Arthur Winter

Article / Updated 07-10-2023

Chiral molecules usually contain at least one carbon atom with four nonidentical substituents. Such a carbon atom is called a chiral center (or sometimes a stereogenic center), using organic-speak. Any molecule that contains a chiral center will be chiral, with the exception of a meso compound (see below for how to identify these). For example, the compound shown here contains a carbon atom with four nonidentical substituents; this carbon atom is a chiral center, and the molecule itself is chiral, because it's nonsuperimposable on its mirror image. A chiral center You need to be able to quickly spot chiral centers in molecules. All straight-chain alkyl group carbons (CH3 or CH2 units) will not be chiral centers because these groups have two or more identical groups (the hydrogens) attached to the carbons. Neither will carbons on double or triple bonds be chiral centers because they can't have bonds to four different groups. When looking at a molecule, look for carbons that are substituted with four different groups. See, for example, if you can spot the two chiral centers in the molecule shown here. A molecule with two chiral centers Because CH3 and CH2 groups cannot be chiral centers, this molecule has only three carbons that could be chiral centers. The two leftmost possibilities, identified in the next figure, have four nonidentical groups and are chiral centers, but the one on the far right has two identical methyl (CH3) groups and so is not a chiral center. The chiral centers in a long molecule How to identify molecules as meso compounds A meso compound contains a plane of symmetry and so is achiral, regardless of whether the molecule has a chiral center. A plane of symmetry is a plane that cuts a molecule in half, yielding two halves that are mirror reflections of each other. By definition, a molecule that's not superimposable on its mirror image is a chiral molecule. Compounds that contain chiral centers are generally chiral, whereas molecules that have planes of symmetry are achiral and have structures that are identical to their mirror images. The plane of symmetry in meso compounds For example, cis-1,2-dibromocyclopentane (shown in the first figure) is meso because a plane cuts the molecule into two halves that are reflections of each other. Trans-1,2-dibromocyclopentane, however, is chiral because no plane splits the molecule into two mirror-image halves. Now look at the mirror images of these two molecules in the second figure to prove this generality to yourself. The mirror images of achiral (meso) and chiral molecules Even though the cis compound has two chiral centers (indicated with asterisks), the molecule is achiral because the mirror image is identical to the original molecule (and is, therefore, superimposable on the original molecule). Molecules with planes of symmetry will always have superimposable mirror images and will be achiral. On the other hand, the trans stereoisomer has no plane of symmetry and is chiral. In organic chemistry, you need to be able to spot planes of symmetry in molecules so you can determine whether a molecule with chiral centers will be chiral or meso. For example, can you spot the planes of symmetry in each of the meso compounds shown in the last figure? Some meso compounds How to Identify the Diastereomers of a Molecule When more than one chiral center is present in a molecule, you have the possibility of having stereoisomers that are not mirror images of each other. Such stereoisomers that are not mirror images are called diastereomers. Typically, you can only have diastereomers when the molecule has two or more chiral centers. The maximum number of possible stereoisomers that a molecule can have is a function of 2n, where n is the number of chiral centers in the molecule. Therefore, a molecule with five chiral centers can have up to 25 or 32 possible stereoisomers! As the number of chiral centers increases, the number of possible stereoisomers for that compound increases rapidly. For example, the molecule shown here has two chiral centers. A molecule with two chiral centers Because this molecule has two chiral centers, it can have a total of 22, or 4, possible stereoisomers, of which only one will be the enantiomer of the original molecule. Enantiomers are stereoisomers that are mirror images of each other. Because both chiral centers in this molecule are of R configuration, the enantiomer of this molecule would have the S configuration for both chiral centers. All the stereoisomers of this molecule are shown in the next figure. Those molecules that are not enantiomers of each other are diastereomers of each other. The four stereoisomers of a molecule with two chiral centers

Step by Step / Updated 07-05-2023

When elements combine through chemical reactions, they form compounds. When compounds contain carbon, they’re called organic compounds. The four families of organic compounds with important biological functions are

Article / Updated 09-27-2022

Studying the elements of the periodic table is vital for understanding organic chemistry. So that you don't have to memorize each element, they're grouped together by their properties.

Cheat Sheet / Updated 02-24-2022

You won't get very far in your study of organic chemistry without the periodic table of elements and an understanding of the common functional groups (or reactive centers) that dictate how most of a compound's chemical reactions occur.

Article / Updated 07-26-2021

Alkanes are not limited to staying in a line — they can have structures that branch. When naming a branched alkane, your first step is to find and number the longest chain. After you number the parent chain, if you want to name the branched alkane, you need to determine the names of all the substituents that stick off of the parent chain, and then order the substituents alphabetically in front of the parent chain. This figure shows an example of a branching alkane. As you can see, the alkane with the formula C4H10 can have two possible chemical structures, or isomers — one alkane that’s a straight chain (butane), and one alkane that’s branched (isobutane). The isomers of C4H10 Find the longest chain in a branched alkane The first, and potentially the trickiest, step in naming a branched alkane is to find the longest chain of carbon atoms in the molecule. This task can be tricky because, as a reader of English, you’re so used to reading from left to right. Often, however, the longest chain of carbons is not the chain that follows simply from left to right, but one that snakes around the molecule in different directions. Organic professors like to make the parent chain one that curves around the molecule and doesn’t necessarily flow from left to right, so you have to keep on your toes to make sure that you’ve spotted the longest carbon chain. The wrong and right ways to count the parent chain The longest carbon chain for the molecule shown here is seven carbons long, so the parent name for this alkane is heptane. Number the longest chain in a branched alkane Number the parent chain starting with the end that reaches a substituent first. A chain can always be numbered in two ways. For the molecule in this example, the numbering could start at the top and go down, or it could start at the bottom and go up. The correct way to number the parent chain is to start with the end that reaches the first substituent sooner. A substituent is organic-speak for a fragment that comes off of the parent chain. The right and wrong ways to number the carbons of the parent chain As you can see here, if you number from the top down, the first substituent comes at carbon number three; if you number from the bottom up, the first substituent comes at carbon number four. The correct numbering in this case, then, starts at the top and goes down.

Article / Updated 07-26-2021

An easy way to find the R / S configuration of a molecule with more than one chiral center is with a Fischer projection. A Fischer projection is a convenient two-dimensional drawing that represents a three-dimensional molecule. To make a Fischer projection, you view a chiral center so that two substituents are coming out of the plane at you, and two substituents are going back into the plane, as shown here. Then the chiral center becomes a cross on the Fischer projection. Every cross on a Fischer projection is a chiral center. Creating a Fischer projection Fischer projections are convenient for comparing the stereochemistries of molecules that have many chiral centers. But these projections have their own sets of rules and conventions for how you can rotate and move them. As shown in the figure below, the two main ways to rotate a Fischer projection are as follows: You can rotate a Fischer projection 180 degrees and retain the stereochemical configuration, but you cannot rotate a Fischer projection 90 degrees. You can rotate any three substituents on a Fischer projection while holding one substituent fixed and retain the stereochemical configuration. Working with Fischer projections Here’s how to determine the configuration of a chiral center drawn in a Fischer projection: First, you prioritize each of the substituents using the Cahn–Ingold–Prelog prioritizing scheme. According to the Cahn–Ingold–Prelog prioritizing scheme, the highest priority goes to the substituent whose first atom has the highest atomic number. (For example, Br would be a higher priority than Cl, because Br has a larger atomic number.) Then, you put the fourth priority substituent on the top, and draw a curve from the first- to the second- to the third-priority substituent. If the curve goes clockwise, the configuration is R; if the curve goes counterclockwise, the configuration is S. To get the number-four priority substituent at the top of the Fischer projection, you have to use one of the two allowed moves diagramed in the second figure. (You can make a 180-degree rotation, or you can hold one substituent fixed and rotate the other three.) Two examples of the determination of the configuration from Fischer projections are shown here. Determining R and S configurations from Fischer projections

Article / Updated 07-26-2021

The first step in drawing the most stable conformation of cyclohexane is to determine — based on whether the substituents are cis or trans to one another, and based on where they're located on the ring — what the choices of axial and equatorial positions are for the substituents. A handy way of determining the substitution alternatives is to use the Haworth projection, as shown here. The Haworth projection This projection is easy to make — simply start at some position on the ring and alternate axial (a) and equatorial (e) from carbon to carbon, and from top to bottom. This projection will tell you what the two options for the two-chair conformations are. For example, if you were asked to draw the most stable conformation of cis-1,3-dimethylcyclohexane, both substituents could be on the top of the ring or both could be on the bottom of the ring, as shown here. (Recall that cis means that both substituents are on the same side of the ring.) As the figure shows, to get the cis stereochemistry, either both of the substituents could be equatorial (both e) or both could be axial (both a). The possible positions of cis substituents in positions 1 and 3 on cyclohexane. Putting large groups in the equatorial position to eliminate 1,3-diaxial strain is energetically favorable. Because large groups prefer to be equatorial, the most stable conformer for cis-1,3-dimethylcyclohexane is the diequatorial conformer, shown here. The diaxial conformer would be higher in energy. The diequatorial conformation of cis-1,3-dimethylcyclohexane If cyclohexane has two substituents and one has to be placed axial and one equatorial (as is the case in trans-1,2-disubstituted cyclohexanes), the lowest-energy conformation will be the one in which the bigger group goes in the equatorial position and the smaller group goes in the axial position.

Cheat Sheet / Updated 07-26-2021

Get a firm grasp on organic chemistry. Successfully studying organic chemistry means getting to know the elements of the periodic table and the important facts that highlight the fundamentals of organic chemistry. This Cheat Sheet shows it all.

Article / Updated 07-26-2021

Whether through alpha cleavage or loss of a water molecule, molecular fragmentation in a mass spectrometer tends to follow certain patterns. You can often predict what peaks will be observed in the mass spectrum simply by looking at a molecule's structure and seeing which pieces would be easy to break off to make stable cations. The ionizer makes the molecules into radical cations (cations with an unpaired electron), which then generally break apart into a cationic piece (which is seen by the detector) plus a neutral radical piece (not seen by the detector). Alkanes generally break apart to make the most highly substituted cation. Tertiary cations (cations substituted with three carbons) are more stable than secondary cations (cations substituted with two carbons), which in turn are more stable than primary cations (cations substituted with only one carbon). (The figure shows an example of tertiary and primary cations.) Therefore, breaks in a molecule that make tertiary cations are likely to give fragments that correspond to large peaks in the mass spectrum, because the most stable fragments produce the largest peaks. Favored and unfavored bond cleavage When a molecule contains heteroatoms (elements such as oxygen, sulfur, and nitrogen), breaking next to these atoms makes cations that are resonance stabilized. For example, breaking the C-C bond next to an alcohol group creates a resonance-stabilized carbocation. This type of break is called alpha cleavage and is commonly seen in alcohols (as shown here). Alcohol alpha cleavage This same pattern of alpha cleavage is observed with amines, as shown in the next figure. Amine alpha cleavage Alpha cleavage is also commonly seen in ethers, where the bond breaks adjacent to the oxygen (shown in the next figure). Ether alpha cleavage Breaks are often seen next to carbonyl groups (C=O groups), because this creates the resonance-stabilized cation (shown in the next figure). Carbonyl alpha cleavage In addition to alpha cleavage, alcohols readily lose a water molecule to form an alkene (a carbon-carbon double bond), as shown in the next figure. This is why the mass spectrum of an alcohol often has a peak corresponding to the loss of 18 mass units (the weight of water). Alcohol dehydration

Article / Updated 07-23-2021

Classifying and naming alcohols is fairly straightforward. For example, to classify an alcohol, you just need to know where the hydroxyl group is in the alcohol molecule. Naming an alcohol does require a few steps, but if you know how to name alkanes, then you'll have no problems. Alcohols are molecules that contain a hydroxyl (OH) group, and they're typically classified by the carbon to which the hydroxyl group is attached. If the carbon bonded to the OH is attached to one other alkyl group, the alcohol is classified as primary (1°); if the carbon is attached to two other alkyl groups, the alcohol is classified as secondary (2°); if the carbon is attached to three alkyl groups, the alcohol is classified as tertiary (3°). The three alcohol classifications are shown here. You can name alcohols just by extending the nomenclature rules used for alkanes. To name an alcohol you follow these five steps: Determine the parent name of the alcohol by looking for the longest chain that includes the alcohol. Snip the e off the suffix for the alkane and replace it with the suffix –ol, which stands for alcohol. For example, a two-carbon alcohol would not be ethane but ethanol. Number the parent chain. Start numbering from the side closer to the hydroxyl group. Identify all the substituents of the parent chain and name them. Order the substituents alphabetically in front of the parent name. Identify the location of the hydroxyl group by placing a number in front of the parent name. Now try naming the alcohol shown here. First, find the parent chain, as shown in the next figure. The parent chain is the longest chain of carbons that contains the hydroxyl group. In this case, the parent chain is seven carbons long, so this is a heptanol. Then number the parent chain, starting from the end that reaches the hydroxyl group sooner. In this case, that's from right to left (see the next figure). Find and name the substituents. The molecule shown in the next figure has two methyl group substituents — one at the number-three carbon and one at the number-five carbon. Then place the substituents (in alphabetical order) in front of the parent group. Indicate the position of the hydroxyl group by placing a number in front of the parent name. The two methyl groups combine to make dimethyl, and the name for this alcohol is, therefore 3,5-dimethyl-3-heptanol.