5.7: Covalent bonds - Biology

5.7: Covalent bonds - Biology

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In the case of van der Waals interactions, the atoms and molecules involved retain their hold on their electrons, they remain distinct and discrete. There are cases, however, where atoms come to "share" each other's electrons. In fact, since one electron cannot even in theory be distinguished from any other electron, they become a part of the molecule’s electron system156. A molecule is stable if the bond energies associated with bonded atoms within the molecule are thigh enough to survive the energy delivered to the molecule through either collisions with neighboring molecules or the absorption of energy (light).

When atoms form a covalent bond, their individual van der Waals surfaces merge to produce a new molecular van der Waals surface. There are a number of ways to draw molecules, but the space-filling or van der Waals surface view is the most realistic (at least for our purposes). While realistic it can also be confusing, since it obscures the underlying molecular structure, that is, how the atoms in the molecule are linked together. This can be seen in this set of representations of the simple molecule 2-methylpropane157. As molecules become larger, as is the case with many biologically important molecules, it can become impossible to appreciate their underlying organization based on a van der Waals surface representation.

Because they form a new stable entity, it is not surprising (perhaps) that the properties of a molecule are quite distinct from, although certainly influenced by, the properties of the atoms from which they are composed. To a first order approximation, a molecule’s properties are based on its shape, which is dictated by how the various atoms withjn the molecule are connected to one another. These geometries are imposed by each atom’s quantum mechanical properties and (particularly as molecules get larger, as they so often do in biological systems) the interactions between different parts of the molecule. Some atoms, common to biological systems, such as hydrogen (H), can form only a single covalent bond. Others can make two (oxygen (O) and sulfur (S)), three (nitrogen (N)), four (carbon (C)), or five (phosphorus (P)) bonds.

In addition to smaller molecules, biological systems contain a number of distinct types of extremely large molecules, composed of thousands of atoms; these are known as macromolecules. Such macromolecules are not rigid; they can often fold back on themselves leading to intramolecular interactions. There are also interactions between molecules. The strength and specificity of these interactions can vary dramatically and even small changes in molecular structure can have dramatic effects.

Molecules and molecular interactions are dynamic. Collisions with other molecules can lead to parts of a molecule rotating around a single bond158. The presence of a double bond restricts these kinds of movements; rotation around a double bond requires what amounts to breaking and then reforming one of the bonds. In addition, and if you have mastered some chemistry you already know this, it is often incorrect to consider bonds as distinct entities, isolated from one another and their surroundings. Adjacent bonds can interact forming what are known as resonance structures that behave as mixtures of single and double bonds. Again this restricts free rotation around the bond axis and acts to constrain molecular geometry. As we we will see later on with the peptide bond, which occurs between a carbon (C) and a nitrogen (N) atom in polypeptide chain, is an example of such a resonance structure. Similarly, the ring structures found in the various “bases” present in nucleic acids produces flat structures that can pack one top of another. These various geometric complexities combine to make predicting a particular molecule’s three dimensional structure increasingly difficult as its size increases.

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Molecular activity

The rate of enzyme activity measured as the number of substrate molecules transformed per minute by a single enzyme molecule.

Turnover number

The rate of enzyme activity measured as the number of substrate molecules transformed per minute by a single enzyme molecule.

Covalent bonds

Formed when atoms share electrons to achieve a stable outer shell a covalent bond is a shared pair of electrons.


The amount of a substance (solute) in a solution


A large organ in the upper abdomen which manufactures, stores and breaks down substances as required by the body

Factors affecting enzyme action

Enzymes are only present in very small amounts in cells but this is all that is needed. Because each enzyme speeds up a reaction by many orders of magnitude, the activity of an enzyme is measured as the molecular activity, also known as the turnover number. This is the number of molecules of reactants (substrate) transformed per minute by a single enzyme molecule. For example catalase is an enzyme found in the liver and in potatoes. It catalyses the breakdown of hydrogen peroxide to oxygen and water.

The turnover number is 6x10 6 min -1 .

Enzymes are such efficient catalysts that they generally speed up reactions by a factor of 10 8 – 10 26 over the uncatalysed rate of reaction. However the rates of enzyme controlled reactions are affected by a number of different factors. In most cases the effect of a factor on the rate of the reaction is due to its influence on the active site.

Substrate concentration

For a given amount of enzyme, an increase in substrate will result in an increase in the rate of reaction. The more substrate molecules there are, the faster the reaction takes place as more of the active sites are used. This continues until the concentration of substrate is so high that all the enzyme molecules are working at their maximum capacity. At this point, however much more substrate is added the reaction will not go any faster.

Graph to show effect of substrate concentration on rate of an enzyme controlled reaction with enzyme in excess


In most chemical reactions an increase in temperature causes an increase in reaction rate. As the reactants are heated, the particles move faster and are more likely to collide with sufficient energy to overcome the activation energy of the substances reacting. We use the temperature coefficient Q10 to express the effect of temperature on the rate of a reaction. For almost all reactions, Q10 is two for every 10 o C rise in temperature in the temperature range 0 o C to 40 o C. In other words, the reaction rate doubles for every 10 o C rise in temperature.

In many reactions Q10 remains around two as the temperature continues to rise. But in most enzyme controlled reactions, once the temperature rises above 40 o C the rate of reaction falls away rapidly and stops.

Graph to show effect of temperature on the rate of an enzyme controlled reaction

  • Initially the rise in temperature above the optimum temperature breaks some of the hydrogen bonds that hold the shape of the active site. This reduces the efficiency of the enzyme and the reaction rate falls.
  • If the temperature falls again the hydrogen bonds reform and the activity of the enzyme is restored.
  • If the temperature continues to rise the disulfide bonds and covalent bonds are broken. This permanently destroys the shape of the active site and so the catalytic activity of the enzyme is lost permanently. The rise in temperature permanently denatures the enzyme.

The effect of temperature on an enzyme controlled reaction

The pH of the environment has a major effect on the rate of enzyme controlled reactions. The intermolecular bonds – particularly the hydrogen bonds – that maintain the tertiary structure and the active site are very vulnerable to changes in hydrogen ion concentration. Each enzyme has an optimum pH at which it works at its optimum rate. A change in pH causes a change in the shape of the active site. It is not so easy for the reactants to fit in and bind to the active site. The activity of the enzyme is reduced and the rate of reaction slows. If the change is too great, the substrate will not be able to bind to the active site at all and the enzyme can no longer catalyse the reaction. In most cases the activity of the enzyme is restored as the pH returns to its optimum level.

Graph to show effect of pH on the rate of an enzyme controlled reaction

The effect of pH on an enzyme controlled reaction

Enzymes in extremophiles

Everything we know about the structure of enzymes tells us that they cannot work in extremes of temperature, in extremes of pH, or in any conditions such as very salty water that would affect the molecular structure of the protein and the shape of the active site.

However living organisms – and the enzymes that enable them to function – have been found in hot springs with water close to boiling point, deep within ice, in extreme salinity (such as some of the small ponds in places such as Death Valley in the USA) and in a wide range of environments with different pHs. Scientists are investigating these extremophile enzymes – not least as they may have many industrial applications (see Enzymes in industry). The proteins have evolved with very high numbers of hydrogen, disulphide and covalent bonds, giving them unusually stable structures that seem to be able to withstand the extremes where they live.

In hot springs, salty pools and ice, the enzymes of extremophiles continue to function.

5.7: Covalent bonds - Biology

When two atoms share electrons to complete their valence shells they create a covalent bond. An atom&rsquos electronegativity&mdashthe force with which shared electrons are pulled towards an atom&mdashdetermines how the electrons are shared. Molecules formed with covalent bonds can be either polar or nonpolar. Atoms with similar electronegativities form nonpolar covalent bonds the electrons are shared equally. Atoms with different electronegativities share electrons unequally, creating polar bonds.

A Covalent Bond Is Formed by Two Shared Electrons

The number of covalent bonds that an atom can form is dictated by how many valence electrons it has. Oxygen, for example, has six out of eight possible valence electrons, meaning that each oxygen atom needs two more electrons to become stable. Oxygen can form single bonds with two other atoms, as it does when it forms water with two hydrogen atoms (chemical formula H2O). Oxygen can also form a double bond with just one other atom that also needs two more electrons to complete its octet (e.g., another oxygen atom). Carbon has four valence electrons and therefore can form four covalent bonds, as it does in methane (CH4).

When a covalent bond is made, both atoms share a pair of electrons in a hybrid orbital that differs in shape from a normal orbital. The electrons participating in the bond thus orbit in a modified path around the nuclei of both atoms. Covalent bonds are strong and, once formed, cannot be broken by physical forces.

Electronegativity Determines Whether a Molecule Is Polar or Nonpolar

Electronegativity is the tendency of an atom to attract electrons in a bond. The most electronegative atom is fluorine. Starting with fluorine at the top right corner of the periodic table (omitting the noble gases in the rightmost column), the electronegativity of atoms tends to decrease with diagonal leftward movement down the periodic table, such that atoms with the lowest electronegativities are at the bottom left corner (e.g., francium, or Fr). If atoms have extremely different electronegativities, they will likely form ions instead of covalent bonds. However, for atoms that form covalent bonds with one another, their electronegativity values determine whether the bond will be polar or nonpolar.

A nonpolar bond is one in which the electrons are shared equally, and there is no charge across the molecule. A polar bond, by contrast, occurs when one atom is more electronegative than another and pulls the electrons toward it. Polar bonds have a partial negative charge on one side and a partial positive charge on the other, which is important because it causes polar molecules to behave differently than nonpolar ones.

Polar molecules are hydrophilic because their partial charges attract them to other charged molecules, which also means they are soluble in water. Nonpolar molecules&mdashthose containing long stretches of hydrocarbons, such as fats&mdashare said to be hydrophobic. Unlike polar molecules, nonpolar molecules will not dissolve in water. Cells are often surrounded by fluid and have cytoplasms that contain water. Thus, the way a molecule interacts with water and other charged molecules impact how it is transported and used by cells.

IB HL Biology 2014-15

Primary Structure
– Linear sequence of amino acids in the ploypeptide chain
– It is held together by covalent bonds such as peptide bonds
– The primary structure is determined by the gene coressponding to the protein
– Controls all subsequent levels of structure

Secondary Structure
– The way amino acids fold or turn upon themselves in regular, repeating patterns
– Formed by hydrogen bonds between amine and carboxyl groups of non-adjacent amino acids
– May form alpha helices or beta-pleated sheets

  • Alpha Helices
    – A righthand-coiled conformation in which every backbone N-H group donates a hydrogen bond to the backbone
    C=O of the amino acid four residues earlier
    – The most predictable and most regular form sequence
  • Beta-pleated sheets
    – Consists of beta strands connected lateral by at least two or three backbone hydrogen bonds, forming a
    twisted, pleated sheet.

Tertiary Structure
– The way a polypeptide folds into a complex 3-D shape
– Caused by interactions between variable R-groups, including H-Bonds, disulphide bonds, etc.
– Determines wether protein is globular or fibrous

Quaternary Structure
– Interactions between multiple ploy peptides or prosthetic groups to form biologically active protein
– Quaternary structure may be help together by a variety of bonds
– Not all proteins will have quaternary structure

5.7: Covalent bonds - Biology

a Department of Organic Chemistry, University of Geneva, Geneva, Switzerland
E-mail: [email protected]
Fax: +41 22 379 5123
Tel: +41 22 379 6523


This review summarizes the use of orthogonal dynamic covalent bonds to build functional systems. Dynamic covalent bonds are unique because of their dual nature. They can be as labile as non-covalent interactions or as permanent as covalent bonds, depending on conditions. Examples from nature, reaching from the role of disulfides in protein folding to thioester exchange in polyketide biosynthesis, indicate how dynamic covalent bonds are best used in functional systems. Several synthetic functional systems that employ a single type of dynamic covalent bonds have been reported. Considering that most functional systems make simultaneous use of several types of non-covalent interactions together, one would expect the literature to contain many examples in which different types of dynamic covalent bonds are similarly used in tandem. However, the incorporation of orthogonal dynamic covalent bonds into functional systems is a surprisingly rare and recent development. This review summarizes the available material comprehensively, covering a remarkably diverse collection of functions. However, probably more revealing than the specific functions addressed is that the questions asked are consistently quite unusual, very demanding and highly original, focusing on molecular systems that can self-sort, self-heal, adapt, exchange, replicate, transcribe, or even walk and “think” (logic gates). This focus on adventurous chemistry off the beaten track supports the promise that with orthogonal dynamic covalent bonds we can ask questions that otherwise cannot be asked. The broad range of functions and concepts covered should appeal to the supramolecular organic chemist but also to the broader community.

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Quaternary structure

In some proteins several polypeptide chains fit together to form a larger molecule. The quaternary structure refers to the way the different polypeptide chains fit together.

Tertiary structure

The final 3D structure of a protein. This structure is produced when the secondary structure of the polypeptide chain is folded.

Disulfide bridge

A covalent S-S bond that joins two cysteine amino acids together, also called an SS-bond or disulfide bond.

Proteins: Protein structures

Proteins have a primary, secondary, tertiary and sometimes a quaternary structure, and each aspect of the structure is important for the protein to carry out its functions. The bonds which hold amino acids together are peptide bonds. However the complex three dimensional shapes of proteins which enable them to carry out their functions in the cells and the body are created and held together by hydrogen bonds, ionic bonds and disulfide bonds.

The primary, secondary tertiary and quaternary structure of proteins

  • The primary structure of a protein is the order of the amino acids joined together to form the polypeptide chain.
  • The secondary structures of proteins - α-helices and β pleated sheets – are held together by hydrogen bonds between polar molecules in the backbone of the polypeptide chain. Hydrogen bonds are relatively weak but there are many of them.
  • The tertiary structure of a protein is produced when the secondary structure of the polypeptide chain is folded up - for example to form a globular protein such as an enzyme. The folds are held in place by
      – there are huge numbers of these relatively weak bonds. – strong bonds form between acid and basic (i.e. has the properties of a base, can accept a proton H+ ion) amine groups of some amino acids in the polypeptide chains.
  • Disulfide bonds - bonds formed between amino acids containing sulfur groups e.g. cysteine or methionine, when they occur close together in polypeptide structures. A covalent bond is formed between the sulfur-containing groups to form a sulfur bridge (also known as a disulfide bridge).
  • Hydrogen bonds and sulfur bridges create the complex 3-D shapes of proteins

    The structure and functions of proteins are affected by both temperature and pH. Understanding the structure of proteins enables you to understand how temperature and pH have their effect.

    Single, double and triple bonds

    The chlorine molecule, Cl2

    Lewis dot structure of a chlorine molecule.

    The chlorine atom has seven valence electrons ⇒ it needs to "borrow" one to get noble gas structure (a "full" outer shell, with eight valence electrons).

    Two chlorine atoms may share an electron pair, each sharing one electron with the other.

    The oxygen molecule, O2

    Lewis dot structure of an oxygen molecule.

    The oxygen atom has six valence electrons ⇒ it needs to "borrow" two to get noble gas structure (a "full" outer shell, with eight valence electrons).

    Two oxygen atoms may share two electron pairs, each sharing two electrons with the other.

    The nitrogen molecule, N2

    Lewis dot structure of a nitrogen molecule.

    The nitrogen atom has five valence electrons ⇒ it needs to "borrow" three to get noble gas structure (a "full" outer shell, with eight valence electrons).

    Two nitrogen atoms may share three electron pairs, each sharing three electrons with the other.


    Before the 18th century, chemists generally believed that compounds obtained from living organisms were endowed with a vital force that distinguished them from inorganic compounds. According to the concept of vitalism (vital force theory), organic matter was endowed with a "vital force". [4] During the first half of the nineteenth century, some of the first systematic studies of organic compounds were reported. Around 1816 Michel Chevreul started a study of soaps made from various fats and alkalis. He separated the acids that, in combination with the alkali, produced the soap. Since these were all individual compounds, he demonstrated that it was possible to make a chemical change in various fats (which traditionally come from organic sources), producing new compounds, without "vital force". In 1828 Friedrich Wöhler produced the organic chemical urea (carbamide), a constituent of urine, from inorganic starting materials (the salts potassium cyanate and ammonium sulfate), in what is now called the Wöhler synthesis. Although Wöhler himself was cautious about claiming he had disproved vitalism, this was the first time a substance thought to be organic was synthesized in the laboratory without biological (organic) starting materials. The event is now generally accepted as indeed disproving the doctrine of vitalism. [5]

    In 1856 William Henry Perkin, while trying to manufacture quinine accidentally produced the organic dye now known as Perkin's mauve. His discovery, made widely known through its financial success, greatly increased interest in organic chemistry. [6]

    A crucial breakthrough for organic chemistry was the concept of chemical structure, developed independently in 1858 by both Friedrich August Kekulé and Archibald Scott Couper. [7] Both researchers suggested that tetravalent carbon atoms could link to each other to form a carbon lattice, and that the detailed patterns of atomic bonding could be discerned by skillful interpretations of appropriate chemical reactions. [8]

    The era of the pharmaceutical industry began in the last decade of the 19th century when the manufacturing of acetylsalicylic acid—more commonly referred to as aspirin—in Germany was started by Bayer. [9] By 1910 Paul Ehrlich and his laboratory group began developing arsenic-based arsphenamine, (Salvarsan), as the first effective medicinal treatment of syphilis, and thereby initiated the medical practice of chemotherapy. Ehrlich popularized the concepts of "magic bullet" drugs and of systematically improving drug therapies. [10] [11] His laboratory made decisive contributions to developing antiserum for diphtheria and standardizing therapeutic serums. [12]

    Early examples of organic reactions and applications were often found because of a combination of luck and preparation for unexpected observations. The latter half of the 19th century however witnessed systematic studies of organic compounds. The development of synthetic indigo is illustrative. The production of indigo from plant sources dropped from 19,000 tons in 1897 to 1,000 tons by 1914 thanks to the synthetic methods developed by Adolf von Baeyer. In 2002, 17,000 tons of synthetic indigo were produced from petrochemicals. [14]

    In the early part of the 20th century, polymers and enzymes were shown to be large organic molecules, and petroleum was shown to be of biological origin.

    The multiple-step synthesis of complex organic compounds is called total synthesis. Total synthesis of complex natural compounds increased in complexity to glucose and terpineol. For example, cholesterol-related compounds have opened ways to synthesize complex human hormones and their modified derivatives. Since the start of the 20th century, complexity of total syntheses has been increased to include molecules of high complexity such as lysergic acid and vitamin B12. [15]

    The discovery of petroleum and the development of the petrochemical industry spurred the development of organic chemistry. Converting individual petroleum compounds into types of compounds by various chemical processes led to organic reactions enabling a broad range of industrial and commercial products including, among (many) others: plastics, synthetic rubber, organic adhesives, and various property-modifying petroleum additives and catalysts.

    The majority of chemical compounds occurring in biological organisms are carbon compounds, so the association between organic chemistry and biochemistry is so close that biochemistry might be regarded as in essence a branch of organic chemistry. Although the history of biochemistry might be taken to span some four centuries, fundamental understanding of the field only began to develop in the late 19th century and the actual term biochemistry was coined around the start of 20th century. Research in the field increased throughout the twentieth century, without any indication of slackening in the rate of increase, as may be verified by inspection of abstraction and indexing services such as BIOSIS Previews and Biological Abstracts, which began in the 1920s as a single annual volume, but has grown so drastically that by the end of the 20th century it was only available to the everyday user as an online electronic database. [16]

    Since organic compounds often exist as mixtures, a variety of techniques have also been developed to assess purity chromatography techniques are especially important for this application, and include HPLC and gas chromatography. Traditional methods of separation include distillation, crystallization, evaporation, magnetic separation and solvent extraction.

    Organic compounds were traditionally characterized by a variety of chemical tests, called "wet methods", but such tests have been largely displaced by spectroscopic or other computer-intensive methods of analysis. [17] Listed in approximate order of utility, the chief analytical methods are:

      is the most commonly used technique, often permitting the complete assignment of atom connectivity and even stereochemistry using correlation spectroscopy. The principal constituent atoms of organic chemistry – hydrogen and carbon – exist naturally with NMR-responsive isotopes, respectively 1 H and 13 C. : A destructive method used to determine the elemental composition of a molecule. See also mass spectrometry, below. indicates the molecular weight of a compound and, from the fragmentation patterns, its structure. High-resolution mass spectrometry can usually identify the exact formula of a compound and is used in place of elemental analysis. In former times, mass spectrometry was restricted to neutral molecules exhibiting some volatility, but advanced ionization techniques allow one to obtain the "mass spec" of virtually any organic compound. can be useful for determining molecular geometry when a single crystal of the material is available. Highly efficient hardware and software allows a structure to be determined within hours of obtaining a suitable crystal.

    Traditional spectroscopic methods such as infrared spectroscopy, optical rotation, and UV/VIS spectroscopy provide relatively nonspecific structural information but remain in use for specific applications. Refractive index and density can also be important for substance identification.

    The physical properties of organic compounds typically of interest include both quantitative and qualitative features. Quantitative information includes a melting point, boiling point, and index of refraction. Qualitative properties include odor, consistency, solubility, and color.

    Melting and boiling properties Edit

    Organic compounds typically melt and many boil. In contrast, while inorganic materials generally can be melted, many do not boil, and instead tend to degrade. In earlier times, the melting point (m.p.) and boiling point (b.p.) provided crucial information on the purity and identity of organic compounds. The melting and boiling points correlate with the polarity of the molecules and their molecular weight. Some organic compounds, especially symmetrical ones, sublime. A well-known example of a sublimable organic compound is para-dichlorobenzene, the odiferous constituent of modern mothballs. Organic compounds are usually not very stable at temperatures above 300 °C, although some exceptions exist.

    Solubility Edit

    Neutral organic compounds tend to be hydrophobic that is, they are less soluble in water than in organic solvents. Exceptions include organic compounds that contain ionizable groups as well as low molecular weight alcohols, amines, and carboxylic acids where hydrogen bonding occurs. Otherwise, organic compounds tend to dissolve in organic solvents. Solubility varies widely with the organic solute and with the organic solvent.

    Solid state properties Edit

    Various specialized properties of molecular crystals and organic polymers with conjugated systems are of interest depending on applications, e.g. thermo-mechanical and electro-mechanical such as piezoelectricity, electrical conductivity (see conductive polymers and organic semiconductors), and electro-optical (e.g. non-linear optics) properties. For historical reasons, such properties are mainly the subjects of the areas of polymer science and materials science.

    The names of organic compounds are either systematic, following logically from a set of rules, or nonsystematic, following various traditions. Systematic nomenclature is stipulated by specifications from IUPAC. Systematic nomenclature starts with the name for a parent structure within the molecule of interest. This parent name is then modified by prefixes, suffixes, and numbers to unambiguously convey the structure. Given that millions of organic compounds are known, rigorous use of systematic names can be cumbersome. Thus, IUPAC recommendations are more closely followed for simple compounds, but not complex molecules. To use the systematic naming, one must know the structures and names of the parent structures. Parent structures include unsubstituted hydrocarbons, heterocycles, and mono functionalized derivatives thereof.

    Nonsystematic nomenclature is simpler and unambiguous, at least to organic chemists. Nonsystematic names do not indicate the structure of the compound. They are common for complex molecules, which include most natural products. Thus, the informally named lysergic acid diethylamide is systematically named (6aR,9R)-N,N-diethyl-7-methyl-4,6,6a,7,8,9-hexahydroindolo-[4,3-fg] quinoline-9-carboxamide.

    With the increased use of computing, other naming methods have evolved that are intended to be interpreted by machines. Two popular formats are SMILES and InChI.

    Structural drawings Edit

    Organic molecules are described more commonly by drawings or structural formulas, combinations of drawings and chemical symbols. The line-angle formula is simple and unambiguous. In this system, the endpoints and intersections of each line represent one carbon, and hydrogen atoms can either be notated explicitly or assumed to be present as implied by tetravalent carbon.

    History Edit

    By 1880 an explosion in the number of chemical compounds being discovered occurred assisted by new synthetic and analytical techniques. Grignard described the situation as "chaos le plus complet" (complete chaos) due to the lack of convention it was possible to have multiple names for the same compound. This led to the creation of the Geneva rules in 1892. [18]

    Functional groups Edit

    The concept of functional groups is central in organic chemistry, both as a means to classify structures and for predicting properties. A functional group is a molecular module, and the reactivity of that functional group is assumed, within limits, to be the same in a variety of molecules. Functional groups can have a decisive influence on the chemical and physical properties of organic compounds. Molecules are classified based on their functional groups. Alcohols, for example, all have the subunit C-O-H. All alcohols tend to be somewhat hydrophilic, usually form esters, and usually can be converted to the corresponding halides. Most functional groups feature heteroatoms (atoms other than C and H). Organic compounds are classified according to functional groups, alcohols, carboxylic acids, amines, etc. [19] Functional groups make the molecule more acidic or basic due to their electronegative influence on surrounding parts of the molecule.

    As the pka (aka basicity) of the molecular addition/functional group increases, there is a corresponding dipole, when measured, increases in strength. A dipole directed towards the functional group (higher pka therefore basic nature of group) points towards it and decreases in strength with increasing distance. Dipole distance (measured in Angstroms) and steric hindrance towards the functional group have an intermolecular and intramolecular effect on the surrounding environment and pH level.

    Different functional groups have different pka values and bond strengths (single, double, triple) leading to increased electrophilicity with lower pka and increased nucleophile strength with higher pka. More basic/nucleophilic functional groups desire to attack an electrophilic functional group with a lower pka on another molecule (intermolecular) or within the same molecule (intramolecular). Any group with a net acidic pka that gets within range, such as an acyl or carbonyl group is fair game. Since the likelihood of being attacked decreases with an increase in pka, acyl chloride components with the lowest measured pka values are most likely to be attacked, followed by carboxylic acids (pka =4), thiols (13), malonates (13), alcohols (17), aldehydes (20), nitriles (25), esters (25), then amines (35). [20] Amines are very basic, and are great nucleophiles/attackers.

    Aliphatic compounds Edit

    The aliphatic hydrocarbons are subdivided into three groups of homologous series according to their state of saturation:

    • alkanes (paraffins): aliphatic hydrocarbons without any double or triple bonds, i.e. just C-C, C-H single bonds
    • alkenes (olefins): aliphatic hydrocarbons that contain one or more double bonds, i.e. di-olefins (dienes) or poly-olefins.
    • alkynes (acetylenes): aliphatic hydrocarbons which have one or more triple bonds.

    The rest of the group is classed according to the functional groups present. Such compounds can be "straight-chain", branched-chain or cyclic. The degree of branching affects characteristics, such as the octane number or cetane number in petroleum chemistry.

    Both saturated (alicyclic) compounds and unsaturated compounds exist as cyclic derivatives. The most stable rings contain five or six carbon atoms, but large rings (macrocycles) and smaller rings are common. The smallest cycloalkane family is the three-membered cyclopropane ((CH2)3). Saturated cyclic compounds contain single bonds only, whereas aromatic rings have an alternating (or conjugated) double bond. Cycloalkanes do not contain multiple bonds, whereas the cycloalkenes and the cycloalkynes do.

    Aromatic compounds Edit

    Aromatic hydrocarbons contain conjugated double bonds. This means that every carbon atom in the ring is sp2 hybridized, allowing for added stability. The most important example is benzene, the structure of which was formulated by Kekulé who first proposed the delocalization or resonance principle for explaining its structure. For "conventional" cyclic compounds, aromaticity is conferred by the presence of 4n + 2 delocalized pi electrons, where n is an integer. Particular instability (antiaromaticity) is conferred by the presence of 4n conjugated pi electrons.

    Heterocyclic compounds Edit

    The characteristics of the cyclic hydrocarbons are again altered if heteroatoms are present, which can exist as either substituents attached externally to the ring (exocyclic) or as a member of the ring itself (endocyclic). In the case of the latter, the ring is termed a heterocycle. Pyridine and furan are examples of aromatic heterocycles while piperidine and tetrahydrofuran are the corresponding alicyclic heterocycles. The heteroatom of heterocyclic molecules is generally oxygen, sulfur, or nitrogen, with the latter being particularly common in biochemical systems.

    Heterocycles are commonly found in a wide range of products including aniline dyes and medicines. Additionally, they are prevalent in a wide range of biochemical compounds such as alkaloids, vitamins, steroids, and nucleic acids (e.g. DNA, RNA).

    Rings can fuse with other rings on an edge to give polycyclic compounds. The purine nucleoside bases are notable polycyclic aromatic heterocycles. Rings can also fuse on a "corner" such that one atom (almost always carbon) has two bonds going to one ring and two to another. Such compounds are termed spiro and are important in several natural products.

    Polymers Edit

    One important property of carbon is that it readily forms chains, or networks, that are linked by carbon-carbon (carbon-to-carbon) bonds. The linking process is called polymerization, while the chains, or networks, are called polymers. The source compound is called a monomer.

    Two main groups of polymers exist synthetic polymers and biopolymers. Synthetic polymers are artificially manufactured, and are commonly referred to as industrial polymers. [21] Biopolymers occur within a respectfully natural environment, or without human intervention.

    Biomolecules Edit

    Biomolecular chemistry is a major category within organic chemistry which is frequently studied by biochemists. Many complex multi-functional group molecules are important in living organisms. Some are long-chain biopolymers, and these include peptides, DNA, RNA and the polysaccharides such as starches in animals and celluloses in plants. The other main classes are amino acids (monomer building blocks of peptides and proteins), carbohydrates (which includes the polysaccharides), the nucleic acids (which include DNA and RNA as polymers), and the lipids. Besides, animal biochemistry contains many small molecule intermediates which assist in energy production through the Krebs cycle, and produces isoprene, the most common hydrocarbon in animals. Isoprenes in animals form the important steroid structural (cholesterol) and steroid hormone compounds and in plants form terpenes, terpenoids, some alkaloids, and a class of hydrocarbons called biopolymer polyisoprenoids present in the latex of various species of plants, which is the basis for making rubber.

    Small molecules Edit

    In pharmacology, an important group of organic compounds is small molecules, also referred to as 'small organic compounds'. In this context, a small molecule is a small organic compound that is biologically active but is not a polymer. In practice, small molecules have a molar mass less than approximately 1000 g/mol.

    Fullerenes Edit

    Fullerenes and carbon nanotubes, carbon compounds with spheroidal and tubular structures, have stimulated much research into the related field of materials science. The first fullerene was discovered in 1985 by Sir Harold W. Kroto of the United Kingdom and by Richard E. Smalley and Robert F. Curl, Jr., of the United States. Using a laser to vaporize graphite rods in an atmosphere of helium gas, these chemists and their assistants obtained cagelike molecules composed of 60 carbon atoms (C60) joined together by single and double bonds to form a hollow sphere with 12 pentagonal and 20 hexagonal faces—a design that resembles a football, or soccer ball. In 1996 the trio was awarded the Nobel Prize for their pioneering efforts. The C60 molecule was named buckminsterfullerene (or, more simply, the buckyball) after the American architect R. Buckminster Fuller, whose geodesic dome is constructed on the same structural principles.

    Others Edit

    Organic compounds containing bonds of carbon to nitrogen, oxygen and the halogens are not normally grouped separately. Others are sometimes put into major groups within organic chemistry and discussed under titles such as organosulfur chemistry, organometallic chemistry, organophosphorus chemistry and organosilicon chemistry.

    Organic reactions are chemical reactions involving organic compounds. Many of these reactions are associated with functional groups. The general theory of these reactions involves careful analysis of such properties as the electron affinity of key atoms, bond strengths and steric hindrance. These factors can determine the relative stability of short-lived reactive intermediates, which usually directly determine the path of the reaction.

    The basic reaction types are: addition reactions, elimination reactions, substitution reactions, pericyclic reactions, rearrangement reactions and redox reactions. An example of a common reaction is a substitution reaction written as:

    where X is some functional group and Nu is a nucleophile.

    The number of possible organic reactions is infinite. However, certain general patterns are observed that can be used to describe many common or useful reactions. Each reaction has a stepwise reaction mechanism that explains how it happens in sequence—although the detailed description of steps is not always clear from a list of reactants alone.

    The stepwise course of any given reaction mechanism can be represented using arrow pushing techniques in which curved arrows are used to track the movement of electrons as starting materials transition through intermediates to final products.

    Synthetic organic chemistry is an applied science as it borders engineering, the "design, analysis, and/or construction of works for practical purposes". Organic synthesis of a novel compound is a problem-solving task, where a synthesis is designed for a target molecule by selecting optimal reactions from optimal starting materials. Complex compounds can have tens of reaction steps that sequentially build the desired molecule. The synthesis proceeds by utilizing the reactivity of the functional groups in the molecule. For example, a carbonyl compound can be used as a nucleophile by converting it into an enolate, or as an electrophile the combination of the two is called the aldol reaction. Designing practically useful syntheses always requires conducting the actual synthesis in the laboratory. The scientific practice of creating novel synthetic routes for complex molecules is called total synthesis.