemistry with Associate Professor and Department Chair, Dr. Lihua Jin.
Accomplished: DePaul University, BS/MS Chemistry 2015 Current: University of Utah, Organic chemistry graduate student
Jin: How has your MS study at DePaul helped you reach where you are now, a PhD student at a top research lab in the country?
Robinson: As an undergraduate, I switched my major to chemistry in the winter quarter of my junior year because I was enjoying my biochemistry class so much. I realized I wanted to have a career in chemistry but felt I had not yet put enough time in at the bench to commit to a PhD program. With more experience in the lab, I became confident that I had the passion for research and personal drive to succeed in a PhD program.
Having an MS was somewhat advantageous for my graduate school applications as it showed my commitment to my education and that despite additional years of study after undergrad; I was still passionate about chemistry and research. Chemistry PhD programs are making an investment in their students and as an applicant it is important to demonstrate your passion for research, chemistry, and that you have the drive to not only finish the program but hopefully make important contributions to science during your time there.
Jin: What aspects of your MS study at DePaul have been the most beneficial to you for your growth as a graduate student?
Robinson: By far the most beneficial aspect of my MS study was my research experience. The MS program gave me the opportunity to have my own research project with more independence and also the valuable experience of writing a thesis. Having written a MS thesis, I feel better prepared for how to approach my PhD dissertation and most importantly, stay organized to keep putting the whole story together much easier.
Hello DePaul Students, Alumni and Friends! Dr. Grice here (@GriceChemistry). One thing we always tell our students in our classes is to use their resources to help them succeed. We want students to read their texts, come to class, go to course assistant (CA) and instructor office hours, and do practice problems so that they can improve. Everyone learns in a different way, so we want to give students various resources to learn how to tackle the concepts. But it doesn’t stop there. As a student you should be building your resume and networking while here at DePaul, so you can be prepared for your life after college (yes, it exists and we want to help you get there!). There are many resources on the internet that can be extremely valuable for other important parts of a student’s time here at DePaul (and beyond). In addition, if you start doing research or plan to go into a research/bench chemistry position, there are many great resources to help you learn about your projects and tackle the challenges that chemistry research throws at you. Maybe you need to write a thesis or research paper and you want to know how approach writing such a large document. Maybe that TLC or column is giving you a lot of trouble. There are resources out there to help!
The Catalyst is a home for links to many resources to help you succeed.
We want the The Catalyst to be your go-to place for online resources. You will find many under the Links to Resources tab at the top of the page. We will try to keep the links updated as new tools come up, so go ahead and bookmark it! We’ve sorted them by area where they may be useful to you and have only included links to things that we have read and/or used ourselves. There’s a lot of not-so-great stuff out there on the internet and we want to help you sort through it by giving you this resource. Future posts to The Catalyst will be dedicated to introducing you to many of these. In the meantime, visit Links to Resources and dive in! All the best, -Dr. Grice
Here are a few links that I have put together for you based on input from faculty and staff.
The Catalyst 