Carbohydrates

• Monosaccharides - simple sugars,  with multiple hydroxyl groups. Based on the number of carbons (e.g., 3, 4, 5, or 6) a monosaccharide is a triose, tetrose, pentose, or hexose, etc.
• Disaccharides - two monosaccharides covalently linked
• Oligosaccharides - a few monosaccharides covalently linked.
• Polysaccharides - polymers consisting of chains of monosaccharide or disaccharide units.

Monosaccharides:

Aldoses (e.g., glucose) have an aldehyde at one end.	Ketoses (e.g., fructose) have a keto group, usually at C #2.

Nomenclature for stereoisomers: D and L designations are based on the configuration about the single asymmetric carbon in glyceraldehyde.  (See also Voet & Voet, 3rd Ed, p. 73). The lower representations are Fischer Projections.

For sugars with more than one chiral center, the D or L designation refers to the asymmetric carbon farthest from the aldehyde or keto group. Most naturally occurring sugars are D isomers. D & L sugars are mirror images of one another. They have the same name. For example, D-glucose and L-glucose are shown at right.

Other stereoisomers have unique names, e.g., glucose, mannose, galactose, etc. The number of stereoisomers is 2 n, where n is the number of asymmetric centers. The six-carbon aldoses have 4 asymmetric centers, and thus 16 stereoisomers (8 D-sugars and 8 L-sugars). See diagrams of D-aldoses in Voet & Voet on p. 357, and D-ketoses on p. 358.

An aldehyde can react with an alcohol to form a hemiacetal. Similarly a ketone can react with an alcohol to form a hemiketal.

Pentoses and hexoses can cyclize, as the aldehyde or keto group reacts with a hydroxyl on one of the distal carbons. E.g., glucose forms an intra-molecular hemiacetal by reaction of the aldehyde on C1 with the hydroxyl on C5, forming a six-member pyranose ring, named after the compound pyran. See also diagrams p. 359. The representations of the cyclic sugars at right are called Haworth projections.

Fructose can form either:  a six-member pyranose ring, by reaction of the C2 keto group with the hydroxyl on C6 a 5-member furanose ring, by reaction of the C2 keto group with the hydroxyl on C5.

Cyclization of glucose produces a new asymmetric center at C1, with the two stereoisomers called anomers, a & b. 

Haworth projections represent the cyclic sugars as having essentially planar rings, with the OH at the anomeric C1 extending either: below the ring (a) above the ring (b).

Because of the tetrahedral nature of carbon bonds, the cyclic form of pyranose sugars actually assume a "chair" or "boat" configuration, depending on the sugar (diagrams p. 360). 

The representation at right reflects the chair configuration of the glucopyranose ring more accurately than the Haworth projection.  The displays below use the Chime plug-in. (These structure files were produced using the program Insight II from Molecular Simulations. )

a-D-glucopyranose	b-D-glucopyranose
C   O   H	C   O   H

Click each image, using the right mouse button to change display selections.
Change the display to sticks, to make the image easier to see.
Drag the images, using the left mouse button, to give the 2 structures the same orientation, as in the diagram above.
In orienting the molecules, look for the ring O that bridges between C1 and C5, and the OH on C6, which sticks up out of the ring.
Identify & compare the orientation of the OH on C1 of each anomer. If you select atom O1 and change the display to ball & stick, the oxygen atom of the OH on C1 will be more prominent. 

Sugar derivatives. Various derivatives of sugars exist (diagrams p. 361-363), including: Sugar alcohol - lacks an aldehyde or ketone. An example is ribitol.

Sugar acid - the aldehyde at C1, or the hydroxyl on the terminal carbon, is oxidized to a carboxylic acid. Examples are gluconic acid and glucuronic acid.

Amino sugar - an amino group substitutes for one of the hydroxyls. An example is glucosamine. The amino group may be acetylated. At right, the acetic acid moiety is shown in red.

N-acetylneuraminate, (N-acetylneuraminic acid, also called sialic acid) is often found as a terminal residue of oligosaccharide chains of glycoproteins. (See also p. 363.) Sialic acid imparts negative charge to glycoproteins, because its carboxyl group tends to dissociate a proton at physiological pH, as shown here.

Glycosidic bonds: The anomeric hydroxyl group and a hydroxyl group of another sugar or some other compound can join together, splitting out water to form a glycosidic bond.

R-OH + HO-R'   --> R-O-R' + H₂O

For example, methanol reacts with the anomeric hydroxyl on glucose to form methyl glucoside (methyl-glucopyranose).

Disaccharides:

Maltose, a cleavage product of starch (e.g., amylose, see below), is a disaccharide with an a(1®4) glycosidic linkage between the C1 hydroxyl of one glucose and the C4 hydroxyl of a second glucose. Maltose is the a anomer, because the O at C1  points down from the ring.
Cellobiose, a product of cellulose breakdown, is the otherwise equivalent b anomer.  The configuration at the anomeric C1 is b (O points up from the ring). The b(1®4) glycosidic linkage is represented as a "zig-zag" line, but one glucose residue is actually flipped over relative to the other. (See Chime view of cellulose below.)

Other disaccharides include (diagrams p. 364):

• Sucrose, common table sugar, has a glycosidic bond linking the anomeric hydroxyls of glucose and fructose. Because the configuration at the anomeric carbon of glucose is a (O points down from the ring), the linkage is designated a(1®2). The full name is a-D-glucopyranosyl-(1®2)b-D- fructopyranose.
• Lactose, milk sugar, is composed of glucose and galactose with b(1®4) linkage from the anomeric hydroxyl of galactose. Its full name is b-D-galactopyranosyl-(1®4)-a-D-glucopyranose. 

Polysaccharides:

Plants store glucose as amylose or amylopectin, glucose polymers collectively called starch. Glucose storage in polymeric form minimizes osmotic effects.

Amylose is a glucose polymer with a(1®4) glycosidic linkages, as represented above (see also diagram p. 366). The end of the polysaccharide with an anomeric carbon (C1) that is not involved in a glycosidic bond is called the reducing end. 

View the structure of amylose at right. (This data file was produced using Chem 3D, with MM2 energy minimization.) Display as sticks, and drag the image. Note the orientation of adjacent glucose residues. Compare to the diagram above. Look for the -CH2OH  at C6, that sticks up out of each pyranose ring. Try other displays. You can make the O atoms more prominent by selecting atom O, and changing the display to ball & stick. Question: What is the overall shape of this polymer?

C   O   H

Amylopectin is a glucose polymer with mainly a(1®4) linkages, but it also has branches formed by a(1®6) linkages. The branches are generally longer than shown above. The branches produce a compact structure, and provide multiple chain ends at which enzymatic cleavage of the polymer can occur. 

Glycogen, the glucose storage polymer in animals, is similar in structure to amylopectin. But glycogen has more a(1®6) branches. See the structure of amylopectin above and diagrams on p. 367. The highly branched structure permits rapid release of glucose from glycogen stores, e.g., in muscle cells during exercise. The ability to rapidly mobilize glucose is more essential to animals than to plants.

Cellulose, a major constituent of plant cell walls, consists of long linear chains of glucose, with b(1®4) linkages. Every other glucose in cellulose is flipped over, due to the b linkages. This promotes intrachain and interchain hydrogen bonds, as well as van der Waals interactions, that cause cellulose chains to be straight and rigid, and pack with a crystalline arrangement in thick bundles called microfibrils. The regular packing of cellulose strands within a microfibril, stabilized by lateral and above/below strand interactions, is schematically represented at right.For additional diagrams see: Voet & Voet text p. 365 the Botany online website a website maintained by L. Williams at Georgia Tech.

Multisubunit Cellulose Synthase complexes in the plasma membrane spin out from the cell surface microfibrils consisting of 36 parallel, interacting cellulose chains. These microfibrils are very strong. The role of cellulose is to impart strength and rigidity to plant cell walls, which can withstand high hydrostatic pressure gradients. Osmotic swelling is prevented.

A short glucose polymer, equivalent to a single cellulose strand with b(1®4) linkages, may be viewed by Chime below right. In cellulose the strand would straighter, due to interactions between adjacent strands in the cellulose fiber bundle.

Display as sticks and drag the image. Note how each glucose residue is flipped over relative to adjacent residues, due to the b(1®4) linkages. To orient yourself, look for the ring oxygen of each residue, as well as the -CH2OH at C6, which sticks up out of each pyranose ring. (See diagram above.) You can make the O atoms prominent by selecting atom O, and changing the display to ball & stick.  (This data file was produced using Chem 3D, with MM2 energy minimization.)

C   O   H

Glycosaminoglycans (mucopolysaccharides) are linear polymers of repeating disaccharides (diagrams p. 368-369). The constituent monosaccharides tend to be modified, with acidic groups, amino groups, sulfated hydroxyl and amino groups, etc. Glycosaminoglycans tend to be negatively charged, because of the prevalence of acidic groups. Hyaluronate (hyaluronan) is a glycosaminoglycan with a repeating disaccharide consisting of two glucose derivatives, glucuronate (glucuronic acid) and N-acetylglucosamine. The glycosidic linkages are b(1®3) and b(1®4).

Proteoglycans are glycosaminoglycans that are covalently linked to serine residues of specific core proteins. The glycosaminoglycan chain is synthesized by sequential addition of sugar residues to the core protein.
Some proteoglycans of the extracellular matrix bind non-covalently to hyaluronate via protein domains called link modules. For example:

• Multiple copies of the aggrecan proteoglycan associate with hyaluronate in cartilage to form large complexes. See diagrams & micrograph p. 371.
• Versican, another proteoglycan, binds hyaluronate in the extracellular matrix of loose connective tissues.  
• See web sites on aggrecan and aggrecan plus versican.

Heparan sulfate is initially synthesized on a membrane-embedded core protein as a polymer of alternating glucuronate and N-acetylglucosamine residues. Later, in segments of the polymer, glucuronate residues may be converted to the sulfated sugar iduronic acid, while N-acetylglucosamine residues may be deacetylated and/or sulfated.

Heparin, a soluble glycosaminoglycan found in granules of mast cells, has a structure similar to that of heparan sulfates, but is relatively highly sulfated. When released into the blood, it inhibits clot formation by interacting with the protein antithrombin. Heparin has an extended helical conformation. Charge repulsion by the many negatively charged groups may contribute to this conformation. The heparin molecule depicted at right includes 10 residues, alternating IDS (iduronate-2-sulfate) and SGN (N-sulfo-glucosamine-6-sulfate). Color key:   C   O  N  S

Some cell surface heparan sulfate glycosaminoglycans remain covalently linked to core proteins associated with the plasma membrane. The core protein of a syndecan heparan sulfate proteoglycan includes a single transmembrane a-helix, as in the simplified diagram at right. The core protein of a glypican heparan sulfate proteoglycan is attached to the outer surface of the plasma membrane via covalent linkage to a modified phosphatidylinositol lipid (see brief description glycosylphosphatidylinositol linkages). Proteins involved in signaling and adhesion at the cell surface recognize and bind heparan sulfate chains. For example, binding of some growth factors (small proteins) to cell surface receptors is enhanced by their binding also to heparan sulfates. Regulated cell surface Sulf enzymes may remove sulfate groups at particular locations on heparan sulfate chains to alter affinity for signal proteins such as growth factors. Structure and roles of cell surface proteoglycans are summarized in a diagram by Kirkpatrick & Selleck (requires a subscription of J Cell Science).

Syndecan

Oligosaccharides of glycoproteins and glycolipids: Oligosaccharides that are covalently attached to proteins or to membrane lipids may be linear or branched chains. They often include modified sugars, e.g., acetylglucosamine, etc. 

O-linked oligosaccharide chains of glycoproteins vary in complexity. They link to a protein via a glycosidic bond between a sugar residue and a serine or threonine hydroxyl (diagram p. 376).  O-linked oligosaccharides have roles in recognition, interaction. (See discussion of lectins below.) N-acetylglucosamine (abbreviated GlcNAc) is a common O-linked glycosylation of protein serine or threonine residues. Many cellular proteins, including enzymes and transcription factors, are regulated by reversible attachment of GlcNAc. Often attachment of GlcNAc to a protein hydroxyl group alternates with phosphorylation, with these two modifications having opposite regulatory effects (stimulation or inhibition).

N-linked oligosaccharides of glycoproteins tend to be complex and branched. Initally N-acetylglucosamine is linked to a protein via the side-chain N of an asparagine residue in a particular 3-amino acid sequence.

Additional monosaccharides are added, and the N-linked oligosaccharide chain is modified by removal and addition of residues, to yield a characteristic branched structure, as at right. (See also p. 376). Many proteins secreted by cells have attached N-linked oligosaccharide chains. Genetic diseases have been attributed to deficiency of particular enzymes involved in synthesizing or modifying oligosaccharide chains of these glycoproteins. Such diseases, and gene knockout studies in mice, have been used to define pathways of modification of oligosaccharide chains of glycoproteins and glycolipids.

Carbohydrate chains of plasma membrane glycoproteins and glycolipids usually face the outside of the cell. They have roles in cell-cell interaction and signaling, and in forming a protective layer on the surface of some cells.

Lectins are glycoproteins that recognize and bind to specific oligosaccharides. Concanavalin A and wheat germ agglutinin are plant lectins that have been useful research tools (discussed p. 363).  The C-type lectin-like domain is a Ca++-binding carbohydrate recognition domain present in many animal lectins. Recognition and binding of carbohydrate moieties of glycoproteins, glycolipids, and proteoglycans by animal lectins is a factor in cell-cell recognition, adhesion of cells to the extracellular matrix, interaction of cells with chemokines and growth factors, recognition of disease-causing microorganisms, and initiation and control of inflammation. For example: Mannan-binding lectin (MBL) is a glycoprotein found in blood plasma. It binds cell surface carbohydrates of disease-causing microorganisms and promotes phagocytosis of these organisms as part of the immune response. Selectins are integral proteins of mammalian cell plasma membranes with roles in cell-cell recognition and binding. The C-type lectin-like domain is at the end of a multi-domain extracellular segment extending outward from the cell surface. A cleavage site just outside the transmembrane a-helix provides a mechanism for regulated release of some lectins from the cell surface. A cytosolic domain participates in regulated interaction with the actin cytoskeleton.

General Organic Chemistry notes

Organic Chemistry, branch of chemistry in which carbon compounds and their reactions are studied. A wide variety of classes of substances—such as drugs, vitamins, plastics, natural and synthetic fibers, as well as carbohydrates, proteins, and fats—consist of organic molecules. Organic chemists determine the structures of organic molecules, study their various reactions, and develop procedures for the synthesis of organic compounds. Organic chemistry has had a profound effect on life in the 20th century: natural materials have been improved and natural and artificial materials have been synthesized, improving health, increasing comfort, and adding to the convenience of many products manufactured today.

The advent of organic chemistry is often associated with the discovery in 1828 by the German chemist Friedrich Wohler that the inorganic, or mineral, substance called ammonium cyanate could be converted in the laboratory to urea, an organic substance found in the urine of many animals. Before this discovery, chemists thought that intervention by a so-called life-force was necessary for the synthesis of organic substances. Wohler’s experiment broke down the barrier between inorganic and organic substances. Modern chemists consider organic compounds to be those containing carbon and one or more other elements, most often hydrogen, oxygen, nitrogen, sulphur, or the halogens, but sometimes others as well.

Organic Formulae and Bonds

The molecular formula of a compound indicates the number of each kind of atom in a molecule of that substance. Fructose, or grape sugar (C6H12O6), consists of molecules containing 6 carbon atoms, 12 hydrogen atoms, and 6 oxygen atoms. At least 15 other compounds have this same molecular formula, so to distinguish one molecule from another a structural formula is used to show the spatial arrangement of the atoms:

An analysis that gives the percentage of carbon, hydrogen, and oxygen cannot distinguish C6H12O6 from ribose, C5H10O5, another sugar in which the ratios of these three elements are the same, namely 1:2:1. The empirical formula, which shows the simplest ratios of the elements that are present, is CH2O for both substances.

The forces that hold atoms together in a molecule are chemical bonds, of which there are three types: ionic, covalent, and metallic. The ability of carbon to form covalent bonds with other carbon atoms in long chains and rings distinguishes carbon from all other elements. Other elements hardly ever form chains of more than eight atoms. This property of carbon, and the fact that carbon nearly always forms four bonds to other atoms, accounts for the large number of known compounds, running into many millions.

Classification and Nomenclature

The consequences of the unique properties of carbon are manifest in the simplest class of organic compounds—the aliphatic hydrocarbons. Hydrocarbons consist of the elements hydrogen and carbon only. Aliphatic hydrocarbons are those in which the carbon atoms form a single straight chain, or a branching one. There are three main types: alkanes, alkenes, and alkynes.

Alkanes

The simplest alkane is methane, CH4. The next members of the family are ethane (C2H6), propane (C3H8), and butane (C4H10), so the general formula for any member of this family is CncH2n+2. For compounds containing more than four carbon atoms, Greek or Latin prefixes are used with the ending “-ane” to name the compounds: pentane, hexane, heptane, octane, and so on.

A formula such as C4H10 does not by itself specify molecular structure. Two different structural formulae, for example, can be drawn for the molecular formula C4H10. Compounds with the same molecular formula but different structural formulae are called isomers. In the case of C4H10, the common isomer names are butane and methylpropane (formerly isobutane). Urea and ammonium cyanate are also isomers; they are structural isomers of the molecular formula CH4 N2O.

The formula C8H18 has 18 isomers and C20H42 has 366,319 theoretical isomers. Thus, unsystematic, or trivial, names commonly used for new compounds when they were discovered must give way to systematic names that can be used in all languages. The International Union of Pure and Applied Chemistry (IUPAC) in 1890 agreed on such a system of nomenclature and has revised it to incorporate new discoveries.

In the IUPAC system of nomenclature, the longest chain of carbon atoms is found. This may have side chains. Two side chains (methyl groups) on the first molecule shown in figure 4 are on carbon atom 2, and another is on carbon atom 4; this can be represented by the prefix 2,2,4-. If the chain were numbered in the opposite direction, the side chains would be on carbon atoms 2, 4, and 4, and would be represented by 2,4,4-. In fact the prefix 2,2,4- is used, because it has the smaller number at the first point of difference. This prefix is attached to the name “trimethylpentane”: the “trimethyl-” signifies the three methyl groups, and “-pentane” signifies a straight hydrocarbon chain with five carbon atoms. The second molecule shown in figure 4 has a single ethyl (CH3CH2-) side chain attached to the third carbon atom of a straight five-carbon hydrocarbon chain, and is therefore called 3-ethylpentane.

Another family of hydrocarbons, the cycloalkanes or cyclanes, has a cyclic or ring structure; the smallest possible ring contains three carbon atoms. The cycloalkanes have the general formula CnH2n, and the IUPAC names are consistent with those of the alkanes (figure 5).

Alkenes and Alkynes

Isomeric with the cycloalkanes are the alkenes, also represented by the general formula CnH2n. This family of hydrocarbons is characterized by one or more double bonds between carbon atoms. Figure 6 shows two examples. Propene and cyclopropane are isomers, as are 1,3-dimethylcyclohexane and 3,4-dimethyl-2-hexene. (The location of the double bond is indicated by the 2-hexene part of the name.) Double bonds may also occur in cyclic compounds—for example, in a-pinene, a constituent of turpentine and vitamin A (figure 7).

Chemists commonly use a shorthand notation when writing the structural formulae of cyclic organic compounds. The apex of the angles in these formulae represents a carbon atom. Each carbon atom is understood to have 2, 1, or 0 hydrogen atoms bound to it, depending on whether there are 2, 3, or 4 bonds to other (usually carbon) atoms. For example, see figure 8 for the full structural formula for a-pinene.

Alkynes, or acetylenes, another major family of hydrocarbons, have the general formula CnH2n-2 and contain still fewer hydrogen atoms than alkanes or alkenes. Acetylene, HC=CH, the most common example, is termed ethyne in the IUPAC system.

Functional Groups

Other atoms, such as chlorine, oxygen, and nitrogen, may be substituted for hydrogen in an alkane, providing that the correct number of chemical bonds is allowed—chlorine forming one bond to other atoms, oxygen forming two bonds to other atoms, and nitrogen three bonds. The chlorine atom in chloroethane (ethyl chloride), the OH group in ethanol (ethyl alcohol), and the NH2 group in aminoethane (ethylamine) are called functional groups. Functional groups determine most of the chemical properties of compounds. Other functional groups are shown in the accompanying table with general formulae, prefixes or suffixes that are added to names, and an example of each class.

Optical and Geometric Isomers

When four different groups of atoms are attached to a central carbon atom, they lie at the corners of a tetrahedron (a figure with four triangular faces). Two different forms of such a molecule can exist. For example, the compound lactic acid, 2-hydroxypropanoic acid (see figure 9), exists in two forms—a phenomenon called optical isomerism. The optical isomers are related in the same way as an object and its mirror image are related: CH3 of one reflecting the position of CH3 in the other, OH reflecting OH, and so on—just as a mirror placed next to a right-hand glove reflects an image of a left-hand glove.

Optical isomers have exactly the same chemical properties and all of the same physical properties except one: the direction in which each type of isomer turns the plane of polarization of plane-polarized light. Dextro-lactic acid or (+)-lactic acid (formerly called d-lactic acid), turns the plane of polarized light to the right and laevo-lactic acid, or (-)-lactic acid (formerly called l-lactic acid), turns it to the left. Racemic lactic acid (a 1:1 mixture of (+)- and (-)-lactic acid) exhibits zero rotation because left and right rotations cancel each other.

Double bonds in carbon compounds give rise to geometric isomerism (not related to optical isomerism) if each double bond has different groups attached. A molecule of 2-heptene, for example, may be arranged in two ways in space because rotation about the double bond is restricted. When the like groups, hydrogen atoms in this case, are on opposite sides of the double-bonded carbon atoms, the isomer is called trans, and when the hydrogens are on the same side, the isomer is called cis.

Saturation

Compounds containing double or triple bonds are said to be unsaturated. Unsaturated compounds can undergo addition reactions with various reagents that cause the double or triple bonds to be replaced with single bonds. Addition reactions cause unsaturated compounds to become saturated. Although saturated compounds are generally more stable than unsaturated compounds, two double bonds in the same molecule cause less instability if they are separated by a single bond. Isoprene, the building block for natural rubber, has this so-called conjugated structure, as do retinal and vitamin A.

Complete conjugation in a six-membered carbon ring has a more profound effect. Benzene, C6H6, and the family of cyclic compounds called aromatic hydrocarbons, do not undergo addition reactions with the reagents that react with isoprene and alkenes. In fact, the properties of aromatic compounds are so different that a more appropriate symbol for benzene is the hexagon on the extreme right of figure 13 rather than the other two. The circle inside the hexagon suggests that the six electrons represented as three conjugated double bonds belong to the entire hexagon and not to individual carbons at the corners of the hexagon. Other aromatic compounds are shown in figure 14.

Cyclic molecules containing atoms of elements other than carbon are called heterocyclic compounds (figure 15). The most common so-called hetero atoms are sulphur, nitrogen, and oxygen.

Sources of Organic Compounds

Coal tar was once the only source of aromatic and some heterocyclic compounds. Petroleum was the source of alkanes that contain such substances as petrol, kerosene, and lubricating oil. Natural gas supplied mainly methane. These three categories of natural substances are still the major sources of organic compounds for most countries. When petroleum is not available, however, a chemical industry can be based on ethyne, which in turn can be synthesized from limestone and coal. During World War II, Germany was forced into just that position when it was cut off from reliable petroleum and natural-gas sources.

Sugar (sucrose) from cane or beet is the most abundant pure chemical from a plant source. Other major substances derived from plants include carbohydrates such as starch and cellulose, alkaloids, caffeine, and amino acids. Animals feed on plants and other animals to synthesize amino acids, proteins, fats, and carbohydrates.

Physical Properties of Organic Compounds

In general, covalent organic compounds are distinguished from inorganic salts by low melting and boiling points. The ionic compound sodium chloride (NaCl), for example, melts at about 800° C (1470° F), but the covalent molecule tetrachloromethane (carbon tetrachloride, CCl4) boils at 76.7° C (170° F). Between these temperatures an arbitrary line may be drawn at about 300° C (570° F) to distinguish most covalent from most ionic compounds. A large fraction of organic compounds melt or boil below 300° C, although exceptions exist. Organic compounds without polar groups generally dissolve in non-polar solvents (liquids that do not have localized electric charges) such as octane or tetrachloromethane and are often insoluble in water, a strongly polar solvent.

Hydrocarbons have low densities, often about 0.8 of that of water, but functional groups may increase the densities of organic compounds. Only a few organic compounds have densities greater than 1.2, generally those containing multiple halogen atoms.

Functional groups capable of forming hydrogen bonds generally increase viscosity (resistance to flow) in molecules. For example, the viscosities of ethanol, ethane-1,2-diol (glycol), and propane-1,2,3-triol (glycerol) increase in that order. These compounds contain one, two, and three OH groups, respectively, which form strong hydrogen bonds

hYBRIDIZATION-SP/SP2/SP3

Molecular Geometry and Bonding Theories
Hybrid Orbitals

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Hybrid Orbitals

For polyatomic molecules we would like to be able to explain:

• The number of bonds formed
• Their geometries

sp Hybrid Orbitals
Consider the Lewis structure of gaseous molecules of BeF₂:

• The VSEPR model predicts this structure will be linear
• What would valence bond theory predict about the structure?

The fluorine atom electron configuration:

• 1s²2s²2p⁵

• There is an unpaired electron in a 2p orbital
• This unpaired 2p electron can be paired with an unpaired electron in the Be atom to form a covalent bond

The Be atom electron configuration:

• 1s²2s²

• In the ground state, there are no unpaired electrons (the Be atom is incapable of forming a covalent bond with a fluorine atom
• However, the Be atom could obtain an unpaired electron by promoting an electron from the 2s orbital to the 2p orbital:

This would actually result in two unpaired electrons, one in a 2s orbital and another in a 2p orbital

• The Be atom can now form two covalent bonds with fluorine atoms
• We would not expect these bonds to be identical (one is with a 2s electron orbital, the other is with a 2p electron orbital)

However, the structure of BeF₂ is linear and the bond lengths are identical

• We can combine wavefunctions for the 2s and 2p electrons to produce a "hybrid" orbital for both electrons
• This hybrid orbital is an "sp" hybrid orbital

• The orbital diagram for this hybridization would be represented as:

Note:

• The Be 2sp orbitals are identical and oriented 180� from one another (i.e. bond lengths will be identical and the molecule linear)
• The promotion of a Be 2s electron to a 2p orbital to allow sp hybrid orbital formation requires energy.
• The elongated sp hybrid orbitals have one large lobe which can overlap (bond) with another atom more effectively
• This produces a stronger bond (higher bond energy) which offsets the energy required to promote the 2s electron

sp² and sp³ Hybrid Orbitals
Whenever orbitals are mixed (hybridized):

• The number of hybrid orbitals produced is equal to the sum of the orbitals being hybridized
• Each hybrid orbital is identical except that they are oriented in different directions

BF₃
Boron electron configuration:

• The three sp² hybrid orbitals have a trigonal planar arrangement to minimize electron repulsion

NOTE: sp² refers to a hybrid orbital being constructed from one s orbital and two p orbitals. Although it looks like an electron configuration notation, the superscript '2' DOES NOT refer to the number of electrons in an orbital.

• An s orbital can also mix with all 3 p orbitals in the same subshell

CH₄

• Thus, using valence bond theory, we would describe the bonds in methane as follows: each of the carbon sp³ hybrid orbitals can overlap with the 1s orbitals of a hydrogen atom to form a bonding pair of electrons

NOTE: sp³ refers to a hybrid orbital being constructed from one s orbital and three p orbitals. Although it looks like an electron configuration notation, the superscript '3' DOES NOT refer to the number of electrons in an orbital.

ANOTHER NOTE: the two steps often observed when constructing hybrid orbitals is to 1) promote a valence electron from the ground state configuration to a higher energy orbital, and then 2) hybridize the appropriate valence electron orbitals to achieve the desired valence electron geometry (i.e. the correct number of hybrid orbitals for the appropriate valence electron geometry)

H₂O
Oxygen

Hybridization Involving d Orbitals
Atoms in the third period and higher can utilize d orbitals to form hybrid orbitals
PF₅

Similarly hybridizing one s, three p and two d orbitals yields six identical hybrid sp³d² orbitals. These would be oriented in an octahedral geometry.

• Hybrid orbitals allows us to use valence bond theory to describe covalent bonds (sharing of electrons in overlapping orbitals of two atoms)
• When we know the molecular geometry, we can use the concept of hybridization to describe the electronic orbitals used by the central atom in bonding

Steps in predicting the hybrid orbitals used by an atom in bonding:
1. Draw the Lewis structure
2. Determine the electron pair geometry using the VSEPR model
3. Specify the hybrid orbitals needed to accommodate the electron pairs in the geometric arrangement
NH₃
1. Lewis structure

2. VSEPR indicates tetrahedral geometry with one non-bonding pair of electrons (structure itself will be trigonal pyramidal)
3. Tetrahedral arrangement indicates four equivalent electron orbitals

Valence Electron Pair Geometry	Number of Orbitals	Hybrid Orbitals
Linear	2	sp
Trigonal Planar	3	sp2
Tetrahedral	4	sp3
Trigonal Bipyramidal	5	sp3d
Octahedral	6	sp3d2