Introduction to Bio-Organic Chemistry
Course No.: Chem 32Course Tiltle: Introduction to Bio-Organic ChemistryCredit: 3 units lec-labPrerequisite: Chem 14
CHEM 32
Lecturer: Dr. Junie B. Billones e-mail: [email protected]
DPSM, CAS, UP Manila
Introduction to Bio-Organic Chemistry
1. To enable the students to know and understand the fundamental concepts of organic and biochemistry in preparation for advance courses in bioinformatics.
General Objectives:
2. To demonstrate to the students the use of computer softwares for molecular modeling and problem solving.
3
Introduction to Bio-Organic Chemistry
Brief Outline:
1. Alkanes and Cycloalkanes
2. Alcohols and Alkyl Halides
3. Alkenes
4. Alkynes
5. Stereochemistry
6. Arenes and Aromaticity
7. Other functional groups
8. Carbohydrates
9. Lipids
10. Proteins
11. Nucleic acids
Grading SystemLecture - 2/3
Lab - 1/3
3 exams, 1 reporting, n exercises
n expts, 1 reporting
Introduction to Bio-Organic Chemistry
Organic chemistry - study of carbon compounds
Origin of Carbon
CHEMICAL BONDING
1.1 ATOMS, ELECTRONS, AND ORBITALS
Introduction to Bio-Organic Chemistry
Probability distribution for an electron in a 1s orbital.
a 2s orbital
Introduction to Bio-Organic Chemistry
Boundary surfaces of the 2p orbitals. The wave function changes sign at the nucleus.
Hydrogen: 1s1
Electronic Configuration
Helium: 1s2 Lithium: 1s2 2s1
1.2 IONIC BONDS
Introduction to Bio-Organic Chemistry
An ionic bond is the force of electrostatic a t t r a c t i o n b e t w e e n oppositely charged ions, illustrated in this case by Na (red) and Cl (green).
Introduction to Bio-Organic Chemistry
1.3 COVALENT BONDS
PROBLEM: Hydrogen is bonded to fluorine in hydrogen fluoride by a covalent bond. Write a Lewis formula for hydrogen fluoride.
Lewis Structures
Introduction to Bio-Organic Chemistry
Octet rule: In forming compounds atoms gain, lose, or share electrons to give a stable electron configuration characterized by eight valence electrons.
PROBLEM: Given the information that it has a carbon–carbon bond, write a satisfactory Lewis structure for C2H6 (ethane).
Introduction to Bio-Organic Chemistry
PROBLEM: Write the most stable Lewis structure for each of the following compounds:
(a) Formaldehyde, CH2O. Both hydrogens are bonded to carbon. (A solution of formaldehyde in water is sometimes used to preserve biological specimens.)
(b) Tetrafluoroethylene, C2F4. (The starting material for the preparation of Teflon.)
(c) Acrylonitrile, C3H3N. The atoms are connected in the order CCCN, and all hydrogens are bonded to carbon.
Introduction to Bio-Organic Chemistry
1.5 POLAR COVALENT BONDS AND ELECTRONEGATIVITY
Polar covalent bond - the electron distribution is polarized, because one atom has a greater tendency to attract electrons toward itself than the other
Electronegativity - the tendency of an atom to draw the electrons in a covalent bond toward itself.
An electronegative element attracts electrons; an electropositive one donates them.
Introduction to Bio-Organic Chemistry
The dipole moment of a molecule is equal to the charge e multiplied by the distance d between the centers of charge:
Centers of positive and negative charge that are separated from each other constitute a dipole.
Introduction to Bio-Organic Chemistry
PROBLEM: Calculate the formal charge on each of the atoms in the Lewis structures given.
Introduction to Bio-Organic Chemistry
1.7 RESONANCEWhen more than one Lewis structure may be written for a molecule, a single structure is not sufficient to describe it.
The true structure has an electron distribution that is a “hybrid” of all the possible Lewis structures.
Introduction to Bio-Organic Chemistry
Rules of Resonance
1. Atomic positions (connectivity) must be the same in all resonance structures; only the electron positions may vary among the various contributing structures.
A and B represent different compounds, not different resonance forms of the same compound.
A is a Lewis structure for nitromethane; B is methyl nitrite.
Introduction to Bio-Organic Chemistry
2. Lewis structures in which second-row elements own or share more than 8 valence electrons are especially unstable and make no contribution to the true structure. (The octet rule may be exceeded for elements beyond the second row.)
C has 10 electrons around nitrogen. It is not a permissible Lewis structure for nitromethane and so cannot be a valid resonance form.
Introduction to Bio-Organic Chemistry
3. When two or more structures satisfy the octet rule, the most stable one is the one with the smallest separation of oppositely charged atoms.
Structure D has no separation of charge and is more stable than E, which does. The true structure of methyl nitrite is more like D than E.
Introduction to Bio-Organic Chemistry
4. Among structural formulas in which the octet rule is satisfied for all atoms and one or more of these atoms bears a formal charge, the most stable resonance form is the one in which negative charge resides on the most electronegative atom (or positive charge on the most electropositive one).
In G the negative charge is on nitrogen. Oxygen is more electronegative than nitrogen and can better support a negative charge.
Introduction to Bio-Organic Chemistry
5. Each contributing Lewis structure must have the same number of electrons and the same net charge, although the formal charges of individual atoms may vary among the various Lewis structures.
H and I are not resonance forms of one another. Structure H has 24 valence electrons and a net charge of 0; I has 26 valence electrons and a net charge of -2.
Introduction to Bio-Organic Chemistry
6. Each contributing Lewis structure must have the same number of unpaired electrons.
Structural formula J is a Lewis structure of nitromethane; K is not, even though it has the same atomic positions and the same number of electrons.
Structure K has 2 unpaired electrons. Structure J has all its electrons paired and is a more stable structure.
Introduction to Bio-Organic Chemistry
7. Electron delocalization stabilizes a molecule. A molecule in which electrons are delocalized is more stable than implied by any of the individual Lewis structures that may be written for it. The degree of stabilization is greatest when the contributing Lewis structures are of equal stability.
Nitromethane is stabilized by electron delocalization more than methyl nitrite is. The two most stable resonance forms of nitromethane are equivalent to each other.
Introduction to Bio-Organic Chemistry
The two most stable resonance forms of methyl nitrite are not equivalent.
PROBLEM: Using curved arrows, show how an equally stable resonance structure can be generated for each of the following anions:
Introduction to Bio-Organic Chemistry
PROBLEM Construct an orbital diagram for nitrogen in ammonia, assuming sp3 hybridization. In what kind of orbital is the unshared pair? What orbital overlaps are involved in the N-H bonds?
Introduction to Bio-Organic Chemistry
sp3 HYBRIDIZATION AND BONDING IN ETHANE
In general, carbon atom is sp3-hybridized when it is directly bonded to four atoms.
Introduction to Bio-Organic Chemistry
In general, a carbon is sp2-hybridized when it is directly bonded to three atoms.
In general, a carbon is sp-hybridized when it is directly bonded to two atoms.
Introduction to Bio-Organic Chemistry
Introduction to Bio-Organic Chemistry
PROBLEM Give the hybridization state of each carbon in the following compounds:
(a) Carbon dioxide (O=C=O) (b) Formaldehyde (H2C=O) (c) Ketene (H2C=C=O)
(e) Acetone [(CH3)2C=O] (d) Propene (CH3CH=CH2) (f) Acrylonitrile (CH2=CHC≡N)
STRUCTURAL FORMULAS OF ORGANIC MOLECULES
Introduction to Bio-Organic Chemistry
Constitution or connectivity - order of attachment of atoms
PROBLEM: Expand the following condensed formulas so as to show all the bonds and unshared electron pairs.
(a) HOCH2CH2NH2 (d) CH3CHCl2(b) (CH3)3CH (e) CH3NHCH2CH3
(c) ClCH2CH2Cl (f) (CH3)2CHCHO
Introduction to Bio-Organic Chemistry
Bond-line formulas or carbon skeleton diagrams - the only atoms specifically written in are those that are neither carbon nor hydrogen bound to carbon.
Hydrogens bound to heteroatoms (not C or H) are shown.
Introduction to Bio-Organic Chemistry
PROBLEM: Expand the following bond-line representations to show all the atoms including carbon and hydrogen.
Introduction to Bio-Organic Chemistry
CONSTITUTIONAL ISOMERS
Isomers - different compounds that have the same molecular formula.
Structural isomers or constitutional isomer - differ in the order in which their atoms are connected.
Ex: Nitromethane and methyl nitrite have the molecular formula CH3NO2.
Introduction to Bio-Organic Chemistry
PROBLEM: Write structural formulas for all the constitutionally isomeric compounds having the given molecular formula.(a) C2H6O (b) C3H8O(c) C4H10O
THE SHAPES OF SOME SIMPLE MOLECULES
Methane, CH4
Tetrahedral
Introduction to Bio-Organic ChemistryA wedge-and-dash drawing of the structure of methane.
A solid wedge projects from the plane of the paper toward you.
A dashed wedge projects away from you.
A bond represented by a line drawn in the customary way lies inthe plane of the paper.
Introduction to Bio-Organic ChemistryH2O, NH3, and CH4 share the common feature of an approximately tetrahedral geometry.
Introduction to Bio-Organic ChemistryRepresentations of the trigonal planar geometry of boron trifluoride (BF3).
Models of formaldehyde (H2C=O) showing the trigonal planar geometry of the bonds to carbon.
Introduction to Bio-Organic Chemistry
PROBLEM: Specify the shape of the following:
Ball-and-spoke and space-filling models showing the linear geometry of carbon dioxide (O=C=O).
Introduction to Bio-Organic Chemistry
MOLECULAR DIPOLE MOMENTS
Molecular dipole moment - resultant of all of the individual bond dipole moments of a substance.
Ex: CO2 has polar bonds, but lack a dipole moment because its shape causes the individual C=O bond dipoles to cancel.
Introduction to Bio-Organic Chemistry
CCl4, with four polar C-Cl bonds and a tetrahedral shape, has no net dipole moment, because the resultant of the four bond dipoles is zero.
Introduction to Bio-Organic ChemistryCH2Cl2, on the other hand, has a dipole moment of 1.62 D. The C=H bond dipoles reinforce the C=Cl bond dipoles.
PROBLEM: Which of the following compounds would you expect to have a dipole moment? If the molecule has a dipole moment, specify its direction. (a) BF3 (c) CH4 (e) CH2O (b) H2O (d) CH3Cl (f) HCN