real life, science developments

Periodic History

I don’t think I’ve mentioned it before, but 2019 is the Year of the Periodic Table, due to the fact that it’s the 150th anniversary of Mendeleev’s creation of his periodic table.  You heard me, his Periodic Table.  No doubt you’ve seen some of the other versions, like the periodic table of chocolate, the periodic table of beer, and the periodic table of the internet.  There’s all sorts of merchandise, such as with cupcakes, the anniversary mugs ACS sends out for its members, and the shirts spelling out various things with element symbols.  However, these are all based on Mendeleev’s version of a periodic table.

There are a couple versions that were actually developed in the mid-1800s as well.  Many different chemists tried their hand at creating a periodic table (starting in the late 1700s), but there were certainly difficulties in doing so.  Periodic tables are used both to communicate known trends and predict new ones.  That is one of the greatest strengths of the most well-known periodic table, since it was able to predict the properties of new elements that had yet to be discovered.  However, at that time, far fewer elements were known, and no elements had been created in the lab.  Discovering trends linking various elements was far more difficult.  Some attempts were generally criticized because they weren’t that useful or even gave incorrect information.

The earliest known attempt was actually by a French geologist (slightly outside of his area of expertise, in other words), Chancourtois.  Some of the data was wrong, and, additionally, Chancourtois published in a geology journal, not a chemistry journal, so it didn’t get quite the attention it deserved.  In addition, the periodic table was designed to be 3D—it was in the shape of a cylinder—but printed in a 2D form.  While this sounds like a fun idea in theory, in practice it’s a lot more difficult, since they didn’t have copy machines and most scientists have better things to do with the journals they bought than cutting out a page to make a cylinder out of it.

Meyer developed his periodic table around the same time as Mendeleev (which is relatively common in the history of science—concurrent discoveries happened all the time, and it’s rare that both groups of researchers get the credit).  He organized his table by atomic weight, while Mendeleev’s table is organized by atomic number (the number of protons).  While there is a general trend of increasing atomic weight in Mendeleev’s more popular periodic table, it’s not the organizational principle by which Meyer created his table.

Someone else had practically discovered the same periodic table as Mendeleev, an academic named Newlands.  However, his presentation was flawed.  To get it to look like he wanted, he placed a few elements in the same box, and didn’t leave space for new elements to be added.  This led to a lot of criticism including a refusal to publish his article, so his discovery was ignored until long after his death.

What’s your favorite version of a periodic table?

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real life, Writing

Reading Scientific Papers

A significant part of several of our classes was learning how to read scientific papers.  I got compliments on my reading comprehension several times, and since reading them might be useful when you’re researching for your writing, I thought I’d share some of the strategies I used.

One key to keep in mind is that you should not necessarily be reaching for the dictionary every three minutes.  Reading scientific papers is not like reading books for fun.  You’re not going to easily understand every word in the sentence.  You’re looking for general understanding.  If a word you don’t recognize is used a few times, then you might want to use that dictionary, but other than that you don’t need to get so focused on understanding every single aspect of every sentence.  Don’t get too hung up on trying to understand every word, and instead concentrate on what you can understand, or what looks super important to understanding the paper.  In addition, you will probably have to read each piece of the article several times.  Largely, you’re looking to understand a few things: what the authors are trying to prove or disprove (i.e. what is their hypothesis), how they went about it (experimental design), and what were their results (did they prove, disprove, or have inconclusive results).  Once you get the hang of it, you can look at the hypothesis, design, and results and make up your own opinion on the conclusions drawn.  Was there a serious flaw in experimental design?  Do the results seem to say something different than the conclusions the authors drew?  If it’s too confusing, don’t automatically assume that you’re terrible at this.  Sometimes that’s the authors’ fault.  (If there seem to be huge differences in the way different sections are written, for instance, this could be due to different authors writing different sections and making no effort to transition between.)  If, for example, you find other articles are easier to read, it might just be that the author(s) is/are terrible at writing, or just not good at writing for a broader audience (some scientists write specifically for others in their field, whereas others write for any scientist that might read the paper, even those not in their field).

I tended to print them out and use highlighters, as well as writing down the gist of every paragraph beside it.  You should at least be able to figure out the point of the paragraph.  Words you don’t understand that seem to be super important should be highlighted and looked up later.

This is one occasion where I actually advocate the use of Wikipedia (though it should always be read with a grain of salt as they can be edited by anyone) or some other beginning resource, as having a background on the data and terminology, even if it’s just a quick check.

Scientific papers tend to have sections.  Paying attention to section titles can often make a world of difference.  One of the most important is the summary or abstract at the beginning, as that generally tells you everything you really need to know, and everything that follows is them backing up that point with evidence.  Stopping between sections is highly recommended.  If the paper cites another paper and isn’t very clear about a similar point or experimental setup used in a previous experiment, you might have to look up that other paper, because they might explain what the new authors didn’t want to use the word count on.

Lastly, graphs and other figures should be well-studied.  Note that not all of them will be well-made or even convey the things the author wishes to convey.  Some of them are even hard to read.  You’ll want to look for the title of the figure, the caption, and then the figure itself.  What does it say about the experiment?  Is it confusing or perfectly clear?

If you can find reviews of that article, too, that can help, because usually they are written to a less technical level and point out the awesome things and flaws in the article.

You can read a few other different points of view on how to read journal articles.

Do any of you have any tips you’d like to share?

real life, Writing

Writing, Ingredient Lists, and Organic Chemistry Terms V

This is probably the last one of these I’m covering, since once I’m done I’ll have covered all the most common substituents.  Amines and amides are really important, since a lot of biologically-important molecules have nitrogen.  Finally, I’ll talk about priority of substituents.

Amines are carbon-groups attached to a nitrogen.  There are a few different types of amines.  R-NH2 amines are called primary amines (1o).  R1-NH-R2 amines are called secondary amines (2o).  Nitrogens attached to three R groups with no hydrogen are called tertiary amines (3o).  The IUPAC nomenclature involves placing amino- in front of the name of the carbon-group.  For example, CH3CH2NH2 would be 1-aminoethane.  It gets slightly more complicated for secondary and tertiary amines, with the amino in the middle.  For example, CH3CH2NHCH3 would be 1-methylaminoethane.  A tertiary amine, such as (CH3CH2)2NCH2CH2CH3, would be diethylaminopropane.  There’s actually a fourth group, the quaternary, which is uncommon—it involves a nitrogen with a positive charge and a fourth R-group.  These have -ammonium at the end, or replace the -e at the end of the alkane with -ium.  As with other charged species, you also have to list the charged counterion (chlorine is common) in a separate word at the end.  These are rare, aside from general ammonium, NH4, which is common as ammonium hydroxide (NH4OH), a cleaning agent. (R-groups can mean just a hydrogen or a carbon group, but their exact definition varies depending on concept and what you want it to be.  For the purposes of primary, tertiary, and secondary, only carbon-groups count as R-groups.) The common name just involves sticking amine at the end no matter whether it’s primary, secondary, or tertiary.  You probably recognize a common amine group biomolecule important to humans, particularly the ones that like to work out: amino acids.

Amides are slightly less common.  Like amines, they exist in primary, secondary, and tertiary forms, and are called that for the same exact reason: the number of R-carbon groups attached.  One of those carbons, though, has a carbonyl, the C=O that exists in the ketone, carboxylic acid, and ester.  Like carboxylic acids, these are named by dropping the -e at the end of the alkane and replacing it with -amide.  For example, ethane (CH3CH3) becomes ethanamide (NH2CH3).  Secondary and tertiary amides act like normal alkane substituents, except the numbers are replaced by N- to indicate that they are attached to a nitrogen.  CH3NHCH2CH3 would be N-methylethananamide.  (CH3)2NCH2CH3 would be N,N-dimethylethananamide.  Like amines, quaternary amides do apparently exist, but we didn’t talk about those during class and apparently naming them is a different matter entirely.  (I don’t think I’ve ever heard of how to do it, and my quick search isn’t coming up with anything either, though if any of you have a burning desire to know how to name quaternary amides I can look into it further.)

I’ll let you read up on imines, imides, and their derivatives yourself, since they’re pretty rare and we barely talked about it in class.  Similarly, there are some other fairly rare substituents, as well as some that are better to talk about with an in-depth look at their properties (nitro for one), but I’ve covered the basics.  (I might delve a little more into “weird ones” when I do spotlights on specific chemicals in use, so stay tuned for that.)

Priority of substituents only matters for when there’s multiple substituents present, because you can’t have them all as prefixes or suffixes.  I’ve only mentioned the suffixes, so I’ll give you the prefixes here, too.  Now, for the priority of substituents for suffix, from highest to lowest: carboxylic acid (carboxy- is the prefix), ester (R-oxycarbonyl- is the prefix), amide (carbamoyl- is the prefix), aldehyde (formyl- is the prefix), ketone (oxo- is the prefix), alcohol (hydroxy- is the prefix), amine (amino- is the prefix), alkene (alkenyl- is the prefix), alkyne (alkynyl- is the prefix), alkane (alkyl- is the prefix), ether (alkoxy- is the prefix), and halide (halo- is the prefix).

Out of the functional groups I’ve covered, which do you most want to know more about their properties?

real life, Writing

Writing, Ingredient Lists, and Organic Chemistry Terms IV

We’re returning to organic chemistry terminology.  I’m probably not going to train you to name chemicals like a chemistry student, partially because there are a lot of situational specific rules like what substituents get naming priority, but I’ll give you a start, especially in deciphering what the labels mean.  If all else fails, you can write something that you think is a reasonable name and ask a forum—scientists love to help people be more accurate about their science in media.  I’ll have a general list on the last blog entry for this topic, but there are other intricacies that I don’t remember or that we didn’t even learn.

Aldehydes also have an oxygen attached (see my previous post).  These occur at the end of a carbon chain, -CHO.  The carbon is attached to a carbon, the hydrogen, and double-bonded to oxygen.  The common name involves just adding -aldehyde at the end, which makes it pretty easy to tell when it’s involved.  The IUPAC version is -anal for a single-bond alkane and -enal for a double bond alkene.  These might sound unfamiliar, but you’ve probably heard of formaldehyde, which also is known as methanal.  As with other chemicals containing oxygen, they are reactive and flammable.

Carboxylic acids are kind of a mix between two other types of chemicals I’ve already talked about—an aldehyde and an alcohol.  The carbon chain has a -COOH at one end, with the first oxygen double-bonded to the end carbon as well as an -OH bonded to the end carbon.  The IUPAC nomenclature here is -oic acid, replacing the -e at the end of the alkane (methane to methanoic acid) if it’s a straight chain, and -carboxylic acid if it’s a ring.  If it’s an alkene, the -oic acid replacing the e thing still applies, but it’s more like propene to propenoic acid.  You might have heard of formic acid (IUPAC methanoic acid), but it is highly unlikely that you haven’t heard of acetic acid (ethanoic acid, better known by its even more common name, vinegar).

Similarly, esters are a mix of an ether and an aldehyde, only it’s -COOR (and therefore doesn’t appear at an end of the chain).  R, in these situations, is used to indicate the rest of a carbon chain, sometimes noted by R’, R”, etc if there’s more than one of them (so in this case it’d be more like R’COOR to indicate the full chemical formula).  The carbon is single-bonded to the carbon chain and one oxygen, and double bonded to the other oxygen.  Esters are more complicated when it comes to naming.  The R-chain is changed to a -yl ending (alkane to alkyl).  The rest of the chain (R’) (don’t forget to count the carbon in the COO portion of the chain) is a separate word in which the carboxylic acid ending is changed to -ate (so it’s -oic to -oate).  Alkanoic acid (example, as this doesn’t actually mean anything) would be alkyl alkanoate (alkyl from the R-chain and alkanoate from the R’ chain).  The simplest would be CH3COOCH3, or methyl ethanoate.

So far, what is the most interesting organic chemistry compound I’ve covered in your opinion?

real life, Writing

Writing, Ingredient Lists, and Organic Chemistry Terms III

Yes, we’re back to the IUPAC organic chemistry terminology.  I’m going to cover a few things you’re likely to see in daily life and a few things you aren’t.

Halogens get named depending on the specific halogen involved—fluoro- for fluorine, chloro- for chlorine, iodo-for iodine, etc.  If multiple halogens are attached, the terminology changes depending on whether multiple halogens are substituents.  I mentioned how the numbering goes in II, but didn’t mention how the numbers work with multiple substituents.  Things get complicated when you have more than one substituent.  If it’s the same type of substituent, x,x-substituentparentcarbonchain is the general pattern, though x,x,x or higher would be used if there are three or more substituents.  For an example, if there’s only one halogen, say, chlorine, we’ve got things like 2,4-chlorohexane.  If multiple substituents are used, it would be more like 2-bromo-2-chlorohexane.  Halogens on their own are also a little reactive, and when added to a carbon chain this doesn’t change (like alcohols).

Ethers, in which there’s a carbon in the middle of a carbon chain, are named in a slightly more complex way.  Remember the number-meaning words from I?  You use one of them (the shorter of the two chains off the oxygen) as that number, like numberwordoxy- (methoxy-).  A CH3OCH2CH2CH3 ether would be methoxypropane.  There are other ways to name them, but this is the way to do it with IUPAC naming.  Ethers are also reactive and flammable (that is pretty common for chemicals with oxygen).

Ketones, a double-bonded oxygen attached to one of the carbons in the carbon chain, have two different possible terms, -one, if it’s on its own, or oxo- if there are other more important suffixes in play.  (I’ll get to the suffix ranking at some point but that’ll be a little ways from now because there’s still a bit to get through.)  If -one is used, then the number occurs in the middle (hexan-3-one).  If oxo- is used, it’ll be x-oxocarbonhighersuffixranking, where x is the number of where the ketone occurs.

Trans and cis also appear as terms in organic chemistry, referring to the location of the attachments (substituents).  Cis means that the substituents are on the same side of the chain, while trans means that the substituents are on opposite sides of the chain.  This can even be used in the case of double bonds.  A cis bond in the chain has both “arms” of the rest of the carbon chain pointing in the same direction, while a trans bond in the chain has both “arms” of the rest of the carbon chain pointing in opposite directions.  (As an aside, this would be the reason why trans fats are named as such.  Saturated and unsaturated also along these lines.  Saturated means that it’s an alkane with no double bonds, so named because it is “saturated” with the maximum number of hydrogens possible, while unsaturated means that some of the hydrogens have been removed to make it an alkene or alkyne.)

Once I get done with the organic chemistry terminology, are there any other chemistry terms you’re curious about?

real life, Writing

Writing, Ingredient Lists, and Organic Chemistry Terms II

We’re returning to the terminology post we started last week.  I’ll add that along with the carbon chain if nothing else is specified (an attachment, a double bond), the carbon will have 3 bonds (as one of the bonds is taken by a carbon), so an end carbon will have 3 hydrogens and one in the middle will have 2 (since it’s attached to two other carbons as well).  So now you can start to guess at the atoms involved, even if you may not have the knowledge of the chemical structure to fully write it down.  (Unless you’re a scientist reading this, in which case, hi!  Practice if you feel like it.)

Interestingly enough, there is a suffix that means essentially the same thing as one of the others we covered last week, -yl.  For example, methane and methyl are identical with one exception—a methyl group is attached to something else, usually a bigger structure, while methane is single and unattached.  Numbers are also used here—in this case, roman numerals.  One example would be 2-methylhexane.  The number is used to indicate which of the carbons on the ‘main chain’ the -yl group is attached to.  The main or parent chain is always considered the longest carbon chain, and numbering is always done so the number is as low as possible (so while 5-methylhexane would be the same thing as 2-methylhexane, you would number it with the 2 because that way the number would be lower).  Also note that 1-methylhexane would not exist, as it would be heptane instead!

Cyclo- indicates that the structure exists in a circular structure.  Cyclohexane, for example, continuing off of last week’s post, is a six-carbon structure with no double bonds in which the first and sixth carbon are connected to each other.

-ol as an ending means that the chemical involved is an alcohol.  This involves having an oxygen-hydrogen group somewhere within the structure.  -OH groups are reactive and flammable, which explains methanol (CH3OH, since you remember from last week meth- means one carbon and there’s an -OH attached) and ethanol (CH3CH2OH, since as we covered eth- means there’s two carbons in the backbone, the number of hydrogens is covered above, and there’s an -OH attached).

We’ll also return to our previous numbering theme.  You might see poly-, which, as you might guess, means ‘many’.  This one is used more often in biochemistry or polymer chemistry (see, there’s that prefix again!) than organic chemistry, such as in polysaccharide (a saccharide is a sugar monomer).  In essence, all carbon chains could be considered polymers.  Polymers are large structures with repeating units (monomers—and yes, there’s one instance in which mono is used).  ‘Large’ is used in a vague way (no, there’s not an especially good, scientific definition of what ‘large’ means or how many monomers are required to make a polymer).  (If you want to be really fancy, you can call small structures with only a few monomers, such as pentane, an oligomer, oligo- here meaning a ‘few’—yeah, I know, that’s not very precise either!)  All plastics are polymers, varying in what monomer is involved (and most are a blend of different plastic types).  The monomer changes the properties of the plastic.

Of the terms we’ve gone over so far, which have you seen most often of the terms you’ve seen on your food?

real life, Writing

Writing, Ingredient Lists, and Organic Chemistry Terms

Organic chemistry is infamous for its difficulty.  There are memes about it, and I can confirm from personal experience it just clicks for a few people and for the others it’s really difficult.

To start with, there’s a bit of a misconception about what Organic Chemistry even entails (which admittedly I’d also had before I’d taken the class).  Organic chemistry has to do with life, true, but to be very specific organic merely means that carbon is present (which could be true of non-living things).  It’s simply that, aside from silicon, carbon is the only element that we know about that is versatile enough to support the number of different reactions that life requires.  Humans need some inorganic chemicals to survive (sodium chloride, iron, magnesium, etc), and a few naturally occurring organic compounds can be found in rocks and other nonliving things.

However difficult I found Organic Chemistry, an interesting and useful part of the subject is the terminology.  You will notice some of these terms if you read the ingredients lists on a number of products on grocery shelves.  You can also use a couple of these (planned) articles on terminology to use terms more meaningfully than simple technobabble.

Organic Chemistry terminology is known as nomenclature, and it’s an entire unit in Organic Chemistry.  (Other versions of chemistry also have a bit of terminology, but most of it is fairly straightforward, such as sodium chloride—organic chemistry is much more complicated.)

The most commonly used is the IUPAC (International Union of Pure and Applied Chemistry); however, this is not the only type used.  Many chemicals also have a common name, a name given to them before anyone had tried to be systematic about it and had been in use so long that changing it is difficult.

The easiest parts to understand are all the number-meaning words.  There are a few of these and you will notice them once you start looking for them.  The most common you’ll see are meth (1), eth (2), prop (3), but (4), pent (5) and hex (6), though there are others.  For example, you’ll see methanol and ethanol, both types of alcohol.  Each of these indicate the number of chemical atoms present, which usually form a backbone of the structure.  There are also ones indicating how many of particular groups are attached—mono (1), di (2), tri (3), tetra (4).  Mono isn’t used especially often, since it’s considered slightly redundant (if there’s more than one, a number would be added), so it’s mostly just used for emphasis (you might have heard of it in monosodium glutamate, i.e. msg).  Some interesting albeit rarely used ones are bis (2), tris (3), tetrakis (4) (used for complicated attached groups).

Similarly, endings are also helpful when understanding the meanings.  -ane, for example, is an indication that the molecule has a single rather than a double or a triple bond between the carbon atoms.  Molecular bonds are created when atoms share electrons with each other.  This forms a springy sort of connection between them that can be broken.  The number of bonds is indicated by the number of lines drawn between the atoms in a specific depiction of the molecule (structural or line drawings) and indicates the number of shared electrons.  -ene indicates that there is a double bond between two or more of the carbon atoms.  -yne indicates that there is a triple bond between two or more of the carbon atoms.

I’ll probably do another one because there is a lot more to say about IUPAC, but in the meantime, I have a different sort of question for you this week—look at your ingredients lists and comment about the most complicated one you can find.  (If you eat all organic, look up the chemical name for one of the vitamins.)