Well, the chemical difference is not the one you hear on the news which distinguishes “organic” vegetables from “non-organic” ones. Guess what, both are made up of organic and inorganic compounds.

Let’s say that the “agriculture industry” definition is not the same as the chemical definition. In chemistry, there is a major difference, which is well defined.

Telling the difference between organic and inorganic compounds is one of the main things you need to make clear while learning chemistry. If you are interested, learn more about thermodynamics and kinetics, another two of thee most important concepts in chemistry.

In this article we will explain it in detail, so at the end you will be able to differentiate both of types of chemicals without any difficulty. We will try to solve all your doubts about this eternal chemistry question!

In the early days, scientists separated organic and inorganic compounds on the fact that the first group was considered as a result of the activity of living beings, whereas the second group belonged to the processes unrelated to any way of life. Now there are much clearer definitions.

Introduction

About 200 years ago, at the transition between alchemy and chemistry, chemists classified the chemical compounds into two main groups.

1. Organic Compounds

An easy, layman-friendly definition for organic compounds is that those are the ones which are derived from living things such as plants and animals are known as organic compounds like sugars, lipids, proteins, nucleic acids, etc.

More strictly speaking, we consider a compound to be organic if it is made of carbon atoms which participate in covalent bonds. Generally (but not always), organic compounds also present covalent C–H bonds.

2. Inorganic Compounds

An easy definition for an outsider, is that those compounds which are obtained from non-living things or mineral sources are known as inorganic compounds like NaCl (table salt) and NaHCO₃, (baking soda), etc.

Defining inorganic compounds is pretty easy after having defined organic compounds. As a rule, every chemical that does not fall into the category of “organic”, is considered an inorganic compound.

The Vital Force Theory and the First Chemical Total Synthesis

Let’s go back in time once again, to the very early days of chemistry. The theory known as the “vital force theory” might ring a bell to you if you are familiar with the history of chemistry.

This theory was proposed by Swedish chemist Berzelius in 1815. This theory states that organic compounds can’t be synthesized in a laboratory. Early chemists believed that organic compounds could only be obtained from living organisms, through “vital forces”. That is why this theory is referred to as “vital force theory”.

In 1828, Friedrich Wohler, a German chemist, synthesized urea in the laboratory. This accounts for the first chemical total synthesis of a natural organic compound ever!

This accomplishment showed that it was possible to synthesize an organic compound (urea), starting from an inorganic compound (ammonium cyanate), in the laboratory: treating silver cyanate with ammonium chloride afforded a crystalline compound that was found to be identical to urea isolated from urine.

This chemical transformation invalidated the vital force theory, and soon after this, chemists began to make organic compounds in the laboratory. Hence the modern definition of organic compounds was introduced in the scientific world. This also marks the very beginning of organic chemistry as a discipline.

The Modern Definitions

Organic Compounds

The compounds which contain carbon atoms as main constituent, which are bonded together through covalent bonds, are called organic compounds. Most organic compounds also contain hydrogen. Other common elements present in organic compounds are oxygen, nitrogen, sulphur, halogens, or phosphorous. But those are not the only ones.

In most cases, all atoms of the different elements are held together through covalent bonds. Some exceptions would be, for example, organic carboxylates, or ammonium salts. But you could argue that those are “inorganic salts of organic compounds”.

Some compounds that might sound “non-organic as hell” such as polymers (a fancy name for plastics), are actually long-chained organic compounds. An example is polystyrene. It’s backbone is basically all covalent C–C and C–H bonds.

Bear in mind that “organic compound” does not imply “biochemical compound”. On the other hand, the backbone of biochemistry is mostly organic compounds (although metals are extremely important in biological systems such as iron in hemoglobin).

Inorganic compounds

Take every organic compound out. You are left with inorganic compounds. If it doesn’t fall into the definition of organic, it is inorganic.

In general, the compounds which do not have C–C or C–H covalent bonds are called inorganic compounds.

There are many compounds that only have covalent bonds, they have carbon atoms, but are not organic compounds. Examples of this type of inorganic compounds include carbon monoxide, carbon dioxide, inorganic carbonates, carbides, etc. Notably, allotropes of carbon such as graphite, graphene or diamond, contain only carbon atoms, but are considered inorganic compounds.

As you can see, sometimes the definition is not so well established. In fact, I couldn’t really find a clear definition for both provided by IUPAC. This illustrates the fact that defining the line between inorganic and organic chemicals.

Some interesting examples of this middle ground are organometallic compounds. These are made up of an organic component, generally bound to an inorganic component through a carbon–metal bond. These are really fun and are one of the most widely explored research topics in modern chemistry!

Major Differences Between Organic and Inorganic Compounds

We will try to sumarize in a quick comparison table the key differences between organic and inorganic compounds.

However, bear in mind that in most cases these are just generalizations and won’t be true for any scenario, and definitely will have exceptions.

And as you can probably guess, the examples for both types of both types can go on forever.

Examples of Organic Compounds

Time to dive into learning organic chemistry! These are just some natural and non-natural examples of organic compounds.

Carbohydrates

These are commonly known as sugars. In terms of functional groups, these are aldehydes or ketones having additional hydroxyl groups. Carbohydrates are a simple way to illustrate organic compounds, since they are just chains of C–C and C–H covalent bonds in the company of some of the most typical organic functional groups (alcohols and carbonyls). Examples of carbohydrates are glucose, fructose, sucrose, etc.

Proteins

Proteins are made up of chains of amino acids joined together to form peptides. Proteins are actually polymers, which can be made up of a single chain of many amino acids, or of several chains that are packed together by non-covalent interactions. Since they are made of amino acids, they contain carbon, hydrogen, oxygen, and also nitrogen atoms, everything held together by covalent bonds, and also non-covalent interactions. A classical example of proteins are enzymes.

Organic Solvents

Organic solvents are organic compounds which are commonly used to dissolve chemicals in the lab, mainly for setting up chemical reactions. “Like dissolves like” they say, so these solvents are a must for carrying out organic reactions. They are usually simple organic compounds made of carbon, hydrogen, and also oxygen or nitrogen, sometimes sulphur. They are usually liquids at room temperature and have boiling points ranging from 40 ºC to 200 ºC. Common examples are hexane, cyclohexane (CyH), acetone, tetrahydrofuran (THF), toluene (PhMe), ethanol (EtOH), methanol (MeOH), benzene (PhH), dimethylsulfoxide (DMSO) or dimethylformamide (DMF).

Whatever Organic Compound that You Can Imagine Making on an Organic Chemistry Lab

The only limit for organic compounds is the imagination of the chemist. Theres is most likely an infinite number of combinations in which you can arrange carbon and hydrogen atoms to form organic compounds. Not to mention other elements.

That’s something I just made up in less than 1 minute in ChemDraw, and it seems like a totally reasonable organic compound.

Examples of Inorganic Compounds

Getting ready to study the realm of inorganic chemistry? These are just some common examples of inorganic molecules.

NaCl – Sodium Chloride or Table Salt

The salt you use for cooking is mostly sodium chloride, NaCl, and this is the most classical example of an inorganic compound. Specifically, it’s an ionic compound composed of an equal number of sodium(I) cations and chloride anions, arranged though a symmetrical three-dimensional network.

Carbon dioxide

Carbon dioxide is another example of inorganic compound with a chemical formula CO₂.  Despite of the presence of carbon atom, CO₂ is considered an inorganic compounds because containing carbon and covalent bonds doesn’t directly make a compound organic. You need a C–H bond or an equivalent.

For example, carbon tetrachloride, CCl4, is considered an organic compound, because instead of C–H covalent bonds it has C–Cl bonds, which are electronically equivalent. The bonding model in carbon dioxide, carbon monoxide, and other small inorganic compounds is quite different.

Diamond and Graphite

Allotropes of carbon such as graphite, graphene or diamond are classified as inorganic compounds, even when they have

Example of an Organometallic Compound

Right in the middle of organic and inorganic compounds, we can find organometallic compounds, which are characterized by having a carbon–metal bond (which in many cases is a “hybrid” between a covalent and an ionic bond).

An example of this are Grignard reagents (such as phenyl magnesium bromide) or organolithium compounds (such as butyl lithium).

To Sum Up

I hope we managed to explain clearly the basic differences between organic and inorganic compounds.

Organic compounds always contain carbon atoms, and almost always hydrogen atoms, all of them held together by covalent forces.

Inorganic compounds are just the rest!

The post What Is the Difference Between Organic and Inorganic Compounds? appeared first on Chemistry Hall.

Let’s set the record straight here. Applying your knowledge of chemistry can help you cut through the marketing hype and fear mongering. The truth is often simpler than you might expect.

What Is Distilled Water?

Distilled water is simply water that has been purified through a process of distillation. That means it has been boiled, and the resulting steam has been collected and condensed, leaving you with what is, in theory, perfectly pure water (it is not a complicated set up, you could even do it at home).

What does “perfectly pure” mean, in this case? Consider tap water, spring water, or any other water you might encounter in daily life. All of this water has some amount of other “stuff” in it besides hydrogen and oxygen.

Some of it might be stuff you can see, like algae in lake water, for example. But most of it will be invisible to the naked eye: dissolved minerals like calcium, sodium, potassium and magnesium, chlorides and bicarbonates, and sometimes additives like chlorine and fluoride in tap water in some regions.

There may even be microscopic critters swimming around in the water. Most of them are harmless, but some pathogenic microorganisms cause very serious illness (this is why so many cities treat their water supplies with a small amount of chlorine).

So, the perfectly pure water that comes from distillation is missing all of the above—it contains no minerals, no bacteria, no nothing. Just plain ol’ H₂O.

Is it Safe to Drink?

The short answer is, yes, it’s safe to drink distilled water. But you might not want to make a habit of it.

Typically, distilled water of different qualities is employed to perform analytical chemistry techniques.

First of all, it’s not going to be any better for you than your regular tap water (assuming you are in an area where the water is safe to drink), and it can actually have certain negative long-term effects in some people.

Because it contains no minerals (i.e. electrolytes), it may be harder for your body to stay hydrated drinking distilled water, or you may get muscle cramps because of low calcium and magnesium. Still, these side effects are far from universal and certainly no reason to avoid distilled water if it is the only uncontaminated source available. You can always replenish electrolytes through food.

To illustrate just how safe it really is, consider that distilled water is often used to prepare formula for infants with particularly weak immune systems.

It has plenty of other uses, too. It’s essential for laboratory tests and chemical preparations like cosmetics, and it is very useful in cars and domestic appliances for reducing limescale and other mineral deposits.

But it’s not the best for drinking if you care at all about how your water tastes. If you look closely at any bottle of purified drinking water, you’ll see that, after purification, minerals have been added back into the water. This is because distilled water, without any minerals, tastes bland and flat.

Finally, it’s a lot more expensive than tap water. It’s worth paying extra to keep your car and clothes iron working smoothly, but for drinking? Why pay more for water that tastes bad and offers no benefits unless it’s really necessary?

What About Alkaline Water?

Speaking of water that is unnecessarily expensive and doesn’t offer any benefits…

I don’t know when this idea first came onto the scene, but I first heard someone peddling the idea of acidic and alkaline diets circa 2007. It didn’t seem terribly harmful at first—the proposed “alkaline diet” was rich in fresh vegetables and fruits, low in sugar and processed foods, and really an undeniably healthy way of eating—but this notion grabbed a foothold and is now being used to scam people out of their money with false health claims.

So now, over a decade later, alkaline water is being sold everywhere you look for exorbitant amounts of money compared to tap water. Depending on who you ask, this water will make sure your blood maintains its proper pH (very slightly basic), doing everything from reducing systemic inflammation to preventing cancer.

For anyone with a rudimentary understanding of chemistry and biochemistry, this is simply preposterous.

Yes, an alteration in your body’s pH is a big problem, but this does not happen as a result of consuming normal foods or drinks. We all eat and drink acidic and alkaline things every single day without any effect on the pH of our bodies. This is because the human body contains numerous regulatory mechanisms and buffering systems to prevent the things we ingest from affecting the pH of our blood or cells.

The body rids itself of excess acid by exhaling carbon dioxide, by excreting it through the kidneys, or by retaining bicarbonate.

So, what happens if you do drink alkaline water? Think about where that water is going: straight into the highly acidic environment of your stomach. Your body has its own built-in water alkalinization system! Before it is absorbed by the colon, the acidic water from your stomach is neutralized by bicarbonate secretions from the pancreas.

Drinking Distilled Water: Water Quality

With all of this in mind, we can say that, in general, it is safe to drink distilled water. Most tap water, however, is equally safe to drink, tastes better and is much cheaper. But if you know that the area you are in does not have safe drinking water, you should not hesitate to drink distilled water if it is the only clean water available.

I guess the same could be said about alkaline water—if there’s nothing else safe to drink, by all means—but that’s the only good reason to do it. Put your chemistry knowledge to use, don’t be fooled by marketing gimmicks, and save your money.

If you want to impress a chemist with a gift, please, don’t even think about these kinds of scammy trends, there are so much better options!

The post Is It Safe To Drink Distilled Water? appeared first on Chemistry Hall.

We have recently reviewed a selection of the best organic chemistry textbooks. Shortly after, we started to receive emails asking for similar recommendations, but directed towards inorganic chemistry. There’s a slight big difference between organic and inorganic chemistry, so different approaches are often employed to teach learn each one of the two.

So we decided to go back to the library a check the best texts for this fascinating and diverse subject. This resulted on a nice and concise review guide of 6 books which we believe are the best for learning inorganic chem.

This reference guide is aimed at education professionals that are looking for a textbook to base their inorganic chemistry syllabus on. But also to all inorganic chem students that do not have a defined textbook on their courses, or want a better one to fully understand the topics on their class.

As always, we start off by cutting right to the chase and present what we believe is the best inorganic chemistry textbook, overall.

What Is the Best Inorganic Chemistry Textbook?

From our point of view, Inorganic Chemistry by C. Housecroft and A. Sharpe is the most recommended textbook for inorganic chemistry. It approaches many areas of this wide subject in a very methodical and logical fashion.

Housecroft Inorganic Chemistry

It is the best book we have put our hands into so far.

This text is very detailed, even in the more specialized chapters. If you buy it, it will probably be the only introductory textbook that you will ever need for any inorganic chemistry university course.

Quick Summary Table of the Best Inorganic Chemistry Textbooks

Here we have condensed the six reviews included on this guide in a reference table. You can take a quick glance at the best features of each option, or continue reading for the complete reviews!

1. Housecroft Inorganic Chemistry

Our number one choice is Inorganic Chemistry by Catherine Housecroft and Alan G. Sharpe. It is the text I used though my undergraduate courses years ago. And it is the first choice for many educators I know.

Housecroft Inorganic Chemistry

Housecroft is greatly organized, and the explanations are easy to understand. But this does not sacrifice level of detail. Most topics are explored deeply.

Many questions and problems are provided in order to help you grasp all the concepts on each chapter. The book has review sections which work greatly for this purpose.

This best inorganic chemistry textbook is filled with beautiful and attractive schemes, pictures and images. Most inorganic chemistry textbooks don’t really have illustrations as powerful and instructive as Housecroft’s.

This textbook is right now on its 5th edition, released in 2018, so its 1300 pages are full of updated content.

It is also worth highlighting how real-life or interdisciplinary applications of pure and basic inorganic chemistry concepts are described throughout the book.

Overall, in our opinion, Housecroft’s is the most complete inorganic chemistry textbook. It is wide, but also deep enough so you will be able to push through any introductory inorganic chemistry course with it.

2. Miessler Inorganic Chemistry

Inorganic chemistry by Miessler and Tarr is another pretty standard option. The last edition brings colored images and diagrams which make the textbook much easier to follow.

Miessler Inorganic Chemistry

This book is very accesible, and describes concepts very visually. It even goes into some computational chemistry. This is generally an advantage, but there is people that, for this reason, find some of the concepts difficult to grasp without a solid basic knowledge on physical chemistry.

For both professors and students, Miessler’s is one of the best options if you want teach or take medium to advanced inorganic chemistry courses. It finds interesctions between physical and organic chemistry, which is good.

As a drawback, it lacks a bit on the problems and exercises department. You will need the corresponding solutions manual, which fortunately is not that expensive. You can find it here.

3. Cotton-Wilkinson Advanced Inorganic Chemistry

Advanced Inorganic Chemistry is probably the best and most complete reference inorganic chem textbook out there.

We wouldn’t choose it as the best option for basing an introductory inorganic chemistry course on, but it is difficult to beat for anything above that. It is a classic masterpiece, written by F. Albert Cotton and the Nobel laureate Sir Geoffrey Wilkinson.

Cotton-Wilkinson Advanced Inorganic Chemistry

If you are either a professional or somebody looking forward to develop a career on inorganic or organometallic chemistry, this textbook should be in your shelf. On the other hand, if you are a student which enjoys inorganic chemistry a lot, and you already have covered the basics of chemistry in class, this book might be your perfect choice. If you want something for self-study or reference, or as a suplement, Advanced Inorganic Chemistry by Cotton and Wilkinson will do the job.

I’m actually an organic chemist and this reference book has been right next to me on my room for a lot of years. It is a great text for both inorganic and organometallic chemistry students (or professionals) alike.

In contrast with other typical textbooks, Cotton-Wilkinson’s Advanced Inorganic Chemistry is organized by elements, describing all the typical compounds for each element, going through bonding and reactivity. This arrangement makes it the absolute best book for just picking it up and starting to get into the inorganic chemistry of one element you are particularly interested in. It has plenty of relevant references to go through and expand your knowledge.

Some describe this book as more like a dictionary or reference guide than a textbook, that’s why using it for introductory courses might not be the best choice. But for reference and self-study, it is the best inorganic chemistry book out there.

4. Weller Inorganic Chemistry (Former Atkins)

Over the years, one of the golden reference textbooks was Inorganic Chemistry by Shriver, Atkins and co-workers. Atkins is no longer updating his book, but his co-workers, Mark Weller, Tina Overton and Jonathan Rourke, took over with this Inorganic Chemistry textbook.

This is the last edition of one of the best inorganic chemistry texbooks out there. Together with Housecroft’s, make up probably the top 2 best textbooks for introductory inorganic chemistry courses.

Weller Inorganic Chemistry

This inorganic chemistry textbook goes generally into more detail than Housecroft’s, but it is generally not as easy to read, especially if you are just getting started.

For chapters such as the ones for the crystal/ligand field theory (the base for coordination chemistry), it is great and very detailed. If you are approaching organometallic chemistry, this text may be the way to go. Another advantage is that it seems to be cheaper than the original Atkins used to be. Also, it was updated in 2018.

Overall, if you want something that goes into a bit more of detail than Housecroft (although covering a less broad amount of material, and with less examples), or if for some reason you don’t like that text, Weller’s Inorganic Chemistry is probably your best bet.

5. Lee Concise Inorganic Chemistry

As you can probably tell from its name, Lee’s Concise Inorganic Chemistry is a textbook that goes right to the point. It does not contain things that the author may consider to be not relevant. This can be good, but it also means that you might find that it lacks examples in some cases.

Lee Concise Inorganic Chemistry

It may be a “concise” textbook, but by no means it is short in content. Throughout its 1000 pages, Concise Inorganic Chemistry is one of the best introductions to the subject there is. I’ve known people that have used it from preparing AP chemistry exams, or SAT chemistry subject tests, to getting through university courses.

As most inorganic chemistry texts, it starts describing the different bonds and trends on the elements of the preiodic table. Then it quickly jumps into describing groups of elements. You won’t find many discussions such as “why is this element important” or “what are the every day uses of this kind of compounds”, instead, Lee focuses on properties, structure and bonding.

However, don’t think that this book would be too boring because of this. It is actually one of the most enjoyable inorganic chemistry textbooks to read. There is a great balance between theory and applications. And it is definitely one of the best choices if you just want to prepare for an inorganic chemistry course.

6. Chemistry: A Molecular Approach

First of all, Chemistry: A Molecular Approach is a general chemistry textbook, not an inorganic chemistry one.

So what’s it doing on this review?

Well, in contrast to the other areas of chemistry (which usually need a more specialized text, even at introductory levels), the content of introductory inorganic chemistry courses usually overlaps with what you can find in most general chemistry textbooks.

This is because most introductions to inorganic chemistry are strongly based and centered around the different concepts of chemical bonding. And this is amazingly well explained in general chemistry textbooks. Specifically, Chemistry: A Molecular Approach by Nivaldo J. Tro does an excellent job on this sense.

Chemistry: A Molecular Approach

If you are just getting into inorganic chemistry, you can perfectly stick to this textbook.

It covers, from the very beginning, all basic concepts of chemical bonding. From the Lewis model to a latter chapter on transition metals and coordination compounds.

However, it is a general chemistry text, after all. If you move deeper into any field within inorganic chemistry, you will probably run out of content pretty soon.

If you want more information about general chemistry textbooks, check out our review post to look for the best one for you!

Overall, this a perfect choice if you are just getting started with inorganic chemistry, and you want a book that can be versatile: you will be able to use it in many other introductory chemistry courses! You need a base to study any field of chemistry. Chemistry: A Molecular Approach does a great job on providing this base, particularly for inorganic chemistry.

Final Thoughts and Summary

To sum up, if you are in doubt, go for Housecroft Inorganic Chemistry. Overall, it is the best option. It will fit any inorganic chemistry course that you want to teach or take.

If you are going to take or teach an advanced inorganic chemistry course, or you want a book that can serve as reference for future courses, or in your chemistry career, go for Advanced Organic Chemistry by Cotton and Wilkinson.

Finally, if you are just taking basic inorganic chemistry courses, and you are just getting started in chemistry, a general chemistry text will be the best fit. It will also be useful for introductory courses on other branches of chemistry. Our best recommendation for this case is Chemistry: A Molecular Approach.

You can take a quick glance or purchase the best option for your needs through the following table:

If you want further information or educational resources, make sure to check our guide to learn chemistry.

Enjoy learning inorganic chemistry!

The post The Best Inorganic Chemistry Textbooks appeared first on Chemistry Hall.

You can find this formations in different places at the US, for example, there is a crystal cave in Wisconsin, a crystal cave in Ohio and a crystal cave in California. Besides, one of the most impressive ones is located in Naica (Mexico).

We will first explain the chemistry behind these natural marvels and then check the best crystal caves that you can find and how to visit them. As a chemist, I find them as a source of inspiration.

1. What Are Crystal Caves and How Do They Form?
2. The Great Cave of Crystals in Mexico
3. Visit the Crystal Cave, Wisconsin
4. Visit a Crystal Cave, Ohio
5. The Crystal Cave in CA: Sequoia National Park

What Are Crystal Caves and How Do They Form?

Many inorganic compounds can form crystals naturally. I spent part of my youth growing crystals as part of chemistry home experiments, and now as a professional chemist, I also have to it on a weekly basis. Crystallisation is an important process in chemistry, but it is nothing new that we discovered in the lab. Nature has been providing examples of growing crystals since forever. And it does it pretty well.

There are different materials that can give rise to crystal caves. Some examples are speleothems (“cave deposits” from Greek). These are deposits of minerals such as limestone (calcium carbone) or dolomite (mixed calcium and magnesium carbonate).

If you are not familiar with these terms, maybe you are interesting in some resources for learning inorganic chemistry.

But this simple deposits don’t give rise to large crystals, they are just microcristaline solids. The best example of a cave with huge crystalline formations is the crystal cave in Naica (Mexico).

Natural Large-Scale Crystal Cave Growing

As you may know, one of the best ways to grow crystals in the lab is using a hot solvent to obtain saturated solution of your compound. Then you let the saturated solution cool down, and if you are lucky, crystals will eventually crash out. But no fancy Nobel-prize wining chemist invented this. Nature did!

Millions of years ago, the caves were filled with water rich in hydrated calcium sulfate (gypsum), in a form called selenite, which gives rise to colorless-white crystals (if want to learn more, you may want to take a look at some of the best inorganic chemistry textbooks). At that time, these waters were heated by magma, above 60 ºC. Over thousands of years, as Earth cooled down, these saturated solutions also got below this temperature. This caused the calcium sulfate to start nucleating and the crystals began to grow. This is a textbook definition of crystallisation by extremely slow cooling, and you can find more details in this original report in Geology. Remember, do your crystallisations slowly (maybe not as slowly as Nature) for them to succeed!

The Great Cave of Crystals in Mexico

Out of all crystal caves, the one located in Naica (Mexico) is definitely the most impressive one. The main chamber contains some of the largest natural crystals ever found. These crystals are mainly selenite, and its formation was described in the last section. The largest weights 55 tons and has 12×4 m dimensions. Simply impressive. The scenery seem like taken right out of a science fiction movie or videogame.

Unfortunately, there are downsides associated with this Mexican wonder. The cave is extremely hot, on average between 45 and 50 ºC, up to a maximum of 58 ºC, with a roughly 100% of humidity. Therefore, visit is limited to authorised trained scientists. Using special suits, it is possible to stay down there no longer 10-15 minutes. These factors result in this crystal cave being relatively unexplored after its discovery in 2000.

Besides, the fact that the crystals are made of hydrated calcium sulfate, makes them very sensitive. The atmosphere saturated in water of the cave allows them to survive, but taking them out of the cave leads to dehydration and subsequent loss of crystallinity.

Maybe it is better for the crystal cave of Naica it to remain fairly unexplored. But don’t worry! There are several nice options across the US to visit a crystal cave, with not-so-extreme conditions.

Speleothem Crystal Cave, Wisconsin

In Pierce County, you can find the crystal cave in Wisconsin. It was discovered much longer ago, in 1881 by W. R. Vanasse. The crystal cave in Wisconsin is filled with speleothems, mostly in the forms of stalagmites, stalactites or columns.

An interesting fact is that this caves were designated as public bomb shelters in 1942. The cave is so massive that it was the only one able to fit the whole population of the town which was using it as a protection element. The Wisconsin crystal caves can be visited any time of the year except for the winter.

Strontium Crystal Cave, Ohio

The next crystal cave, Ohio, is a cave made mainly of limestone (calcium carbonate) and you can find it in Put-in-Bay, in Lake Erie. It was discovered in 1897, and only since 2016, you can visit it!

In this crystal cave you can see crystals of up to 1 m long. These crystals are made of a mineral called celestine, which is a form of strontium sulfate. Strontium salts, specifically strontium carbonate and nitrate, are widely used to make fireworks. The strontium ion gives red fireworks its color. For this reason, the space within this cave is significantly bigger now than when it was discovered. This means more room for visiting and also fireworks. Yay.

The Crystal Cave in CA: Sequoia National Park

You can also find a crystal cave in California, within the magnificent Sequoia National Park. There are more than 200 caves in this National Park, but this one is worth a visit. This cave is usually open for visits from the end of May to the end of September. The crystalline formations in this crystal cave are mostly based in limestone speleothems, so nothing new chemically, but the scenery make it worth checking out if you are a geology enthusiast.

Keep in mind that if you want to visit this crystal cave, you will have to buy the tickets online in advance at the Foothills or Lodgepole Visitor Center, they are not selling them on-site.

As you can see, Nature outranks us chemists in many tasks. Not only builds up extremely complex organic molecules without much effort, but Nature sure also beats us growing crystals! However, to be fair, Nature had millions of years to adapt, but modern science is barely a couple of centuries old. I guess we are on the right path.

Be sure to let us know in the comments which kind of natural wonders would you like to see chemically-explained in the future!

The post Crystal Caves: When Nature Grows Crystals appeared first on Chemistry Hall.

Confirming the actual structure of a molecule, is still a big challenge now-a-days. The advances in techniques such as NMR (Nuclear Magnetic Resonance) spectroscopy, or single-crystal X-ray diffraction have significantly helped speeding up this problem.

Molecular structure determination

Every month we get reports of chemical structures whose structures have to be reassigned or revised after some study (either synthetic or just based on characterization techniques) is carried out. On this regard, it is worth remarking the difference between scientific models and reality.

Truth is, even today, the methods for the characterization of molecules available to use routinely (which are explained in the most basic chemical bibliography), can be consider rather rudimentary, and of difficult interpretation for non-experts. Let me be honest, I am a trained PhD organic chemist and if I had to take a look at the NMR spectra of a complex natural product such as maitotoxin, I would probably have no clue what I am looking at.

Single crystal X-ray diffraction is probably the closest method to easily visualize the structure of a molecule in 3D. However, this is not a bulletproof method. The sample preparation (growing single crystals) required for this indirect technique, renders it useless for a wide variety of chemical compounds.

Can we actually see real molecules or atoms?

Accordingly, I would say that by today, there should already be a method that allows taking a direct microscopic “picture” of any compound you like, and immediately visualizing its structure in a screen. Apparently we are not quite there yet (in regards to “any compound”, keep reading). However, the answer may come under the name of atomic microscopy, and all of its variations.

Atomic force microscopy (AFM) or scanning force microscopy (SFM) is a very high resolution probe-microscopy technique. It allows us to actually “see” or “take real pictures” at the nanometer-scale, in which the molecular realm lies. A picture is worth 1000 words. In the example below, scientists make use of this technique to get pictures of a compound called naphthalenetetracarboxylic diimide. We can actually see a real molecule.

Much more recently, researchers at Oxford and IBM used STM-AFM to generate and visualize in situ the first cyclic allotrope of carbon, cyclo[18]carbon.

Seeing atoms in motion

The world of visualizing at the atomic level took a leap more than ten years ago. In 2008, a research group reported the imaging for the first time of light atoms and molecules on graphene. Subsequently, the same team managed to observe for the first time the actual movement of insolated graphene atoms in real time. The following movie from the Berkeley team shows the growth of a hole in a graphene sheet. For this experiment, a beam of electrons is focused to a specific spot on the graphene sheet, blowing out the focused carbon atoms making a hole. Besides, it can also be observed how the carbon atoms rearrange themselves (edge reconstruction) to adapt a more stable configuration.

The Boy And His Atom: The World’s Smallest Movie

The Guinness World Record for the “Smallest Stop-Motion Film” is held by a movie recorded by IBM scientists. Sometimes, nanophysicists also need to have a bit of fun, and what they decided is to “film” a movie by using scanning tunneling microscopy, a the result is in the following video:

By the use of this technique, the scientists managed to move a lot of molecules of carbon dioxide following their will. The result is a movie you can only see using a microscope that magnifies one hundred million times.

Direct observation of chemical reactions

Obviously, taking real pictures of molecules and atoms was just not enough for the scientific community. If we fast-forward to year 2013, atomic microscopy, more specifically, non-contact atomic force microscopy, allowed the direct imaging of molecular structures during a chemical reaction. Some results of these experiments published in the journal Science are displayed below. We cannot only see actual atoms molecules, we can observe directly chemical reactions!

AFM in structural determination

This field started as a cluster of isolated cases, but as the years went by, more and more examples of the application of this set of physical techniques are being constantly reported. The level at which the studied molecules can be observed is rather impressive. A recent example is the actual structural determination of a natural compound, breitfussin A. Several functional groups of the molecule were derived from classical spectroscopic data (a). Then, an AFM image (c) allowed observing the real structure of the molecule, placing each piece of the puzzle (a) in the correct spot. This established the previously unknown structure of the molecule (b).

Taking real pictures of complex chemical reactions

On the reactivity side of things, much more recently, it was possible to directly image the course of a reaction called the Bergman cyclization. This is one of the most fascinating rearrangements in chemistry. The chemical transformation is directly induced in the metal surface in which the atomic microscopy procedure is carried out.

However, as stated at the end of the introduction, not every molecule or reaction can be a candidate for a STM study as these. Several conditions need to be met. One of them (which might have already called your attention) is that the analyzed compounds need to be near-planar. These techniques rely on depositing the molecules of the compound in a planar metal surface, so planar molecules are the ones that give more interpretable data.

The search for the “Holy Grail” of structural determination

To finish this short essay that does not make justice to the whole field of molecular imaging, a recent application of what is called micro-electron diffraction (MicroED) will be discussed. This brilliant application of electron diffraction, allows overcoming probably the biggest problem on classical X-ray diffraction methods: the requirement of crystalline material of the molecule which structure wants to be elucidated.

This technique allows taking simple powder of any non-crystalline solid, without almost any sample preparation, and getting 3D structures of the powder nano-crystals in a matter of minutes, with extremely high resolutions. The structure of molecules with very high complexity, as thiostrepton, could be obtained unequivocally.

Is this the future of chemistry?

Can we see real atoms and molecules at this point? I would say that we definitely can. All the results that have been described in this article were published only over the last decade. Atomic microscopy seems to be here to stay, and it might be one of the tools that finally allows chemists to stop relying in rudimentary techniques for the determination of molecular structures. Only time will tell.

Stay tuned for more posts about the future of chemistry, share, and post your thoughts in the comment section!

The post Can We See Real Atoms and Molecules? Electron Microscopy at a Glance appeared first on Chemistry Hall.

1. Lab hacks for taking care of air sensitive chemicals: What works and what does not

I have seen people remove the “sureseal” from Aldrich bottles of buthyllithum and exchange it for a rubber septum. This is not the way to go: a piece of rubber full of holes is not protecting you reagent at all. The only long-term reliable method for protecting air-sensitive commercial compounds like BuLi is the metal/plastic seal that originally comes attached to the bottle. Aldrich’s sureseals worked fine in my experience, if you want something more, Acros multi-layer seals provide an even better reliability.

A more useful lab hack is to use a needle that leaves almost no hole while using it to take the reagent out of your bottle. A good choice is using 4 in. 22 ga needles (Fisher #14-817-102). I found them for the first time in my current lab and they work perfectly fine.

But if you really need to store a chemical properly under complete inert conditions you should transfer it into a Schlenk bomb.To do so you can just follow the same procedure than doing a cannula transfer, having throughouly purged it with an inert gas like Ar beforehand. Of course, most of this reagents can be titrated so you can know its exact concentration before using it, which is required especially in cases where you do not want to use an excess but a stoichiometric amount of the compound. Shenvi’s group in Scripps has published online a very nice guide on titration of common soluble RM, R₂NM and ROM reagents.

2. Most commonly used pyrophoric reagents

Most of the fires and explosions that can happen in the labs are usually caused by the same chemicals. We found very interesting to share a list of the most common reagents that might cause a fire or an explosion if not handled properly.

The most popular one would be sodium metal, which is still used in many labs as drying reagent for solvents via distillation. Take special care when handling it under air atmosphere.

Lithium aluminum hydride (LiAlH₄) is a frequently used reagent for performing reductions. It is of extreme importance to add the hydride in very small portions to the substrate, and in a ice/water bath if possible, especially at the beginning of the addition. Another approach would be to add a solution of the substrate to a suspension of LiAlH₄, once again, in a controlled manner.

Palladium on carbon (Pd/C) can also ignite in contact with MeOH (a common solvent for hydrogenations), so it is usually recommended to cover completely the Pd/C with another solvent like toluene, and then add the substrate and the methanol. Obviously, hydrogen can also cause explosions, so if you are planning to do hydrogenations, consider asking for advice or training first. As a general rule, set up the reaction completely under Ar/N₂ atmosphere, only exchange for H₂ last. When the reaction is complete, exchange again H₂ for inert gas and then you can open the flask.

Other common chemicals that may ignite are organolithium reagents, especially tBuLi. Always quench the syringe you used for the addition with not dry Et₂O or THF, you do not want to create a flamethrower!

You can check some guidelines on the safe use of pyrophoric reagents by Columbia University.

3. Short but very useful advices, lab hacks and proverbs

• Labelling a compound takes 5-10 seconds. Identifying an unlabeled compound may take 30 minutes later (if you are lucky).
• A bit of an impurity can make a huge difference in color. If a product that should be colorless looks orange, brown or whatever, do not assume your reaction failed.
• If you do not have time to do something properly/right, make sure you do have time to do it again.
• There is no “having too much starting material”.
• Hofstadter’s law: Everything will take longer time than you think, even if you take into account this rule.
• A week in SciFinder will save months in the lab.
• One gram in hand is worth two in the reaction flask.
• Garbage in, garbage out.
• You get luckier the more you try.

You can find more of them, as well as loads of advice and lab hacks for working in the lab at NotVoodooX (University of Rochester)
This is a really neat website, especially for beginners. I would recommend everyone to have a look at it.

These are general tips that will be useful mainly in professional labs, but you might find something useful even if you just want to do chemistry experiments at home!

4. Plan the project before planning the experiments

Collecting data that will not be publishable is not an efficient way to organize your work. You do not want to end up with a lot of meaningless or unconnected data after weeks or months of work, this just would be a disaster.

The best idea is to always keep in mind the big picture. What do you actually want? Even if the next experiment that you have in mind looks cool, if it does not provide any meaningful insight to the whole project, it is not worth performing. But if it gives you a bit of knowledge about how your reaction works, or puts you in a closer position to your goal, go for it.

5. Lab tricks for weighing compounds

Over the years I have seen people use a lot of different tricks or lab hacks to weigh chemicals. Here I list some of them that can make your life easier every day in the lab.

• If you are weighing a compound from a small container (let’s say, a 5 mg bottle of catalyst), you can just put the container in the balance, set it to 0.0, and then pick with your spatula until the balance reads the negative value of the amount you wanted to measure. I find this very useful when I am setting up several small-scale parallel reactions with the same reagents but different conditions.
• If you need to weigh amounts bellow the accuracy limit of your balance, just weigh a larger amount, dissolve it in a known amount of your reaction solvent, and add the corresponding volume of the resulting solution.

  

• When I find myself with the need of weighing oils/liquids which I do not know the density of, the best solution is to weigh the appropriate empty syringe, then fill it with my reagent and weigh it again. Just adjust until you have picked up the amount you needed. Of course now with the values of weigh and volume you can calculate the density of your product for the next time.
• For very tiny amount of liquids, apply the first point: Weigh the oil container, set the balance to 0.0, dip the tip of a pipette, check the mass that you have taken. Then adjust picking up more amount or dropping some of it. When you have the desired mass on your pipette, rinse it in your reaction solvent and you are done.
• If you want to set up one (or more) small-scale reactions (lets say, 10 mg) but you only have some mg of your starting material (50 mg), you just need to dissolve it in your reaction solvent, for this example 5 mL, and then take 1 mL of the solution to each of your reaction flasks/vials.

6. Lab hacks for TLC

First of all, if you need help on anything related to TLC, check out our complete guide for thin layer chromatography here.

• Do you need to run a lot of TLCs in the same solvent system at the same time? Just get a big glass container that you can close, fill it with sea sand, and then your solvent system. You can now just stick all the TLC plates you want on the sand and they will run at the same time.
• Classic TLC are mandatory before doing a column or preparative TLC purification. This seems obvious, but should always be kept it in mind.

  

• A nice thing to try if you are not getting good TLCs is after spotting your reaction (and the other components/mixtures) eluting it for a few millimeters in pure MeOH. MeOH will concentrate all the spots, and you can now mark the front line and run normal TLC. This gives very nice TLCs and can solve problems like big spots, or spots overlapping.
• If you think a compound is not stable in silica, try running a 2D TLC: Use a square TLC plate and spot the sample in one corner. First run the plate in one direction, then dry it and run it turned 90 degrees (with the line of spots at the bottom). If the compounds are stable in silica, all the spots should appear on the diagonal. If any compound does not, it will probably be decomposing.

7. Dealing with air sensitive compounds NMR

If you have one, you can use a Schlenk line NMR adapter. You can insert the neck of your NMR tube in the bottom hole and do vacuum/Ar cycles. Then you can just fill your tube with your compound in dry deuterated solvent. 

If you do not have one of those adapters, you can use a small rubber septum: it has enough room to insert a needle from your Schlenk line, so you can fill the tube with an inert gas.

You can usually dry your deuterated solvents like CDCl₃ passing them through a plug of activated alumina (A pipette with a cotton plug will work. This will also remove acid traces from chloroform), or adding 4A molecular sieves. You can also try adding some CaH₂ or K₂CO₃ and the filtering them out. If you have access to a glovebox and closed-ampoules of deuterated solvents, you can totally skip the drying step.

8. Organizing your fumehood

• Do you use a certain solvent or bench reagent a lot of times? Instead of wasting every time a new syringe and needle, what I do is sticking some column test tubes in the walls of my fumehood, label them, and put in there a syringe+needle which I use to manipulate a certain solvent or reagent. For example, I have one fo

  

  r my deuterated chloroform, another one for the HPLC grade solvent that I use every day for setting up my reactions and another one for the stock solution of my internal standard to calculate NMR or GC yields.
• Fill and label washing bottles with the technical grade solvents that you use normally.
• If you use reflux condensers in a daily basis, it is probably better if you leave them all permanently connected in series to your cooling water and clamped in the back of your fumehood.

Besides, organizing your lab notebook is just as important!

9. Hacks for pulling solvent off your samples

Sometimes you have a new product, and after checking out your NMR for characterizing it, you find that a lot of solvent shows on the spectra. If you are having a hard time removing the solvent from a sample, there are several things you can try. Place your container (if its hygroscopic or air sensitive, under an inert gas) intro a dry ice or acetone (cryocooled) bath for 30 seconds. Then take it out of the bath and apply high vacuum. Repeat twice more and most solvents will have left.

Another trick that I usually apply, for example right after a column purification, is redisolving my pure product in the solvent (not the deuterated one, of course) I will be getting my NMR with (which is usually chloroform) and then removing it under reduced pressure. This usually helps a lot, since the main traces of solvent will only cause your NMR solvent peak to increase a bit (most of the other solvents will be gone), but you will get a very clean spectra.

10. Miscellaneous lab hacks and tricks

• Multiple rinses using smaller amounts of solvents are better than only one with a large amount, e., 3x1mL is better than 1x3mL.
• If you want to weigh a liquid with very low boiling point, leave it in the fridge or freezer for some minutes before proceeding to do so.
• Rinse your extraction funnel with brine before doing your actual brine wash to the organic phase. It helps removing aqueous residue which remains on the separatory funnel.
• Using a short sentence to describe the result of every reaction (like “the reaction worked well”, “very clean reaction/TLC”, “only SM on GC/TLC”). Writing it down on your notebook is very useful.
• Repeat every new reaction with a positive result. Always make sure that the procedures that you create are reproducible.
• If two pieces are stuck together by a ground glass joint, try heating them up with a burner or other heat source, then it will be easier to separate them.
• If you deal with chemicals that will stick to your gloves a lot (like iodine) you can just double glove. When the moment to manipulate it comes, use the sticky reagent then throw the outer pair of gloves and you will not have to deal with sweaty hands to put new gloves on.

That is all for today, I hope you have enjoyed it and find it useful! I want to thank, apart from the sources cited/linked above, the chemistry reddit community for providing both information and inspiration for making this post. I also wanted to thank Wikimedia for the nice pictures included.

Go check our recommendations of resources if you are looking to prepare for an organic chemistry, inorganic chemistry or, any chemistry lab in particular.

Finally, if you have any doubts or if you feel like contributing with your own tricks/pictures/examples you can do it on the comments. Or even better: contact me so I can include your tricks on a future second edition of this lab hacks post (you can contribute with your own posts if you like).

The post Lab Hacks – How to Increase your Productivity in the Lab appeared first on Chemistry Hall.