Med101 Introduction to Organic Chemistry PDF

In this Chapter; You will learn What is Organic Chemistry? Life and the Chemistry of Carbon Compounds Atomic Structure Isotopes Valence Electrons  What is Organic Chemistry? Organic chemistry plays a role in all aspects of our li...

In this Chapter; You will learn What is Organic Chemistry? Life and the Chemistry of Carbon Compounds Atomic Structure Isotopes Valence Electrons  What is Organic Chemistry? Organic chemistry plays a role in all aspects of our lives, ✔ from the clothing we wear, ✔ to the pixels of our television and computer screens, ✔ to preservatives in food, ✔ to the inks that color the pages of this book. Altınbas University Lecturer: Asst. Prof. Behiye ÖZTÜRK ŞEN [email protected] MED101 MOLECULLAR AND CELLULAR MEDICAL SCIENCES I  What is Organic Chemistry? Indeed, organic chemistry provides ❖ the power to synthesize new drugs, ❖ to engineer molecules that can make computer processors run more quickly, ❖ to understand why grilled meat can cause cancer and how its effects can be combated, and to design ways ❖ to knock the calories out of sugar while still making food taste deliciously sweet. It can explain biochemical processes like aging, neural functioning, and cardiac arrest, and show how we can prolong and improve life. Altınbas University Lecturer: Asst. Prof. Behiye ÖZTÜRK ŞEN [email protected] MED101 MOLECULLAR AND CELLULAR MEDICAL SCIENCES I  1.Life and the Chemistry of Carbon Compounds Organic chemistry is the chemistry of compounds that contain the element carbon. If a compound does not contain the element carbon, it is said to be inorganic Why C is important? There are several reasons, the primary one being this: carbon compounds are central to the structure of living organisms and therefore to the existence of life on Earth. We exist because of carbon compounds Altınbas University Lecturer: Asst. Prof. Behiye ÖZTÜRK ŞEN [email protected] MED101 MOLECULLAR AND CELLULAR MEDICAL SCIENCES I  What is it about carbon that makes it the element that nature has chosen for living organisms? There are two important reasons: 1. CARBON atoms can form strong bonds to other carbon atoms to form rings and chains of carbon atoms, And 2. CARBON atoms can also form strong bonds to elements such as hydrogen, nitrogen, oxygen, and sulfur. Because of these bond-forming properties, carbon can be the basis for the huge diversity of compounds necessary for the emergence of living organisms Altınbas University Lecturer: Asst. Prof. Behiye ÖZTÜRK ŞEN [email protected] MED101 MOLECULLAR AND CELLULAR MEDICAL SCIENCES I  1.2 Atomic Structure The compounds we encounter in chemistry are made up of elements combined in different proportions. Elements are made up of atoms. An atom consists of a dense, positively charged nucleus containing protons and neutrons and a surrounding cloud of electrons. Structure of Atom Altınbas University Lecturer: Asst. Prof. Behiye ÖZTÜRK ŞEN [email protected] MED101 MOLECULLAR AND CELLULAR MEDICAL SCIENCES I  1.2B Valence Electrons The most important shell, called the valence shell, is the outermost shell because the electrons of this shell are the ones that an atom uses in making chemical bonds with other atoms to form compounds. How do we know how many electrons an atom has in its valence shell? We look at the periodic table. The number of electrons in the valence shell (called valence electrons) is equal to the group number of the atom. For example, carbon is in group IVA and carbon has four valence electrons; oxygen is in group VIA and oxygen has six valence electrons. The halogens of group VIIA all have seven electrons. Altınbas University Lecturer: Asst. Prof. Behiye ÖZTÜRK ŞEN [email protected] MED101 MOLECULLAR AND CELLULAR MEDICAL SCIENCES I  Exercise How many valence electrons does each of the following atoms have? a) Na b) Cl c) Si d) B e) Ne f) N Altınbas University Lecturer: Asst. Prof. Behiye ÖZTÜRK ŞEN [email protected] MED101 MOLECULLAR AND CELLULAR MEDICAL SCIENCES I  Everywhere on Earth, organisms make organic molecules comprised almost exclusively of carbon, hydrogen, nitrogen, and oxygen. Sometimes a few slightly more exotic atoms, such as halogens and sulfur, are present. Globally, these compounds aid in day-to-day functioning of these organisms and/or their survival against predators. Organic molecules include many different compounds with diverse properties. For example, chlorophyll in green plants harnesses the energy of sunlight while vitamin C in citrus trees protects them against oxidative stress. Other molecules include capsaicin, a compound synthesized by pepper plants that wards off insects and birds that might try to eat them and is responsible for the “hotness” that we taste when we bite into a pepper. They also include salicylic acid, a signaling hormone made by willow trees, and lovastatin, a material found in oyster mushrooms that protects the mushroom against bacterial attacks. Altınbas University Lecturer: Asst. Prof. Behiye ÖZTÜRK ŞEN [email protected] MED101 MOLECULLAR AND CELLULAR MEDICAL SCIENCES I  Analgesic. It can modulate pain when applied to the skin and is currently sold under the tradename Capzacin a painkiller as well as an anti-acne medication a drug to decrease levels of cholesterol in human blood Altınbas University Lecturer: Asst. Prof. Behiye ÖZTÜRK ŞEN [email protected] MED101 MOLECULLAR AND CELLULAR MEDICAL SCIENCES I Altınbas University Lecturer: Asst. Prof. Behiye ÖZTÜRK ŞEN [email protected] MED101 MOLECULLAR AND CELLULAR MEDICAL SCIENCES I MED100 MOLECULAR AND CELLULAR MEDICAL SCIENCES I Asst. Prof. Behiye ÖZTÜRK ŞEN [email protected]  Lecture Presentation Basic concepts Chemical bonds Altınbas University Lecturer: Asst. Prof. Behiye ÖZTÜRK ŞEN [email protected] MED101 MOLECULLAR AND CELLULAR MEDICAL SCIENCES I In this Chapter; You will learn Chemical Bonds: The Octet Rule Ionic Bonds Covalent Bonds and Lewis Structures How To Write Lewis Structures Exceptions to the Octet Rule Formal Charges and How To Calculate Them A Summary of Formal Charges How To Write and Interpret Structural Formulas More About Dash Structural Formulas Condensed Structural Formulas Rules for Writing Resonance Structures  Chemical Bonds: The Octet Rule 1. Ionic (or electrovalent) bonds are formed by the transfer of one or more electrons from one atom to another to create ions. 2. Covalent bonds result when atoms share electrons. The central idea in their work on bonding is that atoms without the electronic configuration of a noble gas generally react to produce such a configuration because these configurations are known to be highly stable. For all of the noble gases except helium, this means achieving an octet of electrons in the valence shell. The valence shell is the outermost shell of electrons in an atom. The tendency for an atom to achieve a configuration where its valence shell contains eight electrons is called the octet rule. Altınbas University Lecturer: Asst. Prof. Behiye ÖZTÜRK ŞEN [email protected] MED101 MOLECULLAR AND CELLULAR MEDICAL SCIENCES I  Chemical Bonds: The Octet Rule 1. Ionic (or electrovalent) bonds are formed by the transfer of one or more electrons from one atom to another to create ions. 2. Covalent bonds result when atoms share electrons. The central idea in their work on bonding is that atoms without the electronic configuration of a noble gas generally react to produce such a configuration because these configurations are known to be highly stable. For all of the noble gases except helium, this means achieving an octet of electrons in the valence shell. The valence shell is the outermost shell of electrons in an atom. The tendency for an atom to achieve a configuration where its valence shell contains eight electrons is called the octet rule. Altınbas University Lecturer: Asst. Prof. Behiye ÖZTÜRK ŞEN [email protected] MED101 MOLECULLAR AND CELLULAR MEDICAL SCIENCES I  Ionic Bonds Atoms may gain or lose electrons and form charged particles called ions. An ionic bond is an attractive force between oppositely charged ions. One source of such ions is a reaction between atoms of widely differing electronegativities Electronegativity is a measure of the ability of an atom to attract electrons. Altınbas University Lecturer: Asst. Prof. Behiye ÖZTÜRK ŞEN [email protected] MED101 MOLECULLAR AND CELLULAR MEDICAL SCIENCES I  Exercise Altınbas University Lecturer: Asst. Prof. Behiye ÖZTÜRK ŞEN [email protected] MED101 MOLECULLAR AND CELLULAR MEDICAL SCIENCES I  Covalent Bonds and Lewis Structures Covalent bonds form by sharing of electrons between atoms of similar electronegativities to achieve the configuration of a noble gas. Molecules are composed of atoms joined exclusively or predominantly by covalent bonds. Molecules may be represented by electron-dot formulas or, more conveniently, by formulas where each pair of electrons shared by two atoms is represented by a line. A dash structural formula has lines that show bonding electron pairs and includes elemental symbols for the atoms in a molecule. Altınbas University Lecturer: Asst. Prof. Behiye ÖZTÜRK ŞEN [email protected] MED101 MOLECULLAR AND CELLULAR MEDICAL SCIENCES I  Covalent Bonds and Lewis Structures 1. Hydrogen, being in group IA of the periodic table, has one valence electron. Two hydrogen atoms share electrons to form a hydrogen molecule, H2. 2. Because chlorine is in group VIIA, its atoms have seven valence electrons. Two chlorine atoms can share electrons (one electron from each) to form a molecule of Cl2. Altınbas University Lecturer: Asst. Prof. Behiye ÖZTÜRK ŞEN [email protected] MED101 MOLECULLAR AND CELLULAR MEDICAL SCIENCES I  Exercise Consider the following compounds and decide whether the bond in them would be IONIC Por COVALENT. (a) KCl (b) F2 (c) PH3 (d) CBr4 Altınbas University Lecturer: Asst. Prof. Behiye ÖZTÜRK ŞEN [email protected] MED101 MOLECULLAR AND CELLULAR MEDICAL SCIENCES I  How To Write Lewis Structures Several simple rules allow us to draw proper Lewis structures: 1. Lewis structures show the connections between atoms in a molecule or ion using only the valence electrons of the atoms involved. Valence electrons are those of an atom’s outermost shell. 2. For main group elements, the number of valence electrons a neutral atom brings to a Lewis structure is the same as its group number in the periodic table. Carbon, for example, is in group IVA and has four valence electrons; the halogens (e.g.,fluorine) are in group VIIA and each has seven valence electrons; hydrogen is in group IA and has one valence electron. Altınbas University Lecturer: Asst. Prof. Behiye ÖZTÜRK ŞEN [email protected] MED101 MOLECULLAR AND CELLULAR MEDICAL SCIENCES I  How To Write Lewis Structures 3. If the structure we are drawing is a negative ion (an anion), we add one electron for each negative charge to the original count of valence electrons. If the structure is a positive ion (a cation), we subtract one electron for each positive charge. Altınbas University Lecturer: Asst. Prof. Behiye ÖZTÜRK ŞEN [email protected] MED101 MOLECULLAR AND CELLULAR MEDICAL SCIENCES I  How To Write Lewis Structures 4. In drawing Lewis structures we try to give each atom the electron configuration of a noble gas. To do so, we draw structures where atoms share electrons to form covalent bonds or transfer electrons to form ions. a. Hydrogen forms one covalent bond by sharing its electron with an electron of another atom so that it can have two valence electrons, the same number as in the noble gas helium. b. Carbon forms four covalent bonds by sharing its four valence electrons with four valence electrons from other atoms, so that it can have eight electrons (the same as the electron configuration of neon, satisfying the octet rule). c. To achieve an octet of valence electrons, elements such as nitrogen, oxygen, and the halogens typically share only some of their valence electrons through covalent bonding, leaving others as unshared electron pairs. Nitrogen typically shares three electrons, oxygen two, and the halogens one. Altınbas University Lecturer: Asst. Prof. Behiye ÖZTÜRK ŞEN [email protected] MED101 MOLECULLAR AND CELLULAR MEDICAL SCIENCES I  Exercise Write the Lewis structure of CH3F. 1. We find the total number of valence electrons of all the atoms: Altınbas University Lecturer: Asst. Prof. Behiye ÖZTÜRK ŞEN [email protected] MED101 MOLECULLAR AND CELLULAR MEDICAL SCIENCES I  2. We use pairs of electrons to form bonds between all atoms that are bonded to each other. We represent these bonding pairs with lines. In our example this requires four pairs of electrons (8 of the 14 valence electrons). Altınbas University Lecturer: Asst. Prof. Behiye ÖZTÜRK ŞEN [email protected] MED101 MOLECULLAR AND CELLULAR MEDICAL SCIENCES I  3.We then add the remaining electrons in pairs so as to give each hydrogen 2 electrons (a duet) and every other atom 8 electrons (an octet). In our example, we assign the remaining 6 valence electrons to the fluorine atom in three nonbonding pairs. Altınbas University Lecturer: Asst. Prof. Behiye ÖZTÜRK ŞEN [email protected] MED101 MOLECULLAR AND CELLULAR MEDICAL SCIENCES I  Exercise Write a Lewis structure for methylamine (CH3NH2). 1. We find the total number of valence electrons for all the atoms. Altınbas University Lecturer: Asst. Prof. Behiye ÖZTÜRK ŞEN [email protected] MED101 MOLECULLAR AND CELLULAR MEDICAL SCIENCES I  2. We use one electron pair to join the carbon and nitrogen. Altınbas University Lecturer: Asst. Prof. Behiye ÖZTÜRK ŞEN [email protected] MED101 MOLECULLAR AND CELLULAR MEDICAL SCIENCES I  3. We use three pairs to form single bonds between the carbon and three hydrogen atoms. 4. We use two pairs to form single bonds between the nitrogen atom and two hydrogen atoms. 5. This leaves one electron pair, which we use as a lone pair on the nitrogen atom. Altınbas University Lecturer: Asst. Prof. Behiye ÖZTÜRK ŞEN [email protected] MED101 MOLECULLAR AND CELLULAR MEDICAL SCIENCES I  Exercise Write the Lewis structure of CH3OH. 5. If necessary, we use multiple bonds to satisfy the octet rule (i.e., give atoms the noble gas configuration). The carbonate ion (CO32−) illustrates this: Altınbas University Lecturer: Asst. Prof. Behiye ÖZTÜRK ŞEN [email protected] MED101 MOLECULLAR AND CELLULAR MEDICAL SCIENCES I  Exercise Write the Lewis structure of CH2O (formaldehyde). 1. Find the total number of valence electrons of all the atoms: Altınbas University Lecturer: Asst. Prof. Behiye ÖZTÜRK ŞEN [email protected] MED101 MOLECULLAR AND CELLULAR MEDICAL SCIENCES I  2. (a) Use pairs of electrons to form single bonds. Altınbas University Lecturer: Asst. Prof. Behiye ÖZTÜRK ŞEN [email protected] MED101 MOLECULLAR AND CELLULAR MEDICAL SCIENCES I  (b)Determine which atoms already have a full valence shell and which ones do not, and how many valence electrons we have used so far. In this case, we have used 6 valence electrons, and the valence shell is full for the hydrogen atoms but not for the carbon and oxygen atoms. (c) We use the remaining electrons as bonds or unshared electron pairs, to fill the valence shell of any atoms whose valence shell is not yet full, taking care not to exceed the octet rule. In this case 6 of the initial 12 valence electrons are left to use. We use 2 electrons to fill the valence shell of the carbon by another bond to the oxygen, and the remaining 4 electrons as two unshared electron pairs with the oxygen, filling its valence shell. Altınbas University Lecturer: Asst. Prof. Behiye ÖZTÜRK ŞEN [email protected] MED101 MOLECULLAR AND CELLULAR MEDICAL SCIENCES I  Exercise Write a Lewis structure for the toxic gas hydrogen cyanide (HCN). 1. We find the total number of valence electrons on all of the atoms: Altınbas University Lecturer: Asst. Prof. Behiye ÖZTÜRK ŞEN [email protected] MED101 MOLECULLAR AND CELLULAR MEDICAL SCIENCES I  2. We use one pair of electrons to form a single bond between the hydrogen atom and the carbon atom, and we use three pairs to form a triple bond between the carbon atom and the nitrogen atom. This leaves two electrons. We use these as an unshared pair on the nitrogen atom. Now each atom has the electronic structure of a noble gas. The hydrogen atom has two electrons (like helium) and the carbon and nitrogen atoms each have eight electrons (like neon). Altınbas University Lecturer: Asst. Prof. Behiye ÖZTÜRK ŞEN [email protected] MED101 MOLECULLAR AND CELLULAR MEDICAL SCIENCES I  Exceptions to the Octet Rule Elements of the second period of the periodic table can have a maximum of four bonds (i.e., have eight electrons around them) because these elements have only one 2s and three 2p orbitals available for bonding. Each orbital can contain two electrons, and a total of eight electrons fills these orbitals. The octet rule, therefore, only applies to these elements, and even here, as we shall see in compounds of beryllium and boron, fewer than eight electrons are possible. Elements of the third period and beyond have d orbitals that can be used for bonding. These elements can accommodate more than eight electrons in their valence shells and therefore can form more than four covalent bonds. Examples are compounds such as PCl5 and SF6. Altınbas University Lecturer: Asst. Prof. Behiye ÖZTÜRK ŞEN [email protected] MED101 MOLECULLAR AND CELLULAR MEDICAL SCIENCES I  Exceptions to the Octet Rule Altınbas University Lecturer: Asst. Prof. Behiye ÖZTÜRK ŞEN [email protected] MED101 MOLECULLAR AND CELLULAR MEDICAL SCIENCES I  Exercise Write a Lewis structure for the sulfate ion (SO42−) 1.We find the total number of valence electrons including the extra 2 electrons needed to give the ion the double negative charge: Altınbas University Lecturer: Asst. Prof. Behiye ÖZTÜRK ŞEN [email protected] MED101 MOLECULLAR AND CELLULAR MEDICAL SCIENCES I  2.We use four pairs of electrons to form bonds between the sulfur atom and the four oxygen atoms: Altınbas University Lecturer: Asst. Prof. Behiye ÖZTÜRK ŞEN [email protected] MED101 MOLECULLAR AND CELLULAR MEDICAL SCIENCES I  3.We add the remaining 24 electrons as unshared pairs on oxygen atoms and as double bonds between the sülfür atom and two oxygen atoms. This gives each oxygen 8 electrons and the sulfur atom 12: Altınbas University Lecturer: Asst. Prof. Behiye ÖZTÜRK ŞEN [email protected] MED101 MOLECULLAR AND CELLULAR MEDICAL SCIENCES I  Formal Charges and How To Calculate Them Many Lewis structures are incomplete until we decide whether any of their atoms have a formal charge. Calculating the formal charge on an atom in a Lewis structure is simply a bookkeeping method for its valence electrons. First, we examine each atom and, using the periodic table, we determine how many valence electrons it would have if it were an isolated atom. This is equal to the group number of the atom in the periodic table. For hydrogen this number equals 1, for carbon it equals 4, for nitrogen it equals 5, and for oxygen it equals 6. Next, we examine the atom in the Lewis structure and we assign the valence electrons in the following way: Altınbas University Lecturer: Asst. Prof. Behiye ÖZTÜRK ŞEN [email protected] MED101 MOLECULLAR AND CELLULAR MEDICAL SCIENCES I  Formal Charges and How To Calculate Them We assign to each atom half of the electrons it is sharing with another atom and all of its unshared (lone) electron pairs. Then we do the following calculation for the atom: Formal charge = number of valence electrons − 1/2 number of shared electrons − number of unshared electrons or F = Z − (1/2)S − U the number of unshared electrons formal charge group number of the element the number of shared electrons It is important to note, too, that the arithmetic sum of all the formal charges in a molecule or ion will equal the overall charge on the molecule or ion. Altınbas University Lecturer: Asst. Prof. Behiye ÖZTÜRK ŞEN [email protected] MED101 MOLECULLAR AND CELLULAR MEDICAL SCIENCES I  Exercise Formal Charges of Ammonium Ion or Altınbas University Lecturer: Asst. Prof. Behiye ÖZTÜRK ŞEN [email protected] MED101 MOLECULLAR AND CELLULAR MEDICAL SCIENCES I  Exercise Nitrate Ion or Altınbas University Lecturer: Asst. Prof. Behiye ÖZTÜRK ŞEN [email protected] MED101 MOLECULLAR AND CELLULAR MEDICAL SCIENCES I  Exercise Water or Altınbas University Lecturer: Asst. Prof. Behiye ÖZTÜRK ŞEN [email protected] MED101 MOLECULLAR AND CELLULAR MEDICAL SCIENCES I  Exercise Ammonia or Altınbas University Lecturer: Asst. Prof. Behiye ÖZTÜRK ŞEN [email protected] MED101 MOLECULLAR AND CELLULAR MEDICAL SCIENCES I  A Summary of Formal Charges Altınbas University Lecturer: Asst. Prof. Behiye ÖZTÜRK ŞEN [email protected] MED101 MOLECULLAR AND CELLULAR MEDICAL SCIENCES I  How To Write and Interpret Structural Formulas Altınbas University Lecturer: Asst. Prof. Behiye ÖZTÜRK ŞEN [email protected] MED101 MOLECULLAR AND CELLULAR MEDICAL SCIENCES I  More About Dash Structural Formulas Dash structural formulas have lines that show bonding electron pairs, and include elemental symbols for all of the atoms in a molecule.  Condensed Structural Formulas In condensed formulas all of the hydrogen atoms that are attached to a particular carbon are usually written immediately after the carbon Altınbas University Lecturer: Asst. Prof. Behiye ÖZTÜRK ŞEN [email protected] MED101 MOLECULLAR AND CELLULAR MEDICAL SCIENCES I  Condensed Structural Formulas The condensed formula for isopropyl alcohol can be written in four different ways: Altınbas University Lecturer: Asst. Prof. Behiye ÖZTÜRK ŞEN [email protected] MED101 MOLECULLAR AND CELLULAR MEDICAL SCIENCES I  Rules for Writing Resonance Structures 1. Resonance structures exist only on paper. Although they have no real existence of their own, resonance structures are useful because they allow us to describe molecules and ions for which a single Lewis structure is inadequate. We write two or more Lewis structures, calling them resonance structures or resonance contributors. We connect these structures by double-headed arrows (←→ ), and we say that the real molecule or ion is a hybrid of all of them. 2. We are only allowed to move electrons in writing resonance structures. The positions of the nuclei of the atoms must remain the same in all of the structures. Structure 3 is not a resonance structure of 1 or 2, for example, because in order to form it we would have to move a hydrogen atom and this is not permitted: Altınbas University Lecturer: Asst. Prof. Behiye ÖZTÜRK ŞEN [email protected] MED101 MOLECULLAR AND CELLULAR MEDICAL SCIENCES I  Rules for Writing Resonance Structures Altınbas University Lecturer: Asst. Prof. Behiye ÖZTÜRK ŞEN [email protected] MED101 MOLECULLAR AND CELLULAR MEDICAL SCIENCES I  3. All of the structures must be proper Lewis structures. We should not write structures in which carbon has five bonds, for example: Altınbas University Lecturer: Asst. Prof. Behiye ÖZTÜRK ŞEN [email protected] MED101 MOLECULLAR AND CELLULAR MEDICAL SCIENCES I  4. The energy of the resonance hybrid is lower than the energy of any contributing structure. Resonance stabilizes a molecule or ion. This is especially true when the resonance structures are equivalent. Chemists call this stabilization resonance stabilization. If the resonance structures are equivalent, then the resonance stabilization is large. Altınbas University Lecturer: Asst. Prof. Behiye ÖZTÜRK ŞEN [email protected] MED101 MOLECULLAR AND CELLULAR MEDICAL SCIENCES I  5. The more stable a structure is (when taken by itself ), the greater is its contribution to the hybrid. Altınbas University Lecturer: Asst. Prof. Behiye ÖZTÜRK ŞEN [email protected] MED101 MOLECULLAR AND CELLULAR MEDICAL SCIENCES I Altınbas University Lecturer: Asst. Prof. Behiye ÖZTÜRK ŞEN [email protected] MED101 MOLECULLAR AND CELLULAR MEDICAL SCIENCES I MED100 MOLECULAR AND CELLULAR MEDICAL SCIENCES I Asst. Prof. Behiye ÖZTÜRK ŞEN [email protected]  Lecture Presentation Alkanes, Alkenes, Alkynes Altınbas University Lecturer: Asst. Prof. Behiye ÖZTÜRK ŞEN [email protected] MED101 MOLECULLAR AND CELLULAR MEDICAL SCIENCES I  Introduction to Alkanes and Cycloalkanes Hydrocarbons in which all of the carbon–carbon bonds are single bonds are called alkanes, those hydrocarbons that contain a carbon–carbon double bond are called alkenes, and those with a carbon– carbon triple bond are called alkynes. Cycloalkanes are alkanes in which all or some of the carbon atoms are arranged in a ring. Alkanes have the general formula CnH2n+2; cycloalkanes containing a single ring have two fewer hydrogen atoms and thus have the general formula CnH2n. Altınbas University Lecturer: Asst. Prof. Behiye ÖZTÜRK ŞEN [email protected] MED100 MOLECULLAR AND CELLULAR MEDICAL SCIENCES I In this Chapter; You will learn Introduction to Alkanes and Cycloalkanes Shapes of Alkanes How To NAME Alkanes How To Name Unbranched Alkyl Groups How To Name Branched-Chain Alkanes How To Name Branched Alkyl Groups How To NAME cycloalkanes How To Name Alkenes and Cycloalkenes How To Name Alkynes  Shapes of Alkanes Unbranced Alkanes Altınbas University Lecturer: Asst. Prof. Behiye ÖZTÜRK ŞEN [email protected] MED100 MOLECULLAR AND CELLULAR MEDICAL SCIENCES I  Shapes of Alkanes Branched Alkanes Altınbas University Lecturer: Asst. Prof. Behiye ÖZTÜRK ŞEN [email protected] MED100 MOLECULLAR AND CELLULAR MEDICAL SCIENCES I  How To NAME Alkanes Today, chemists use a systematic nomenclature developed and updated by the International Union of Pure and Applied Chemistry (IUPAC). The ending for all of the names of alkanes is -ane. Altınbas University Lecturer: Asst. Prof. Behiye ÖZTÜRK ŞEN [email protected] MED100 MOLECULLAR AND CELLULAR MEDICAL SCIENCES I  How To Name Unbranched Alkyl Groups If we remove one hydrogen atom from an alkane, we obtain what is called an alkyl group. These alkyl groups have names that end in -yl. When the alkane is unbranched, and the hydrogen atom that is removed is a terminal hydrogen atom, the names are straightforward: Altınbas University Lecturer: Asst. Prof. Behiye ÖZTÜRK ŞEN [email protected] MED100 MOLECULLAR AND CELLULAR MEDICAL SCIENCES I  How To Name Branched-Chain Alkanes 1. Locate the longest continuous chain of carbon atoms; this chain determines the parent name for the alkane. We designate the following compound, for example, as a hexane because the longest continuous chain contains six carbon atoms: Altınbas University Lecturer: Asst. Prof. Behiye ÖZTÜRK ŞEN [email protected] MED100 MOLECULLAR AND CELLULAR MEDICAL SCIENCES I  How To Name Branched-Chain Alkanes 2. Number the longest chain beginning with the end of the chain nearer the substituent. Applying this rule, we number the two alkanes that we illustrated previously in the following way: Altınbas University Lecturer: Asst. Prof. Behiye ÖZTÜRK ŞEN [email protected] MED100 MOLECULLAR AND CELLULAR MEDICAL SCIENCES I  How To Name Branched-Chain Alkanes 3. Use the numbers obtained by application of rule 2 to designate the location of the substituent group. The parent name is placed last, and the substituent group, preceded by the number designating its location on the chain, is placed first. Numbers are separated from words by a hyphen. Our two examples are; 2-methylhexane and 3-methylheptane, respectively: Altınbas University Lecturer: Asst. Prof. Behiye ÖZTÜRK ŞEN [email protected] MED100 MOLECULLAR AND CELLULAR MEDICAL SCIENCES I  How To Name Branched-Chain Alkanes 4. When two or more substituents are present, give each substituent a number corresponding to its location on the longest chain. For example, we designate the following compound as 4-ethyl-2-methylhexane: The substituent groups should be listed alphabetically (i.e., ethyl before methyl).* In deciding on alphabetical order, disregard multiplying prefixes such as “di” and “tri.” Altınbas University Lecturer: Asst. Prof. Behiye ÖZTÜRK ŞEN [email protected] MED100 MOLECULLAR AND CELLULAR MEDICAL SCIENCES I  How To Name Branched-Chain Alkanes 5. When two substituents are present on the same carbon atom, use that number twice: Altınbas University Lecturer: Asst. Prof. Behiye ÖZTÜRK ŞEN [email protected] MED100 MOLECULLAR AND CELLULAR MEDICAL SCIENCES I  How To Name Branched-Chain Alkanes Altınbas University Lecturer: Asst. Prof. Behiye ÖZTÜRK ŞEN [email protected] MED100 MOLECULLAR AND CELLULAR MEDICAL SCIENCES I  How To Name Branched-Chain Alkanes 7. When two chains of equal length compete for selection as the parent chain, choose the chain with the greater number of substituents: Altınbas University Lecturer: Asst. Prof. Behiye ÖZTÜRK ŞEN [email protected] MED100 MOLECULLAR AND CELLULAR MEDICAL SCIENCES I  How To Name Branched-Chain Alkanes 8. When branching first occurs at an equal distance from either end of the longest chain, choose the name that gives the lower number at the first point of difference: Altınbas University Lecturer: Asst. Prof. Behiye ÖZTÜRK ŞEN [email protected] MED100 MOLECULLAR AND CELLULAR MEDICAL SCIENCES I  Exercise: Provide an IUPAC name for the following alkane Answer: Altınbas University Lecturer: Asst. Prof. Behiye ÖZTÜRK ŞEN [email protected] MED100 MOLECULLAR AND CELLULAR MEDICAL SCIENCES I  Exercise: Which structure does not represent 2-methylpentane? Altınbas University Lecturer: Asst. Prof. Behiye ÖZTÜRK ŞEN [email protected] MED100 MOLECULLAR AND CELLULAR MEDICAL SCIENCES I  How To Name Branched Alkyl Groups For alkanes with more than two carbon atoms, more than one derived group is possible. Two groups can be derived from propane, for example; the propyl group is derived by removal of a terminal hydrogen, and the 1-methylethyl or isopropyl group is derived by removal of a hydrogen from the central carbon: Altınbas University Lecturer: Asst. Prof. Behiye ÖZTÜRK ŞEN [email protected] MED100 MOLECULLAR AND CELLULAR MEDICAL SCIENCES I  How To Name Branched Alkyl Groups Altınbas University Lecturer: Asst. Prof. Behiye ÖZTÜRK ŞEN [email protected] MED100 MOLECULLAR AND CELLULAR MEDICAL SCIENCES I  How To Name Branched Alkyl Groups Altınbas University Lecturer: Asst. Prof. Behiye ÖZTÜRK ŞEN [email protected] MED100 MOLECULLAR AND CELLULAR MEDICAL SCIENCES I  How To NAME cycloalkanes How To Name Monocyclic Cycloalkanes Cycloalkanes are named by adding “cyclo” before the parent name. 1. Cycloalkanes with one ring and no substituents: Count the number of carbon atoms in the ring, then add “cyclo” to the beginning of the name of the alkane with that number of carbons. For example, cyclopropane has three carbons and cyclopentane has five carbons. Altınbas University Lecturer: Asst. Prof. Behiye ÖZTÜRK ŞEN [email protected] MED100 MOLECULLAR AND CELLULAR MEDICAL SCIENCES I  How To NAME cycloalkanes 2. Cycloalkanes with one ring and one substituent: Add the name of the substituent to the beginning of the parent name. For example, cyclohexane with an attached isopropyl group is isopropylcyclohexane. For compounds with only one substituent, it is not necessary to specify a number (locant) for the carbon bearing the substituent. Altınbas University Lecturer: Asst. Prof. Behiye ÖZTÜRK ŞEN [email protected] MED100 MOLECULLAR AND CELLULAR MEDICAL SCIENCES I  How To NAME cycloalkanes 3. Cycloalkanes with one ring and two or more substituents: For a ring with two substituents, begin by numbering the carbons in the ring, starting at the carbon with the substituent that is first in the alphabet and number in the direction that gives the next substituent the lower number possible. When there are three or more substituents, begin at the substituent that leads to the lowest set of numbers (locants). The substituents are listed in alphabetical order, not according to the number of their carbon atom. Altınbas University Lecturer: Asst. Prof. Behiye ÖZTÜRK ŞEN [email protected] MED100 MOLECULLAR AND CELLULAR MEDICAL SCIENCES I  How To NAME cycloalkanes 4. When a single ring system is attached to a single chain with a greater number of carbon atoms, or when more than one ring system is attached to a single chain, then it is appropriate to name the compounds as cycloalkylalkanes. For example, Altınbas University Lecturer: Asst. Prof. Behiye ÖZTÜRK ŞEN [email protected] MED100 MOLECULLAR AND CELLULAR MEDICAL SCIENCES I  How To Name Alkenes and Cycloalkenes The IUPAC rules for naming alkenes are similar in many respects to those for naming alkanes: 1. Determine the parent name by selecting the longest chain that contains the double bond and change the ending of the name of the alkane of identical length from –ane to -ene. Thus, if the longest chain contains five carbon atoms, the parent name for the alkene is pentene; if it contains six carbon atoms, the parent name is hexene, and so on. Altınbas University Lecturer: Asst. Prof. Behiye ÖZTÜRK ŞEN [email protected] MED100 MOLECULLAR AND CELLULAR MEDICAL SCIENCES I  How To Name Alkenes and Cycloalkenes 2. Number the chain so as to include both carbon atoms of the double bond and begin numbering at the end of the chain nearer the double bond. Designate the location of the double bond by using the number of the first atom of the double bond as a prefix. The locant for the alkene suffix may precede the parent name or be placed immediately before the suffix. We will show examples of both styles: Altınbas University Lecturer: Asst. Prof. Behiye ÖZTÜRK ŞEN [email protected] MED100 MOLECULLAR AND CELLULAR MEDICAL SCIENCES I  How To Name Alkenes and Cycloalkenes 3. Indicate the locations of the substituent groups by the numbers of the carbon atoms to which they are attached: Altınbas University Lecturer: Asst. Prof. Behiye ÖZTÜRK ŞEN [email protected] MED100 MOLECULLAR AND CELLULAR MEDICAL SCIENCES I  How To Name Alkenes and Cycloalkenes 4. Number substituted cycloalkenes in the way that gives the carbon atoms of the double bond the 1 and 2 positions and that also gives the substituent groups the lower numbers at the first point of difference. With substituted cycloalkenes it is not necessary to specify the position of the double bond since it will always begin with C1 and C2. The two examples shown here illustrate the application of these rules: Altınbas University Lecturer: Asst. Prof. Behiye ÖZTÜRK ŞEN [email protected] MED100 MOLECULLAR AND CELLULAR MEDICAL SCIENCES I  How To Name Alkenes and Cycloalkenes 5. Name compounds containing a double bond and an alcohol group as alkenols (or cycloalkenols) and give the alcohol carbon the lower number: Altınbas University Lecturer: Asst. Prof. Behiye ÖZTÜRK ŞEN [email protected] MED100 MOLECULLAR AND CELLULAR MEDICAL SCIENCES I  How To Name Alkenes and Cycloalkenes 6. Two frequently encountered alkenyl groups are the vinyl group and the allyl group: Using substitutive nomenclature, the vinyl and allyl groups are called ethenyl and prop-2-en-1-yl, respectively. The following examples illustrate how these names are employed: Altınbas University Lecturer: Asst. Prof. Behiye ÖZTÜRK ŞEN [email protected] MED100 MOLECULLAR AND CELLULAR MEDICAL SCIENCES I  Exercise: Give an IUPAC name for the molecule shown Answer: We number the ring as shown below starting with the hydroxyl group so as to give the double bond the lower possible number. We include in the name the substituent (an ethenyl group) and the double bond (-ene-), and the hydroxyl group (-ol) with numbers for their respective positions. Hence the IUPAC name is 3- ethenyl-2-cyclopenten-1-ol. Altınbas University Lecturer: Asst. Prof. Behiye ÖZTÜRK ŞEN [email protected] MED100 MOLECULLAR AND CELLULAR MEDICAL SCIENCES I  How To Name Alkenes and Cycloalkenes 7. If two identical or substantial groups are on the same side of the double bond, the compound can be designated cis; if they are on opposite sides it can be designated trans: Altınbas University Lecturer: Asst. Prof. Behiye ÖZTÜRK ŞEN [email protected] MED100 MOLECULLAR AND CELLULAR MEDICAL SCIENCES I  Exercise: Give IUPAC names for the following alkenes: Altınbas University Lecturer: Asst. Prof. Behiye ÖZTÜRK ŞEN [email protected] MED100 MOLECULLAR AND CELLULAR MEDICAL SCIENCES I  Exercise: Write bond-line formulas for the following: (a) cis-3-Octene (b) trans-2-Hexene (c) 2,4-Dimethyl-2-pentene (d) trans-1-Chlorobut-2-ene (e) 4,5-Dibromo-1-pentene (f) 1-Bromo-2-methyl-1-(prop-2-en-1-yl)cyclopentane (g) 3,4-Dimethylcyclopentene (h) Vinylcyclopentane (i) 1,2-Dichlorocyclohexene (j) trans-1,4-Dichloro-2-pentene Altınbas University Lecturer: Asst. Prof. Behiye ÖZTÜRK ŞEN [email protected] MED100 MOLECULLAR AND CELLULAR MEDICAL SCIENCES I  How To Name Alkynes Alkynes are named in much the same way as alkenes. Unbranched alkynes, for example, are named by replacing the -ane of the name of the corresponding alkane with the ending -yne. The chain is numbered to give the carbon atoms of the triple bond the lower possible numbers. The lower number of the two carbon atoms of the triple bond is used to designate the location of the triple bond. When double and triple bonds are present, the direction of numbering is chosen so as to give the lowest overall set of locants. In the face of equivalent options, then preference is given to assigning lowest numbers to the double bonds. The IUPAC names of three unbranched alkynes are shown here: Altınbas University Lecturer: Asst. Prof. Behiye ÖZTÜRK ŞEN [email protected] MED100 MOLECULLAR AND CELLULAR MEDICAL SCIENCES I  How To Name Alkynes The locations of substituent groups of branched alkynes and substituted alkynes are also indicated with numbers. An −OH group has priority over the triple bond when numbering the chain of an alkynol: Altınbas University Lecturer: Asst. Prof. Behiye ÖZTÜRK ŞEN [email protected] MED100 MOLECULLAR AND CELLULAR MEDICAL SCIENCES I Altınbas University Lecturer: Asst. Prof. Behiye ÖZTÜRK ŞEN [email protected] MED100 MOLECULLAR AND CELLULAR MEDICAL SCIENCES I MED100 MOLECULAR AND CELLULAR MEDICAL SCIENCES I Asst. Prof. Behiye ÖZTÜRK ŞEN [email protected]  Lecture Presentation Alcohols, Phenols, Ethers Altınbas University Lecturer: Asst. Prof. Behiye ÖZTÜRK ŞEN [email protected] MED101 MOLECULLAR AND CELLULAR MEDICAL SCIENCES I In this Chapter; You will learn Structure and Nomenclature Nomenclature of Alcohols Ethers Nomenclature of Ethers Exercises  Have you ever walked into a bakery and caught a whiff of vanilla or peppermint emanating from a cake or pastry? Maybe you like to snack on licorice. These smells and flavors, as well as many others that you encounter in daily life, arise from naturally occurring molecules that contain either an alcohol or an ether functional group. Hundreds of such molecules are known, and in addition to their use as flavorings, some have other commercial roles, for example, as antifreezes or pharmaceuticals. An understanding of the physical properties and reactivity of these compounds will enable you to see how they can be used to create new materials with different and even more valuable characteristics. Altınbas University Lecturer: Asst. Prof. Behiye ÖZTÜRK ŞEN [email protected] MED100 MOLECULLAR AND CELLULAR MEDICAL SCIENCES I  Structure and Nomenclature Alcohols have a hydroxyl (−OH) group bonded to a saturated carbon atom. The alcohol carbon atom may be part of a simple alkyl group, as in some of the following examples, or it may be part of a more complex molecule, such as cholesterol. Alcohols are classified as 1°, 2°, or 3°, depending on the number of carbons bonded to the alcohol carbon. Altınbas University Lecturer: Asst. Prof. Behiye ÖZTÜRK ŞEN [email protected] MED100 MOLECULLAR AND CELLULAR MEDICAL SCIENCES I  Structure and Nomenclature Altınbas University Lecturer: Asst. Prof. Behiye ÖZTÜRK ŞEN [email protected] MED100 MOLECULLAR AND CELLULAR MEDICAL SCIENCES I  Structure and Nomenclature The alcohol carbon atom may also be a saturated carbon atom adjacent to an alkenyl group, in which case it is called allylic, or the carbon atom may be a saturated carbon atom that is attached to a benzene ring in which case it is called benzylic. Altınbas University Lecturer: Asst. Prof. Behiye ÖZTÜRK ŞEN [email protected] MED100 MOLECULLAR AND CELLULAR MEDICAL SCIENCES I  Structure and Nomenclature Compounds that have a hydroxyl group attached directly to a benzene ring are called phenols. Altınbas University Lecturer: Asst. Prof. Behiye ÖZTÜRK ŞEN [email protected] MED100 MOLECULLAR AND CELLULAR MEDICAL SCIENCES I  Structure and Nomenclature Ethers differ from alcohols in that the oxygen atom of an ether is bonded to two carbon atoms. The hydrocarbon groups may be alkyl, alkenyl, vinyl, alkynyl, or aryl. Several examples are shown here: Altınbas University Lecturer: Asst. Prof. Behiye ÖZTÜRK ŞEN [email protected] MED100 MOLECULLAR AND CELLULAR MEDICAL SCIENCES I  Nomenclature of Alcohols Methyl alcohol (also called methanol) has the structural formula CH3OH and is the simplest member of a family of organic compounds known as alcohols. The characteristic functional group of this family is the hydroxyl (−OH) group attached to an sp3- hybridized carbon atom. Another example of an alcohol is ethyl alcohol, CH3CH2OH (also called ethanol). Altınbas University Lecturer: Asst. Prof. Behiye ÖZTÜRK ŞEN [email protected] MED100 MOLECULLAR AND CELLULAR MEDICAL SCIENCES I  Nomenclature of Alcohols Alcohols may be viewed structurally in two ways: (1) as hydroxyl derivatives of alkanes and (2) as alkyl derivatives of water. Ethyl alcohol, for example, can be seen as an ethane molecule in which one hydrogen has been replaced by a hydroxyl group or as a water molecule in which one hydrogen has been replaced by an ethyl group: Altınbas University Lecturer: Asst. Prof. Behiye ÖZTÜRK ŞEN [email protected] MED100 MOLECULLAR AND CELLULAR MEDICAL SCIENCES I  Nomenclature of Alcohols As with alkyl halides, alcohols are classified into three groups: ✔ Primary (1°), ✔ Secondary (2°), and ✔ Tertiary (3°) alcohols. This classification is based on the degree of substitution of the carbon to which the hydroxyl group is directly attached. If the carbon has only one other carbon attached to it, the carbon is said to be a primary carbon and the alcohol is a primary alcohol: Altınbas University Lecturer: Asst. Prof. Behiye ÖZTÜRK ŞEN [email protected] MED100 MOLECULLAR AND CELLULAR MEDICAL SCIENCES I  Nomenclature of Alcohols If the carbon atom that bears the hydroxyl group also has two other carbon atoms attached to it, this carbon is called a secondary carbon, and the alcohol is a secondary alcohol: Altınbas University Lecturer: Asst. Prof. Behiye ÖZTÜRK ŞEN [email protected] MED100 MOLECULLAR AND CELLULAR MEDICAL SCIENCES I  Nomenclature of Alcohols If the carbon atom that bears the hydroxyl group has three other carbons attached to it, this carbon is called a tertiary carbon, and the alcohol is a tertiary alcohol: Altınbas University Lecturer: Asst. Prof. Behiye ÖZTÜRK ŞEN [email protected] MED100 MOLECULLAR AND CELLULAR MEDICAL SCIENCES I  Nomenclature of Alcohols Exercises: Give IUPAC names for the following alcohols: Answers: The longest chain to which the hydroxyl group is attached gives us the base name. The ending is -ol. We then number the longest chain from the end that gives the carbon bearing the hydroxyl group the lower number. Altınbas University Lecturer: Asst. Prof. Behiye ÖZTÜRK ŞEN [email protected] MED100 MOLECULLAR AND CELLULAR MEDICAL SCIENCES I  Ethers Ethers have the general formula R−O−R or R−O−R′, where R′ may be an alkyl (or phenyl) group different from R. Ethers can be thought of as derivatives of water in which both hydrogen atoms have been replaced by alkyl groups. The bond angle at the oxygen atom of an ether is only slightly larger than that of water: Altınbas University Lecturer: Asst. Prof. Behiye ÖZTÜRK ŞEN [email protected] MED100 MOLECULLAR AND CELLULAR MEDICAL SCIENCES I  Ethers One way of naming ethers is to name the two alkyl groups attached to the oxygen atom in alphabetical order and add the word ether. If the two alkyl groups are the same, we use the prefix di-, for example, as in dimethyl ether. Write bond-line structural formulas for (a) diethyl ether, (b) ethyl propyl ether, and (c) ethyl isopropyl ether. (b) (c) (a) Altınbas University Lecturer: Asst. Prof. Behiye ÖZTÜRK ŞEN [email protected] MED100 MOLECULLAR AND CELLULAR MEDICAL SCIENCES I  Ethers What name would you give to Me- methyl Altınbas University Lecturer: Asst. Prof. Behiye ÖZTÜRK ŞEN [email protected] MED100 MOLECULLAR AND CELLULAR MEDICAL SCIENCES I  Nomenclature of Ethers Simple ethers are frequently given common functional class names. One simply lists (in alphabetical order) both groups that are attached to the oxygen atom and adds the word ether: IUPAC substitutive names should be used for complicated ethers, however, and for compounds with more than one ether linkage. In this IUPAC style, ethers are named as alkoxyalkanes, alkoxyalkenes, and alkoxyarenes. The −OR group is an alkoxy group. Altınbas University Lecturer: Asst. Prof. Behiye ÖZTÜRK ŞEN [email protected] MED100 MOLECULLAR AND CELLULAR MEDICAL SCIENCES I  Nomenclature of Ethers Cyclic ethers can be named in several ways. One simple way is to use replacement nomenclature, in which we relate the cyclic ether to the corresponding hydrocarbon ring system and use the prefix oxa- to indicate that an oxygen atom replaces a CH2 group. In another system, a cyclic three-membered ether is named oxirane and a four-membered ether is called oxetane. Several simple cyclic ethers also have common names; in the examples below, these common names are given in parentheses. Tetrahydrofuran (THF) and 1,4-dioxane are useful solvents: Altınbas University Lecturer: Asst. Prof. Behiye ÖZTÜRK ŞEN [email protected] MED100 MOLECULLAR AND CELLULAR MEDICAL SCIENCES I  Exercises Give an IUPAC substitutive name for each of the following alcohols Altınbas University Lecturer: Asst. Prof. Behiye ÖZTÜRK ŞEN [email protected] MED100 MOLECULLAR AND CELLULAR MEDICAL SCIENCES I  Exercises Write structural formulas for each of the following A. 1-Ethylcyclobutanol B. 2-Ethoxypentane C. 2-Ethoxyethanol D. 2-Chlorohex-3-yn-1-ol E. Ethyl phenyl ether F. Tetrahydrofuran Altınbas University Lecturer: Asst. Prof. Behiye ÖZTÜRK ŞEN [email protected] MED100 MOLECULLAR AND CELLULAR MEDICAL SCIENCES I Altınbas University Lecturer: Asst. Prof. Behiye ÖZTÜRK ŞEN [email protected] MED101 MOLECULLAR AND CELLULAR MEDICAL SCIENCES I MED100 MOLECULAR AND CELLULAR MEDICAL SCIENCES I Asst. Prof. Behiye ÖZTÜRK ŞEN [email protected]  Carbonyl Compounds A sk organic chemists about favorite functional group, and a good percentage of their them will name a group that contains a carbonyl group. Why? Because carbonyl groups are at the heart of many key functional groups, including aldehydes, ketones, carboxylic acids, and amides. Moreover, carbonyl groups are versatile, serving as a nexus for interconversions between many other kinds of functional groups. Altınbas University Lecturer: Asst. Prof. Behiye ÖZTÜRK ŞEN [email protected] MED101 MOLECULLAR AND CELLULAR MEDICAL SCIENCES I  Lecture Presentation Carboxylic acids & Their Derivatives Altınbas University Lecturer: Asst. Prof. Behiye ÖZTÜRK ŞEN [email protected] MED101 MOLECULLAR AND CELLULAR MEDICAL SCIENCES I In this Chapter; You will learn Chemical Bonds: The Octet Rule Ionic Bonds Covalent Bonds and Lewis Structures How To Write Lewis Structures Exceptions to the Octet Rule Formal Charges and How To Calculate Them A Summary of Formal Charges How To Write and Interpret Structural Formulas More About Dash Structural Formulas Condensed Structural Formulas Rules for Writing Resonance Structures  Structure of the Carbonyl Group Carbonyl compounds are a broad group of compounds that includes aldehydes, ketones, carboxylic acids, esters, and amides Altınbas University Lecturer: Asst. Prof. Behiye ÖZTÜRK ŞEN [email protected] MED101 MOLECULLAR AND CELLULAR MEDICAL SCIENCES I  Structure of the Carbonyl Group Altınbas University Lecturer: Asst. Prof. Behiye ÖZTÜRK ŞEN [email protected] MED101 MOLECULLAR AND CELLULAR MEDICAL SCIENCES I  Vanillin is responsible for the smell of vanilla, while almond flavor results from benzaldehyde, cinnamon from cinnamaldehyde, and spearmint from (R)-carvone. Other odors and sensations that are far less pleasant can also be caused by aldehydes and ketones—for example, the pungent odor of formaldehyde or acetone, or the hangover caused by acetaldehyde that results from drinking too many alcoholic beverages Altınbas University Lecturer: Asst. Prof. Behiye ÖZTÜRK ŞEN [email protected] MED101 MOLECULLAR AND CELLULAR MEDICAL SCIENCES I  Aldehydes and Ketones Aldehydes have a carbonyl group bonded to a carbon atom on one side and a hydrogen atom on the other side. (Formaldehyde is an exception because it has hydrogen atoms on both sides.) Ketones have a carbonyl group bonded to carbon atoms on both sides. Altınbas University Lecturer: Asst. Prof. Behiye ÖZTÜRK ŞEN [email protected] MED101 MOLECULLAR AND CELLULAR MEDICAL SCIENCES I  Nomenclature of Aldehydes and Ketones Aliphatic aldehydes are named substitutively in the IUPAC system by replacing the final -e of the name of the corresponding alkane with -al Since the aldehyde group must be at an end of the carbon chain, there is no need to indicate its position. When other substituents are present the carbonyl group carbon is assigned position 1. Many aldehydes also have common names; these are given below in parentheses. These common names are derived from the common names for the corresponding carboxylic acids, and some of them are retained by the IUPAC as acceptable names. Altınbas University Lecturer: Asst. Prof. Behiye ÖZTÜRK ŞEN [email protected] MED101 MOLECULLAR AND CELLULAR MEDICAL SCIENCES I  Nomenclature of Aldehydes and Ketones Altınbas University Lecturer: Asst. Prof. Behiye ÖZTÜRK ŞEN [email protected] MED101 MOLECULLAR AND CELLULAR MEDICAL SCIENCES I  Nomenclature of Aldehydes and Ketones Aldehydes in which the −CHO group is attached to a ring system are named substitutively by adding the suffix carbaldehyde. Several examples follow: Altınbas University Lecturer: Asst. Prof. Behiye ÖZTÜRK ŞEN [email protected] MED101 MOLECULLAR AND CELLULAR MEDICAL SCIENCES I  Nomenclature of Aldehydes and Ketones The common name benzaldehyde is far more frequently used than benzenecarbaldehyde for C6H5CHO, and it is the name we shall use in this text. Aliphatic ketones are named substitutively by replacing the final -e of the name of the corresponding alkane with -one. The chain is then numbered in the way that gives the carbonyl carbon atom the lower possible number, and this number is used to designate its position. Altınbas University Lecturer: Asst. Prof. Behiye ÖZTÜRK ŞEN [email protected] MED101 MOLECULLAR AND CELLULAR MEDICAL SCIENCES I  Nomenclature of Aldehydes and Ketones Common functional group names for ketones (in parentheses above) are obtained simply by separately naming the two groups attached to the carbonyl group and adding the word ketone as a separate word. Altınbas University Lecturer: Asst. Prof. Behiye ÖZTÜRK ŞEN [email protected] MED101 MOLECULLAR AND CELLULAR MEDICAL SCIENCES I  Nomenclature of Aldehydes and Ketones Some ketones have common names that are retained in the IUPAC system: Altınbas University Lecturer: Asst. Prof. Behiye ÖZTÜRK ŞEN [email protected] MED101 MOLECULLAR AND CELLULAR MEDICAL SCIENCES I  Nomenclature of Aldehydes and Ketones Exercises: Give a structural formula and another acceptable name for each of the following compounds: a) Formaldehyde b) Acetaldehyde c) Phenylacetaldehyde d) Acetone e) Ethyl methyl ketone f) Acetophenone g) Benzophenone h) Diethyl ketone i) Ethyl isopropyl ketone j) Diisopropyl ketone k) Dibutyl ketone l) Dipropyl ketone Altınbas University Lecturer: Asst. Prof. Behiye ÖZTÜRK ŞEN [email protected] MED101 MOLECULLAR AND CELLULAR MEDICAL SCIENCES I Altınbas University Lecturer: Asst. Prof. Behiye ÖZTÜRK ŞEN [email protected] MED101 MOLECULLAR AND CELLULAR MEDICAL SCIENCES I  Carboxylic Acid and Derivatives Altınbas University Lecturer: Asst. Prof. Behiye ÖZTÜRK ŞEN [email protected] MED101 MOLECULLAR AND CELLULAR MEDICAL SCIENCES I  Nomenclature of Carboxylic Acids Systematic or substitutive names for carboxylic acids are obtained by dropping the final -e of the name of the alkane corresponding to the longest chain in the acid and by adding -oic acid. The carboxyl carbon atom is assigned number 1. Altınbas University Lecturer: Asst. Prof. Behiye ÖZTÜRK ŞEN [email protected] MED101 MOLECULLAR AND CELLULAR MEDICAL SCIENCES I  Properties of Carboxylic Acids ✔ Carboxylic acids are polar substances. ✔ Their molecules can form strong hydrogen bonds with each other and with water. ✔ As a result, carboxylic acids generally have high boiling points, and low-molecular- weight carboxylic acids show appreciable solubility in water. ✔ As the length of the carbon chain increases, water solubility declines Altınbas University Lecturer: Asst. Prof. Behiye ÖZTÜRK ŞEN [email protected] MED101 MOLECULLAR AND CELLULAR MEDICAL SCIENCES I  Nomenclature of Carboxylic Acids Exercises: Give an IUPAC systematic name for each of the following: Altınbas University Lecturer: Asst. Prof. Behiye ÖZTÜRK ŞEN [email protected] MED101 MOLECULLAR AND CELLULAR MEDICAL SCIENCES I  Esters The names of esters are derived from the names of the alcohol (with the ending -yl) and the acid (with the ending -ate or -oate). The portion of the name derived from the alcohol comes first: Altınbas University Lecturer: Asst. Prof. Behiye ÖZTÜRK ŞEN [email protected] MED101 MOLECULLAR AND CELLULAR MEDICAL SCIENCES I  Esters Esters are polar compounds, but lacking a hydrogen attached to oxygen, their molecules cannot form strong hydrogen bonds to each other. As a result, esters have boiling points that are lower than those of acids and alcohols of comparable molecular weight. The boiling points of esters are about the same as those of comparable aldehydes and ketones. Unlike the low-molecular-weight acids, esters usually have pleasant odors, some resembling those of fruits, and these are used in the manufacture of synthetic flavors: Altınbas University Lecturer: Asst. Prof. Behiye ÖZTÜRK ŞEN [email protected] MED101 MOLECULLAR AND CELLULAR MEDICAL SCIENCES I  Amides Amides that have no substituent on nitrogen are named by dropping -ic acid from the common name of the acid (or -oic acid from the substitutive name) and then adding -amide. Alkyl groups on the nitrogen atom of amides are named as substituents, and the named substituent is prefaced by N- or N,N-. Examples are Altınbas University Lecturer: Asst. Prof. Behiye ÖZTÜRK ŞEN [email protected] MED101 MOLECULLAR AND CELLULAR MEDICAL SCIENCES I  Amides Amides with nitrogen atoms bearing one or two hydrogen atoms are able to form strong hydrogen bonds to each other. Such amides have high melting points and boiling points. On the other hand, molecules of N,N- disubstituted amides cannot form strong hydrogen bonds to each other, and they have lower melting points and boiling points. The melting and boiling data given above illustrate this trend. Hydrogen bonding between amide groups plays a key role in the way proteins and peptides fold to achieve their overall shape. Altınbas University Lecturer: Asst. Prof. Behiye ÖZTÜRK ŞEN [email protected] MED101 MOLECULLAR AND CELLULAR MEDICAL SCIENCES I  Amides Proteins and peptides (short proteins) are polymers of amino acids joined by amide groups. One feature common to the structure of many proteins is the β sheet, shown below: Altınbas University Lecturer: Asst. Prof. Behiye ÖZTÜRK ŞEN [email protected] MED101 MOLECULLAR AND CELLULAR MEDICAL SCIENCES I  Amides Exercises: Write structural formulas for the following: a) Methyl propanoate b) Ethyl p-nitrobenzoate c) N,N-Dimethylbenzamide d) N,N-Dimethylformamide e) 2-Bromopropanoyl bromide Altınbas University Lecturer: Asst. Prof. Behiye ÖZTÜRK ŞEN [email protected] MED101 MOLECULLAR AND CELLULAR MEDICAL SCIENCES I  Amine-containing compounds have an incredible range of biochemical properties. Some, like acetylcholine, act as neurotransmitters, control muscle function, enhance sensory perceptions, and sustain attention span. Others play far more sinister roles. Colombian poison dart frogs, for example, are tiny and beautiful, but they are also deadly. They produce a compound known as histrionicotoxin, an amine that causes paralysis and eventually death through suffocation. The respiratory muscles cease to function because acetylcholine cannot act, preventing it from initiating the electrical signaling that makes the muscles of our lungs function. Altınbas University Lecturer: Asst. Prof. Behiye ÖZTÜRK ŞEN [email protected] MED101 MOLECULLAR AND CELLULAR MEDICAL SCIENCES I Altınbas University Lecturer: Asst. Prof. Behiye ÖZTÜRK ŞEN [email protected] MED101 MOLECULLAR AND CELLULAR MEDICAL SCIENCES I  Nomenclature of Amines In common nomenclature most primary amines are named as alkylamines. In systematic nomenclature (blue names in parentheses below) they are named by adding the suffix -amine to the name of the chain or ring system to which the NH2 group is attached with replacement of the final -e. Amines are classified as being primary (1°), secondary (2°), or tertiary (3°) on the basis of the number of organic groups attached to the nitrogen. PRIMARY AMINES Altınbas University Lecturer: Asst. Prof. Behiye ÖZTÜRK ŞEN [email protected] MED101 MOLECULLAR AND CELLULAR MEDICAL SCIENCES I  Nomenclature of Amines Most secondary and tertiary amines are named in the same general way. In common nomenclature we either designate the organic groups individually if they are different or use the prefixes di- or tri- if they are the same. In systematic nomenclature we use the locant N to designate substituents attached to a nitrogen atom. SECONDARY AMINES Altınbas University Lecturer: Asst. Prof. Behiye ÖZTÜRK ŞEN [email protected] MED101 MOLECULLAR AND CELLULAR MEDICAL SCIENCES I  Nomenclature of Amines TERTIARY AMINES Altınbas University Lecturer: Asst. Prof. Behiye ÖZTÜRK ŞEN [email protected] MED101 MOLECULLAR AND CELLULAR MEDICAL SCIENCES I  Nomenclature of Amines In the IUPAC system, the substituent −NH2 is called the amino group. We often use this system for naming amines containing an OH group or a CO2H group: Altınbas University Lecturer: Asst. Prof. Behiye ÖZTÜRK ŞEN [email protected] MED101 MOLECULLAR AND CELLULAR MEDICAL SCIENCES I Altınbas University Lecturer: Asst. Prof. Behiye ÖZTÜRK ŞEN [email protected] MED101 MOLECULLAR AND CELLULAR MEDICAL SCIENCES I