Yesterday, the good folks at Beersmith (the popular brewing software) announced an open beta for their new linux version. Sadly, they are currently only releasing the install package in the .deb form. The following is a guide to how to install BeerSmith 2 on Fedora 16.

• Download the BeerSmith-2.0.60.deb file here.
• ar p BeerSmith-2.0.60.deb data.tar.gz | tar zx
• mkdir -p /etc/xdg/menus/applications-merged/
• sudo cp usr/bin/beersmith2 /usr/bin
• sudo cp usr/lib/* /usr/lib/
• sudo cp usr/share/applications/beersmith2.desktop /usr/share/applications/beersmith2.desktop
• sudo cp -R usr/share/BeerSmith2/ /usr/share
• sudo cp usr/share/icons/hicolor/128×128/apps/beersmith.png /usr/share/icons/hicolor/128×128/apps/beersmith.png
• sudo cp usr/share/icons/hicolor/16×16/apps/beersmith.png /usr/share/icons/hicolor/16×16/apps/beersmith.png
• sudo cp usr/share/icons/hicolor/24×24/apps/beersmith.png /usr/share/icons/hicolor/24×24/apps/beersmith.png
• sudo cp usr/share/icons/hicolor/32×32/apps/beersmith.png /usr/share/icons/hicolor/32×32/apps/beersmith.png
• sudo cp usr/share/icons/hicolor/48×48/apps/beersmith.png /usr/share/icons/hicolor/48×48/apps/beersmith.png
• sudo cp usr/share/icons/hicolor/64×64/apps/beersmith.png /usr/share/icons/hicolor/64×64/apps/beersmith.png
• sudo cp -R usr/share/menu /usr/share/

The Beersmith2 binary should now show up under applications. If not, you can always run it from /usr/bin/beersmith2 or create a shortcut to that binary. I haven’t had a chance to play around with it yet, but it at least launches successfully.

Tags: beersmith linux fedora rpm deb

 

If you are like me, you are daunted by the names thrown around in organic chemistry. As it turns out though, there is a very systematic process behind it. I will attempt to explain. First off, let’s start by defining what I will call the root names. The root names are assigned to the largest carbon chain in the molecule.

Root Names

• 1 carbon = meth
• 2 carbons = eth
• 3 carbons = prop
• 4 carbons = but
• 5 carbons = pent
• 6 carbons = hex
• 7 carbons = hept
• 8 carbons = oct
• 9 carbons = non
• 10 carbons = dec
• 11 carbons = undec
• 12 carbons = dodec
• 13 carbons = tridec
• 14 carbons = tetradec
• 15 carbons = pentadec
• 16 carbons = hexadec
• …
• 20 carbons = iso

Largest Chain

What do I mean by largest chain? Take for example the structure of 4-methylnonane:

In organic chemistry, on any point of a line structure that doesn’t have a label, it is assumed to contain a carbon atom, and that there are hydrogen atoms bonded to that carbon atom. Remember, a carbon atom has 4 valence electrons (or electrons in its outer electron orbital), and a Hydrogen atom has 1 valence electron, and that carbon wants to have 8, and really wants them from hydrogen. Anyway, without getting too much into basic chemistry, if you look at 4-methylnonane above, you see that the longest chain is 9 carbons long. At each point in the chain, you can assume a carbon. Count the points, and you get your root name. In this case, consult the chart above, and you see 9 carbons = non.

How many bonds?

Next, you look at the bonds. Are there any double bonds? Double bonds are usually notated by a double line at the bond, instead of a single line. If there are, you would use the suffix
-ene, triple bonds would use the suffix -ine. In our case, 4-methylnonane does not have any double bonds, so we would use the suffix -ane. So we add -ane to the root, non+ane, nonane. Carbon chains without double bonds are called alkanes. All carbon chains that are alkanes, get the suffix -ane. Carbon chains with double bonds are called alkenes, and carbon chains with triple bonds are called alkynes.

alkyl groups

So where does the 4-methyl come from? If you look at the original structure, you’ll notice that there is a branch coming off of the 9-carbon chain. When you have a branch off the longest chain, you count the “branch” chain and use the prefix for that. In our case, the 9-carbon longest chain has a 1-carbon chain branch, so we would use meth, and then you apply the suffix -yl (methyl nonane).

Next, number the carbons on the longest chain, starting from the side of the chain that would be closest to the branch. In our case, the branch is on the 4th carbon, and the name would be 4-methyl nonane, because the methyl group is attached to the 4th carbon on the nonane chain. Makes sense, right?

Let’s take another example.

Now what happens if the chain is a ring? Take buytlcyclopentane:

If a carbon chain forms a ring you add the prefix cyclo- to it. Easy as that.

Common vs. Systematic

Just to make things more complicated, there are two ways of naming. Common naming, and Systematic naming.

Common Name

Common naming uses the additional prefixes sec-, iso-, and tert- to explain where the branch or group is attached to the ring or chain. If the group is attached on the first carbon in the straight chain, there are no prefixes added. For example, in butylcyclopentane, the butyl group attaches to the ring at the point of the first carbon in the chain. For sec-butylcyclopentane, the butyl group is attached on the second carbon atom in the chain where that carbon is bonded with 2 other carbon atoms. For iso-buytlcyclopentane, the butyl group is attached to the ring at one end of the 4 carbon chain, but it also branches off on the other end of the chain. This only tends to happen with groups below 5-6 carbons. For tert-butylcyclopentane, the butyl group would attach to the ring on a carbon that is also bonded with 3 other carbon atoms. The following will try to explain that in image form:

Systematic Naming

For me, systematic naming makes more sense and is easier to use. Systematic naming basically repeats the naming scheme used for the root, when naming the groups attached to the ring or chain. For example, take butylcyclopentane again.

butyl cyclopentane is still butyl cyclopentane

sec-butyl cyclopentane becomes (1-methyl propyl)cyclopentane. The longest chain on the group attached to the ring is 3 carbons long (propyl), and branch off that chain is 1 carbon long (methyl), and that branch is attached on the first carbon (1-methyl).

iso-butyl cyclopentane becomes (2-methyl propyl)cyclopentane. The longest chain on the group attached to the ring is 3 carbons long (propyl), and branch off that chain is 1 carbon long (methyl), and that branch is attached by the 2nd carbon (2-methyl).

tert-butyl cyclopentane becomes (1,1-dimethyl ethyl)cyclopentane. The longest chain on the group attached to the ring is 2 carbons long (ethyl), and branch off that chain is 1 carbon long (methyl), but there are two of them (dimethyl), and the branches are attached by the first carbon (1,1-dimethyl).

Difficult example

How about 5,6 – diethyl – 6-(1-methylethyl) decane?

Tags: chains, names, Organic Chemistry, rings

 

Higher Alcohols

Higher alcohols contribute to beer flavor, but are also involved in ester formation. They have strong flavors, producing an “alcoholic” or “solvent-like” aroma, and can have a warming effect on the palate. Most higher alcohols are formed during primary fermentation.

There are 45 different alcohols identified in beer. They are named higher alcohols because thier molecular weight is greater than ethanol (C2H5OH).

There are two classes of higher alcohols: aliphatic (volatile and contribute hot, solvent, and alcoholic taste and smell), and aromatic (not volatile and can give beer “drinkability”).

Aliphatic Alcohols

Aliphatic alcohols are organic compounds with with open chains of carbon atoms volatile and contribute hot, solvent, and alcoholic taste and smell.

Examples of Aliphatic alcohols

n-propanol:
(CH3CH2CH2OH)

iso-amyl alcohol:
((CH3)2CHCH2CH2OH)

active amyl alcohol:
(C5H12O)

iso-butyl alcohol:
((CH3)2CHCH2OH)

Aromatic Alcohols

Aromatic alcohols are not volatile and are organic compounds containing one or more 6-carbon rings. They contain phenols (meaning they have a carboxyl group –OH bonded with aromatic hydrocarbon group) which are benzene based molecules.

Examples of Aromatic alcohols

2-phenylethanol:
(C6H5CH2CH2OH)

All higher alcohol production occurs during primary fermentation as byproducts of amino acid synthesis. Unlike Diacetyl, higher alcohols are not reabsorbed and reused by the yeast cell

Increased higher Alcohol factors: yeast strain, fermentation temperature, pitch rate, wort gravity, wort O2, wort FAN, fermentation vessel design.

Esters

Esters are formed by combining a higher alcohol with an organic acid. A organic acid is an organic compound with acidic properties. The most common organic acids are the carboxylic acids, whose acidity is associated with their carboxyl group –COOH. Sulfonic acids, containing the group –SO2OH, are relatively stronger acids. Alcohols, with –OH, can act as acids but they are usually very weak.

Ester aromas

• ethyl acetate: solvent, nail polish
• isoamyl acetate: banana
• ethyl caproate: apple, aniseed
• ethyl caprylate: apple
• phenylethylacetate: roses

Tags: aroma, esters, higher alcohols, solvent

 

Most content that follows was taken from the various forgotten sources on the internet, most of which was probably wikipedia

Organic Compound: any member of a large class of gaseous, liquid, or solid chemical compounds whose molecules contain carbon.

Carbon has the ability to form very long chains of interconnecting C-C bonds. This property is called catenation. Carbon-carbon bonds are strong, and stable. This property allows carbon to form an almost infinite number of compounds; in fact, there are more known carbon-containing compounds than all the compounds of the other chemical elements combined except those of hydrogen (because almost all organic compounds contain hydrogen too).

In organic chemistry, there are a few basic structural shapes that you will encounter. They are open chains and rings. There are also two types of chains, a straight chain, and a branched chain. In a straight chain, one carbon atom holds no more than two other carbon atoms. As its name implies, the straight chain is a straight link of carbon, sometimes oxygen or nitrogen, atoms, in structural formula that is. Because of twisting and contouring, they chain may have several conformations. Branched chains have at least one carbon holding more than two other carbon atoms. It will, as its name implies, have branches of other chains coming off another chain. Branching is one of the reasons why there are so many isomers for each compound.

Straight Chain

Branched Chain

Rings (or cyclic compounds) are composed of rings of carbon and sometimes oxygen or nitrogen.

Benzene Ring

aldehyde: organic compound containing a carbon atom double bonded to Oxygen and that same carbon atom bonded to Hydrogen (H-C=O)

ketone: organic compound with the structure RC(=O)R’, where R and R’ can be a variety of atoms and groups of atoms

diketone: A diketone is a molecule containing two ketone groups.

Aldehydes and ketones play an important role in the chemistry of carbohydrates. The term carbohydrate literally means a “hydrate” of carbon, and was introduced to describe a family of compounds with the empirical formula CH2O. Glucose and fructose, for example, are carbohydrates with the formula C6H12O6. These sugars differ in the location of the C=O double bond on the six-carbon chain, as shown in the figure below. Glucose is an aldehyde; fructose is a ketone.

carboxylic acid: organic acids characterized by the presence of at least one carboxyl group (–COOH).

organic acid: an organic compound with acidic properties. The most common organic acids are the carboxylic acids, whose acidity is associated with their carboxyl group –COOH. Sulfonic acids, containing the group –SO2OH, are relatively stronger acids. Alcohols, with –OH, can act as acids but they are usually very weak.

hydrocarbon: organic compound consisting entirely of hydrogen and carbon.

aromatic hydrocarbon group: hydrocarbon with alternating double and single bonds between carbon atoms.

isomer: are compounds with the same molecular formula but different structural formulas.

metabolic pathways: series of chemical reactions occurring within a cell.

anabolism: set of metabolic pathways that construct molecules from smaller units.

catabolism: set of metabolic pathways that break down molecules into smaller units and release energy.

synthesis: an enzyme-catalyzed process in cells of living organisms by which substrates are converted to more complex products.

synthase: an enzyme that catalyses a synthesis process.

decarboxylation: a chemical reaction that releases carbon dioxide (CO2).

alcohol: is an organic compound in which the hydroxy functional group (-OH) is bound to a carbon atom. In particular, this carbon center should be saturated, having single bonds to three other atoms.

.

Images of Functional Groups

Tags: Organic Chemistry, Study Guide

 

Today I was reading “Brewing,” by Alfred Chaston Chapman and came upon this morsel:

Cane sugar itself is not directly fermentable but is first converted by the enzyme invertase contained in the yeast cell into invert sugar which then undergoes decomposition into alcohol and carbon dioxide. Cane sugar may therefore be directly employed as a brewing material but inasmuch as its use is thought by many brewers to conduce to yeast weakness it is more usual to employ the invert sugar made from it. On the manufacturing scale the invert sugar is prepared by heating a solution of cane sugar with a small amount of a mineral acid until the desired change is complete. The acid is then neutralized and the solution after more or less decolorization is evaporated in a vacuum pan to the consistency of a syrup. In this process the cane sugar undergoes hydrolysis and is converted into a mixture of dextrose and laevulose in nearly equal proportions which is known as invert sugar. The change may be represented by the following equation:

C12H22O11 + H20 -> C6H120 + C6H1206

Cane sugar + Water -> Dextrose + Laevulose = Invert sugar

As used by the brewer invert sugar is a product closely resembling golden syrup in appearance and in flavour but when allowed to stand for some time it sets to a soft solid mass owing to the crystallization of the dextrose the laevulose which crystallizes only with great difficulty remaining in the syrupy condition. The commercial syrups usually contain about 75 per cent of invert sugar the balance consisting of water with small quantities of cane sugar and a little mineral matter. In its composition therefore it is very similar to honey.

This got me thinking about making invert sugar from cane sugar any time I might normally add straight cane sugar. Though of course it would be easier to just buy candi sugar, but where is the fun in that? This post has a good description of the process. Essentailly the steps are:

• Boil water
• Desolve Cane Sugar
• Add acid (lactic, lemon juice)
• stir
• chill

Again, check out this post for the detailed method.

Tags: Cane Sugar, Invert Sugar, Yeast