Groups, functional

Functional Group Type of Compound Suffix/ prefix Sample Name 

R-COOH Carboxylic acid -oic acid CHjCHj-COOH Propanoic acid 

The polar hydroxyl group (-OH) present in alcohols makes alcohols more soluble in polar solvents than other hydrocarbons and also increases the boiling temperature of these compounds (because of increased hydrogen bonding). The boiling temperatures of alcohols are much higher than the boiling temperatures of the alkanes to which they are attached. 

When naming alcohols, the ending of the hydrocarbon is removed and the suffix -ol is used instead. For example, when a hydroxyl group attaches to an ethane molecule, CH.CH,. the resulting alcohol, CH CH OH, is known as ethanol. 

Ethers are formed from condensation reactions (result in the formation of water) between two alcohols. The main function of ethers is their use as solvents. Ethers are named by placing the names of the two R groups (R and 

Functional group Name ending Compound name Example 

COOR -oate Ester CH3COOCH3, methyl ethanoate 

The functional group of an alkene, for example, is its carbon-carbon double bond. When we study the reactions of alkenes in greater detail in Chapter 8, we shall find that most of the chemical reactions of alkenes are the chemical reactions of the carbon-carbon double bond. 

Alkyl groups are the groups that we identify for purposes of naming compounds. They are groups that would be obtained by removing a hydrogen atom from an alkane  

ALKANE ALKYL GROUP ABBREVIATION BOND-LINE model 

When a benzene ring is attached to some other group of atoms in a molecule, it is called a phenyl group, and it is represented in several ways  

4 — or Ar— (if ring substituents are present) Ways of representing a phenyl group 

Functional groups, nomenclature and drawing organic compounds 

Key point. Organic compounds are classified by functional groups, which determine their chemistry. The names of organic compounds are derived from the functional group (or groups) and the main carbon chain. From the name, the structure of organic compounds can be drawn using full structural formulae, 

Carboxylic acids have at least one carboxyl group this functional group has the formula HO -CO2H (or-COOH) 

The longest chain has four carbons - it is a derivative of butane 

A functional group is made up of an atom or atoms with characteristic chemical properties. The chemistry of organic compounds is determined by the functional groups that are present. 

Many functional groups can be identified conclusively by their 1H chemical shifts 1 3. Important examples are listed in Table 2.1, where the ranges for the proton shifts are shown in decreasing sequence aldehydes (SH = 9.5 - 10.5), acetals (SH = 4.5 - 6), alkoxy (SH = 4 - 5.5) and methoxy functions (SH = 3.5 - 4), //-methyl groups SH = 3 - 3.5) and methyl residues attached to double bonds such as C=C or C=X (X = N, 0,S) or to aromatic and heteroaromatic skeletons (SH = 1.8 -2.5). 

Small shift values for CH or CH2 protons may indicate cyclopropane units. Proton shifts distinguish between alkyne CH (generally SH= 2.5 - 3.2), alkene CH (generally SH = 4.5 - 6) and aro-matic/heteroaromatic CH (SH = 6 - 9.5), and also between n-electron-rich (pyrrole, furan, thiophene, SH = 6 - 7) and rc-electron-deficient heteroaromatic compounds (pyridine, 5H-7.5 - 9.5). 

The 13C chemical shift ranges for organic compounds 4 6 in Table 2.2 show that many carbon-containing functional groups can be identified by the characteristic shift values in the l3C NMR 

Other functional groups that are easily differentiated are cyanide (5C =110-120) from isocyanide (8C = 135- 150), thiocyanate (5c = 110-120) from isothiocyanate (5c = 125 - 140), cyanate (5C = 105 - 120) from isocyanate (5c = 120 - 135) and aliphatic C atoms which are bonded to different heteroatoms or substituents (Table 2.2). Thus ether-methoxy generally appears between 5c = 55 and 62, ester-methoxy at 5C = 52 TV-methyl generally lies between 5c = 30 and 45 and S-methyl at about 5C = 25. However, methyl signals at 5C = 20 may also arise from methyl groups attached to C=X or C=C double bonds, e.g. as in acetyl, CH3-CO-.--------------------------------------------- 

Carbonyl functional groups bound to a carbon bearing fluorine give rise to significant shielding of the fluorine. 

Dickie et al derivitivized surface hydroxy groups on acrylic copolymers with ammonia then characterized them by x-ray photoelectron microscopy. 

Kim et al examined the strong infi ared band at 3450cm of tetrahydrofiiran associated hydroxy groups in dinitropropyl acrylate prepolym in order to det mine hydroxy groups. 

A group of organic compotmds witii the same functional group forms a family. The members of the family of alcohols have an —OH functional group and the general formula R—OH. Some specific examples of alcohols are methanol and isopropyl alcohol. 

As previously mentioned, alcohols are organic compounds containing the —OH funchonal group. They have the general formula R—OH. In addition to methanol and isopropyl alcohol (shown previously), other common alcohols include ethanol and 1-butanol  

In another example for functional groups, Gower and Ruparelia (1993) noted that the odoriferous steroids that play a role in communication share certain 

FIGURE 2.1 Hypoxanthine oxide, a fish alarm pheromone. 

Further examples of the importance of functional groups for behavior are the responses of simfish to steroids in beetles, their prey reactions of birds and mammals to capsaicin-related compounds and fear behavior of rats when exposed to sulfur compoimds from fox urine and feces. 

Of several related steroids in the defensive secretion of dytiscid beetles, deoxycorticosterone was most effective. It deterred simfish from feeding in 94% of the tests. Other steroids (pregnolones) that differed only by lacking a keto group at one carbon atom were either intermediate or not active at all (Gerhart etal., 1991). 

Capsaicin analogues that differ in only one functional group affect birds and mammals differently. A change from an acidic phenolic hydroxyl group in vanil-lyl acetamide to a methoxy group in veratryl acetamide reverses the effect on starlings and rats. The first was aversive to starlings, but attractive to rats, while the opposite was true for veratryl acetamide (Mason etal., 1991). 

I AIM To learn the common functional groups in organic molecules. 

Class Functional Group General Formula Example 

I AIM To learn about simple alcohols and explain how to name them. 

Alcohols are characterized by the presence of the —OH group. Some common alcohols are listed in Table 19.6. The systematic name for an alcohol is obtained by replacing the final -e of the parent hydrocarbon name 

Select the longest chain of carbon atoms containing the —OH group. 

The vast majority of organic molecules contain elements in addition to carbon and hydrogen. However, most of these substances can be viewed as 

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This type of reaction is similar to its chemical counterpart, in that a functional group is reduced or oxidized to another one, e.g. as in eqns (6)—(8)  

It is difficult to give a general formula covering all electrochemical functional group conversions, but these examples should be suf- 

Nuclear resonance spectroscopy is one method which can be applied to gain functional group information. H, C NMR with results of Norwood and Christman (1987) demonstrating that the 

Organic Type Aliphatic Carboh) cirate Aromatic Carboxyl Other 

Functional Groups with Carbon-Carbon Multiple Bonds 

Alkenes, alkynes, and arenes (aromatic compounds) all contain carbon-carbon multiple bonds. Alkenes have a double bond, alkynes have a triple bond, and cneues have alternating double and single bonds in a six-membered ring of carbon atoms. Because of their structural similarities, these compounds also have chemical similarities. 

Alkyl halide (haloallcane) Alcohol Ether Phosphate 

Inline (Sdiiff base) N II X C /C VC / / / None NH II ch3cch3 Acetone imine 

Alkanes are saturated as they contain the maximum number of hydrogen atoms per carbon (C I I2 +2). Alkenes, alkynes and arenes are un saturated. 

Aldehyde Ketone Acid halide X = Br, Cl Carboxylic acid 

Chapter 3 Introduction to Organic Molecules and Functional Groups 

Having learned some basic concepts about structure, bonding, and acid-base chanis-try in Chapters 1 and 2, we will now concentrate on organic molecules. 

After these questions are answered, we can understand some important phenomena. For example, why do we store some vitamins in the body and readily excrete others How does soap clean away dirt We will also use the properties of organic molecules to explain some basic biological phenomena, such as the structure of cell membranes and the transport of species across these membranes. 

What are the characteristic features of an organic compound Most organic molecules have C - C and C - H o bonds. These bonds are strong, nonpolar, and not readily broken. Organic molecules may have the following structural features as well  

These structural features distinguish one organic molecule from another. They determine a molecule s geometry, physical properties, and reactivity, and comprise what is called a functional group. 

Fimctional groups am reactive, non-alkane portions of molecules. The following two lists display functional groups. Memorization of List 1 is absolutely vital to success on the MCAT. List 2 is less important, but should still be memorized. 

Unsaturation may need to be determined, as well as functional groups such as hydroxy, carbonyl, carboxyl, alkyl, aryl, alkoxy, oxyalkylene, nitrile, ester, amino, nitro, amide, amido, imino, epoxy cyano and organosilicon groups. 

In our study of the simple hydrocarbons, there are only two functional groups. One is a carbon-to-carbon double bond. Hydrocarbons that contain a carbon-to-carbon double bond are called alkenes. Naming alkenes is very similar to naming alkanes. The major difference is that the carbon base has an -ene ending instead of the -ane ending. The carbon backbone of the base hydrocarbon is numbered so the position of the double bond has the lowest location number. 

The other hydrocarbon functional group is a carbon-to-carbon triple bond. Hydrocarbons that contain a triple bond are called alkynes. Alkynes use the -yne ending on the base hydrocarbon. The presence of a double or triple bond make these hydrocarbons unsaturated. 

The introduction of other atoms (N, O, Cl, etc.) to organic compounds gives rise to many other functional groups. The major functional groups are shown in Table 18.2. 

As we mentioned in the introduction to this chapter, carbon has the ability to bond to itself in long and complex chains. These large molecules, called macromolecules, may have 

FUNCTIONAL GROUP COMPOUND TYPE SUFFIX OR PREFIX OF NAME EXAMPLE SYSTEMATIC NAME (COMMON NAME) 

Click Coached Problems for a self-study module on identifying functional groups. 

About 3 X 109 kg of methanol are produced annually in the United States from synthesis gas, a mixture of carbon monoxide and hydrogen  

Physical Properties of Simple Alkanes, Alcohols, and Ethers 

Name Structure Molar Mass Point Solubility 

Making wine. Wine (farritfit) is produced from the glucose in grape juice (left) by fermentation. The reaction is 

According to Chemical Abslracts, the publication that abstracts and indexes the ciiemical literature, there are more than 30 million known organic compounds. Each of these compounds has its own physical properties, such as melting ] )oint and boiling point, and each has its own chemical reactivity. 

Chemists have learned through many years of experience that organic compounds can be classified into families according to their structural features and that the members of a given family often have similar chejnical behavior. Instead of 30 million compounds with random reactivity, tliere are a few dozen families of organic compounds whose chemistry is reasonably redictable. We ll study the chemistry of specific families throughout much of this book, beginning in this chapter with a look at the simplest family, the alkanes. 

Atoms of these elements occur in organic substances as parts of functional groups. A functional group in an organic molecule is an atom or group of atoms that always reacts in a certain way. The addition of a functional group 

Many organic compounds contain atoms of eiements in addition to carbon and hydrogen. 

For exampie, caffeine, a compound found in many beverages, contains both oxygen and nitrogen atoms. Refer to Table C-1 in Appendix C for a key to atom coior conventions. 

Compound type General formula Functional group 

See page 963 in Appendix E for Modeling Basic Organic Compounds 

Not all organic compounds that contain —OH groups are alcohols. Carbo ylic acids contain a —COOH functional group, for example. 

Carboxylic acid anhydride 0 0 II II O C / / -ok aiilmiride 0 0 II II CH3COCCH3 Ethanoic aniiydride 

If more than one type of functional group is present, the one highest in the list is treated as the principal functional group (Table 3.5). Some groups can never be functional groups, only substituents, e.g., chloro-, nitro- (distinct from the very early literature where nitro, for example, was treated as a functional group). 

Organic Chemist s Desk Reference, Second Edition 

Fully substitutive names for certain types of compounds, especially heterocyclic, also occur. Examples are 2-aminopyridine for 2-pyridinamine, 2-formylpyridine for 2-pyridinecarboxaldehyde, and 2-cyanopyridine for 2-pyridinecarbonitrile. Such forms are technically incorrect, but frequently occur. Others, such as 2-carboxypyridine for 2-pyridinecarboxylic acid, are sometimes encountered but should not be used. 

It is convenient in equations such as this to represent generic alcohols and alkyl hahdes as ROH and RX, respectively, where R stands for an alkyl group. In addition to convenience, this notation lets us focus more clearly on the functional group transformation the OH functional group of an alcohol is replaced by a halogen, such as chlorine (X = Cl) or bromine (X = Br). 

While developing the connections between structure, reaction, and mechanism, we will also extend the fundamentals of lUPAC nomenclature to functional group families, beginning with alcohols and alkyl halides. 

Sample Solution (a) According to Table 4.1, sulfides have the general formula RSR and the Rs may be the same or different. The only possible connectivity for a sulfide with three carbons is C—S—C—C. Therefore, the sulfide is CH3SCH2CH3. 

We have already touched on some of these functional-group families in our discussion of acids and bases. We have seen that alcohols resemble water in and that carboxy- 

Carbonyl group chemistry is discussed in a block of four chapters (Chapters 17-20). 

The requirement for diverse compound libraries by means of solid-phase synthesis led to the development of hnkers for most functional groups found in organic synthesis. The number of hnkers developed for a specific group also reflects the distribution of pharmacophoric groups present in natural products and other bioactive compounds. Tab. 3.16 gives an overview of examples of hnkers for different functional groups. 

Oxidation and reduction reactions are very important processes in organic synthesis and they have been used for various transformations. 

It is particularly important that when we look at the strnctnre of a complex molecule we should visualize it in terms of the functional groups it contains. The properties and reactivity of the molecule can 

Carboxylic acid Carboxylic acid anhydride (anhydride) 0 // —c OH 0 0 II II c c —C02H -oic acid -oic anhydride carboxy- 

Carboxylic acid ester (ester) 0 // —c 0 — —C02R alkyl -oate alkoxylcarbonyl- (or carbalkoxy-) 

Atoms of other elements, typically oxygen, nitrogen and sulphur, are incorporated into the basic hydrocarbon structures, usually as peripheral components known as functional groups (Table 2.1). Each functional group confers specific properties on the compound, and can be a major factor in determining the chemical behaviour of the compound. Functional groups include the hydroxyl (-OH), carboxyl (-COOH), amino (-NH2) and nitro groups (-N02). The -OH and 

Symbol Group name Resulting compound name 

R— OH Hydroxyl Alcohol (R = aliphatic group) Phenol (R = aromatic group) 

Ethers make bonds in biopolymers such as cellulose (see Box 4.11). 

The word acid indicates that these substances act as a weak acid (see Box 3.3) in water, releasing H+ by dissociation from the carboxyl group (see Box 4.5). Some molecules contain more than one functional group, for example the amino acids contain both -COOH and -NH2  

The vast majority of organic molecules contain elements in addition to carbon and hydrogen. Most of these substances are fundamentally hydrocarbons that have additional atoms or groups of atoms called functional groups. The common functional groups are listed in Table 20.6 one example of a compound that contains that functional group is given for each. 

A hydrocarbon derivative in which the hydroxyl group (-OH) is the functional group 

OUR FIRST THREE CHAPTERS established some fundamental principles concerning the structure of organic molecules and introduced the connection between structure and reactivity with a review of acid-base reactions. In this chapter we explore structure and reactivity in more detail by developing two concepts functional groups and reaction mechanisms. A functional group is the atom or group in a molecule most responsible for the reaction the compound undergoes under a prescribed set of conditions. How the structure of the reactant is transformed to that of the product is what we mean by the reaction mechanism. 

Organic compounds are grouped into families according to the functional groups they contain. Two of the most important families are alcohols and alkyl halides. Alcohols and alkyl halides are especially useful because they are versatile starting materials for preparing numerous other families. Indeed, alcohols or alkyl halides—often both— will appear in virtually all of the remaining chapters of this text. 

The major portion of the present chapter concerns the conversion of alcohols to alkyl halides by reaction with hydrogen halides  

Problem 1.13 Methane, CH ethane. C,H and propane. C,are the first three members of the alkane homologous series. By what structural unit does each member differ from its predecessor -4 

These members differ by a C and two H s the unit is —CH,— (a methylene group). 

The atom with the higher valence is usually the one to which most of the other atoms are bonded. 

Structure Elucidation By NMR In Organic Chemistry A Practical Guide. 

Eberhard Breitmaier Copyright e 2002 John Wiley Sons, Ltd. ISBNs 0-470-85006-X (HB) 0-470-85007-8 (PB) 

Organic Carboxylic Acids — (RCOOH) are usually weak acids but can be very corrosive to skin. However, The substitution of Cl atoms on die carbon next to the carboxylic carbon, produces a stronger acid. Thus, trichloracetic acid is almost a strong acid whereas acetic acid is a weak one. 

Organic Sulfonic Acids — (RS02H) are generally stronger acids than organic carboxylic acids. 

Organic Bases — (such as amines, RNH2) are weak bases but can be corrosive to skin or other tissue. 

Alcohols — (ROH) are not very reactive. The lower molecular weight alcohols (methanol, ethanol, propanol) are completely miscible with water, but the heavier alcohols tend to be less soluble. Most common alcohols are flammable. Aromatic alcohols like phenol are not as flammable (flashpoint = 79°C) and are fairly water soluble ( 9 g/L). 

Alkenes — Also known as olefins, and denoted as CuH2u the compounds are unsaturated hydrocarbons widr a single carbon-to-carbon double bond per molecule. The alkenes are very similar to the alkanes in boiling point, specific gravity, and other physical characteristics. Like alkanes, alkenes are at most only weakly polar. 

Organic Chemistry An Intermediate Text, Second Edition, by Robert V. Hoffman ISBN 0-471-45024-3 Copyright 2004 John Wiley Sons, Inc. 

Since most organic reactions involve die conversion of one functional group to another, it follows that most organic reactions quite simply involve bond 

Having presented the concept of arrow pushing in context of the steps that initiate chemical reactions, some factors impacting the flow of electrons leading from starting materials to products can now be explored. 

As a mle, electrons will flow from atomic centers high in electron density to atomic centers low in electron density. This dependence on polarity is similar to the way that 

While functional groups can be either electron donating or electron withdrawing, these properties rely upon the specific heteroatoms the functional group is composed of as well as the configuration of these heteroatoms relative to one another. With respect to 

R-COOH Carboxylic -oic CH3CH2-COOH Propanoic acid 

Aldehydes contain a carbonyl group (C=0) to which at least one hydrogen atom is attached. The suffix -al is placed on the end of the name of aldehydes. For example, the molecule CH3CH2COH is known as propanal. Aldehydes must have the carbonyl on the last carbon on the chain (in order to have the hydrogen atom attached to the carbon). As a result, there is no need for the use of numbers to distinguish the position of the carbonyl group. 

Why do heteroatoms and n bonds confer reactivity on a particular molecule  

Don t think, though, that the C - C and C - H o bonds are unimportant. They form the carbon backbone or skeleton to which the functional groups are bonded. A functional group usually behaves the same whether it is bonded to a carbon skeleton having as few as two or as many as twenty carbons. For this reason, we often abbreviate the carbon and hydrogen portion of the molecule by a capital letter R, and draw the R bonded to a particular functional group. 

Ethane, for example, has only C-C and C - H a bonds, so it has no functional group. Ethane has no polar bonds, no lone pairs, and no n bonds, so it has no reactive sites. Because of this, ethane and molecules like it are very unreactive. 

The strong acid cation exchange resins are made by the sulfonation of the matrix copolymer. Strong acid cation resins are characterized by their ability to exchange cations or split neutral salts. They will function throughout the entire pH range. 

The synthesis of weak acid cation resins has been described above. The ability of this type of resin to split neutral salts is very limited. The resin has the greatest affinity for alkaline earth metal ions in the presence of alkalinity. Only limited capacities for the alkali metals are obtained when alkalinity other than hydroxide is present. Effective use is limited to solutions above pH 4.0. 

The anion exchange resins require the synthesis of an active intermediate. This is usually performed in the process called c/j/orc wet/jy/ofto . The subsequent intermediate is reactive with a wide variety of amines which form different functional groups. 

The Type I resin is a quatemized amine resin resulting from the reaction of trimethylamine with the chloromethylated copolymer. This functionalized resin has the most strongly basic functional group available and has the greatest affinity for weak acids. However, the efficiency of regenerating the resin to the hydroxide form is somewhat lower than Type II resins, particularly when the resin is exhausted with monovalent anions. 

The Type II resin results when dimethylethanolamine is reacted with the chloromethylated copolymer. This quaternary amine has lower basicity than that of the Type I resin, yet it is high enough to remove the anions of weak acids in most applications. While the caustic regeneration efficiency is significantly greater with Type II resins, their thermal and chemical stability is not as good as Type I resins. 

The biological properties of a molecule are determined by the molecule itself - the atoms in it and the way they are bonded to one another, its flexibility and shape. 

Carbon can share its electrons with any number of other elements or functional groups. Each of these must be able to share 2 electrons. For instance, carbon readily bonds with hydrogen to form hydrocarbons  

or CH4, is methane, the simplest hydrocarbon. Hydrocarbons may be either satu-H 

Hydrogen is often the additional element added to the unsaturated compound to produce the saturated compound. 

Source Campbell, N.A. et al.. Biology, 5th edn., Addison Wesley Longman, Menlo Park, CA, 1999. With permission. 

The preparation of cyclopropyl ketones can be achieved in good yields, and with a minimum of ring-cleaved by-products, from the reaction between an acid chloride and cyclopropyltrimethylsilane in the presence of aluminium trichloride. The same authors have generated cyclopropanesulphonic acid for the first time. Cyclopropyl ketones can also be obtained by treatment of the corresponding hydrocarbon with ozone adsorbed on silica. This dry ozonolysis method is widely applicable and yields are generally good. 

Reduction of the cyano function of (434) to aldehyde proceeds in very high yield on employing di-isobutylaluminium hydride. Acid-catalysed cleavage of (435) (Bn = benzyl) leads only to the trans-diaminocyclopropane (436) and not to the 

The Schmidt reaction of cyclopropyl alkyl ketones is remarkably dependent on the strength of the acid used. Whereas the use of 83 % HjSO gives N-cyclopropylamides predominantly (74— 92 %), trichloroacetic acid yields unrearranged cyclopropane-carboxamides, Cyclopropyl ethers have been used for the production of alkoxy-containing polymers.  

Grignon-Dubois, J. Dunogu6s, and R. Galas, Synthesis, 1976,737 Tetrahedron Letters, 1976,1197. 

Proksch and A. de Meijere, Angew. Chem. Internat. Edn., 1976, 15, 761 Tetrahedron Letters, 1976, 

SR 1 at least 1 fragment funcn-C4H9-0 SR 0 no fragments funcn-C4H9-0 

12 The condensed rings are represented as MMGs using an arbitrary atom type and alternatives for the bonds. 

Schreiner, W. Ahrens, and A. Berndt, Angew. Chem. Internai. Edn., 1975,14, 550. 

The synthesis of 5-cyclopropyl-6-azauracil has been effected in three steps from acetylcyclopropane.  

A complex reaction occurs between 1,1-dimethylcyclopropane and acetic anhydride in the presence of chloroplatinic acid.  

Enamines can be obtained from cyclopropyl, cyclopentyl, methyl, and ethyl ketones [the latter affording the (jE)-isomer stereoselectively] but the reaction of amines with dicyclopropyl and cyclopropyl phenyl or a-thienyl ketones results in homoallylic rearrangement to 1-substituted 1,4-diaminobut-l-enes.  

The kinetics and stereochemistry of deacetylation of 1,1-diacety 1-2-aryIcyclo-propanes have been studied. Base-catalysed cleavage of the three-membered ring (see p. 52) apparently does not occur, and the cis-disubstituted cyclopropane predominates at low temperature (0 

Alkanes are relatively unreactive and are rarely involved in chemical reactions, but they nevertheless provide a useful vehicle for introducing some important general ideas. In this chapter, we ll use alkanes to introduce the basic approach to naming organic compounds and to take an initial look at some of the three-dimensional aspects of molecules, a topic of particular importance in understanding biological organic chemistry. 

The structural featmes that make it possible to classify compounds into families are called functional groups. A functional group is a group of atoms within a molecule that has a characteristic chemical hehavior. Chemically, a given 

Online homework forth is chapter can be assigned in Organic OWL. 

For example, compounds that contain only carbon and hydrogen are called hydrocarbons. The carbon atoms can be arranged in straight chains, branched chains, or rings. To understand these arrangements, consider a carbon molecule that has six carbon atoms. 

There are a number of different structures that are possible. If we did not show each molecule s structure, just writing or would not tell us which compound we were discussing. Nor would we readily see that some compounds have all single bonds, some have multiple bonds, some are branched, and some are rings. 

We will continue by looking at examples of compounds with each kind of functional group. We will see how to name them, and get a feeling for some of their properties. 

The prefixes for one to four carbon atoms in a chain are different than the prefixes we used in Chapter 6 for inorganic compounds. For five to ten carbon atoms, however, the prefixes are the same. The prefixes used for organic compounds are the following  

Examples of substances that use these prefixes include methane (CEl ) and methanol (CEljOH), each with only one carbon atom propane (CjEl ) and propylene (CjH ), each with three carbon atoms cyclohexane (CgHj ) and 2,4-hexadiene (CHj - CH = CH - CH CEl - CHj), each with six carbon atoms and octane (CgHj ), with eight carbon atoms. 

A large palette of often very selective and efficient reactions is now 

Mortreux and F. Petit (Eds.), Industrial Applications of Homogeneous Catalysis, 93—139. 1988 D. Reidel Publishing Company. All Rights Reserved. 

The stmctural features that make it possible to classify compoimds into families are called functional groups. A functional group is a group of atoms within a molecule that has a characteristic chemical behavior. Chemically, a given functional group behaves in nearly the same way in every molecule it s a part of. For example, compare ethylene, a plant hormone that causes fmit to ripen, with menthene, a much more complicated molecule found in peppermint oil. Both substances contain a carbon-carbon double-bond functional group, and both therefore react with Br2 in the same way to give a product in which a Br atom 

II — C—OH Carboxylic acids CH3—C—OH Ethanoic acid (acetic acid) 

Methanol is also formed as a byproduct when charcoal is made by heating wood in the absence of air. For this reason, it is sometimes called wood alcohol. Methanol is used in jet fuels and as a solvent, gasohne additive, and starting material for several industrial syntheses. It is a deadly poison ingestion of as little as 25 mL can be fatal. The antidote in this case is a solution of sodium hydrogen carbonate, NaHC03. 

Industrial ethanol is made by the reaction of ethylene with water, using sulfuric acid as a catalyst. 

Halocarbons are named by the use of the prefixes chloro-, bromo-, and iodo- attached to the name of the alkane structure. If there is more than one kind of halogen present, the atoms are listed alphabetically. Numbers are used to identify the positions of the halogens. The chain is numbered in such a way that the lowest possible position number is given to the substituent that comes first alphabetically. In the case of aryl halides, the additional rule is that the numbering gives the substituents the lowest numbers possible. 

The alkyl chain has three carbon atoms and is therefore that of propane. The halogens present are bromine and fluorine. The prefixes to be used, in alphabetical order, are bromo- ondfluoro-. The chain is numbered so that the bromine atoms, which are first alphabetically, are on the lowest-numbered carbon atoms possible. The right-hand carbon must be carbon 1. Because two of the bromine atoms are on carbon 1 and one is on carbon 2, the 1 position is indicated twice and the 2 position once. Because there are three 

Solving Problems A Chemistry Handbook Chemistry Matter and Change 233 

Write a balanced chenfical equation for the substitution reaction in which one of the hydrogens on an end carbon of butane is replaced by a chlorine atom through reaction with elemental chlorine. Name the resulting compound. 

Butane is a four-carbon alkane and thus has the formula C4HJQ, which can be represented as CH3CH2CH2CH3. 

---

Analysis of organic functional groups Infra-Red Absorption... 

Of the general formula, R - S — H, where R represents an aliphatic or cyclic radical, the thiols —also known as mercaptans— are acidic in behavior owing to their S—H functional group they are corrosive and malodorous. Their concentration in crude oils is very low if not zero, but they are created from other sulfur compounds during refining operations and show up in the light cuts, as illustrated in Table 8.6. 

Two main viscosity additive families are used hydrocarbon polymers and polymers containing ester functional groups. 

Quack M and Stohner J 1993 Femtosecond quantum dynamics of functional groups under coherent infrared multiphoton excitation as derived from the analysis of high-resolution spectra J. Rhys. Chem. 97 12 574-90... 

This tliird part can be substituted by a functional group, a small fragment or even a polymer, where alkanetliiols are only used to attach tire whole compound to tire surface. This potential makes compounds modified witli SA molecules attractive in a whole variety of areas and teclmologies. 

The strong bond fonned between tire tliiol endgroups and gold and silver surfaces allows tire possibility of fonning molecules tliat have a wide variety of different functional groups at tire opposite end and tluis of coating a noble metal surface witli a variety of differently functionalized molecules and mixtures. 

If a catalyst is to work well in solution, it (and tire reactants) must be sufficiently soluble and stable. Most polar catalysts (e.g., acids and bases) are used in water and most organometallic catalysts (compounds of metals witli organic ligands bonded to tliem) are used in organic solvents. Some enzymes function in aqueous biological solutions, witli tlieir solubilities detennined by the polar functional groups (R groups) on tlieir outer surfaces. 

The Wiswesser Line Notation (WLN) was introduced in 1946, in order to organize and to systematically describe the cornucopia of compounds in a more concise manner. A line notation represents a chemical structure by an alphanumeric sequence, which significantly simplifies the processing by the computer [9-11], (n many cases the WLN uses the standard symbols for the chemical elements. Additionally, functional groups, ring systems, positions of ring substituents, and posi-... 

The great advantage of WLN codes is their compactness. Both compactness and unambiguity are achieved only by a complex set of rules, which make the notation difficult to code and error-prone. Since much information had been stored in the WLN code (functional groups, fragments, etc.), much effort was spent in the devel-... 

Constitutional isomers are molecules with different connectivities between the atoms. Either the structures have different functional groups (these are called structural isomers), or the same functional group is placed in different positions (positional isomers). 

Consideration of the reaction center or reaction site is of central importance in reaction searching. It does not suffice to specify the functional groups in the starting materials and in the products of a reaction when one is interested in a certain transformation. On top of that, one also has to specify that these functional groups shotfid participate directly in the reaction - that they should be part of the reaction center. 

Next, an attempt was made to evaluate the quantitative importance of the various reaction schemes [19]. To this effect, a printed compilation of 1900 reactions dealing with the introduction of one carbon atom bearing a functional group [20] was analyzed and each reaction assigned manually to a corresponding reaction scheme. The results are Hsted in Table 3-3. 

Gelemter and Rose [25] used machine learning techniques Chapter IX, Section 1.1 of the Handbook) to analyze the reaction center. Based on the functionalities attached to the reaction center, the method of conceptual clustering derived the features a reaction needed to possess for it to be assigned to a certain reaction type. A drawback of this approach was that it only used topological features, the functional groups at the reaction center, and its immediate environment, and did not consider the physicochemical effects which are so important for determining a reaction mechanism and thus a reaction type. 

A wider variety of reaction types involving reactions at bonds to oxygen atom bearing functional groups was investigated by the same kind of methodology [30]. Reaction classification is an essential step in knowledge extraction from reaction databases. This topic is discussed in Section 10.3.1 of this book. 

Once we have the measures, we have to apply them to chemical objects. Objects of interest to a chemist include molecules, reactions, mbrtures, spectra, patents, journal articles, atoms, functional groups, and complex chemical systems. Most frequently, the objects studied for similarity/dissimilarity are molecular structures. 

D similarity search methods are quite well developed. Thus, methods which attempt to find overlapping parts (atoms and functional groups) of the molecular moieties studied were reported first [31]. As discussed above for the case of 2D searching, these methods are of combinatorial complexity. To reduce this complexity some field-based methods have been introduced. In this case, the overlap of the fields of two structures is considered as a similarity measure. 

Inadequate availability of experimental data can considerably inhibit the development of improved energy functions for more accurate simulations of energetic, structural, and spectroscopic properties. This has led to the development of class II force fields such as CFF and the Merck Molecular Force Field (MMFF), which are both based primarily on quantum mechanical calculations of the energy surface. The purpose of MMFF, which has been developed by Thomas Halgren at Merck and Co., is to be able to handle all functional groups of interest in pharmaceutical design. 

Structural keys describe the chemical composition and structural motifs of molecules represented as a Boolean array. If a certain structural feature is present in a molecule or a substructure, a particular bit is set to 1 (true), otherwise to 0 (false). A bit in this array may encode a particular functional group (such as a carboxylic acid or an amidelinkage), a structural element (e.g., a substituted cyclohexane), or at least n occurrences of a particular element (e.g., a carbon atom). Alternatively, the structural key can be defined as an array of integers where the elements of this array contain the frequency of a specific feature in the molecule. 

Descriptors have to be found representing the structural features which are related to the target property. This is the most important step in QSPR, and the development of powerful descriptors is of central interest in this field. Descriptors can range from simple atom- or functional group counts to quantum chemical descriptors. They can be derived on the basis of the connectivity (topological or... 

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