Organic-Biological Chemistry - Brief - Principles of Chemistry II - Lecture Slides, Slides of Chemistry

Download Organic-Biological Chemistry - Brief - Principles of Chemistry II - Lecture Slides and more Slides Chemistry in PDF only on Docsity! Organic & Biological Chemistry Chemistry of Life Alkanes (Saturated HC’s) Hydrocarbons Alkenes (Unsaturated HC’s) Alcohols Ethers Chirality Functional Groups Biochemistry Carbohydrates Proteins Nucleic Acids 9/7/2013 The Structures of Organic Molecules • Organic molecules exhibit three different types of hybridization at the carbon center: – sp3 hybridized carbons for tetrahedral geometries; – sp2 hybridized carbons for trigonal planar geometries; and – sp hybridized carbons for linear geometries. Some General Characteristics of Organic Molecules Summary of VSEPR Molecular Shapes e-pairs Notation Name of VSEPR shape Examples 2 AX2 Linear HgCl2 , ZnI2 , CS2 , CO2 3 AX3 Trigonal planar BF3 , GaI3 AX2E Non-linear (Bent) SO2 , SnCl2 4 AX4 Tetrahedral CCl4 , CH4 , BF4 - AX3E (Trigonal) Pyramidal NH3 , OH3 - AX2E2 Non-Linear (Bent) H2O , SeCl2 5 AX5 Trigonal bipyramidal PCl5 , PF5 AX4E Distorted tetrahedral (see-sawed) TeCl4 , SF4 AX3E2 T-Shaped ClF3 , BrF3 AX2E3 Linear I3 - , ICl2 - 6 AX6 Octahedral SF6 , PF6 - AX5E Square Pyramidal IF5 , BrF5 AX4E2 Square Planar ICl4 - , BrF4 - See Ng Web-site HyperChem CyberChem video Methane Ethene Ethyne sp3 Hybridzation in Carbon Bonding ALKANE Ethane CH3CH3 ALKENE Ethylene =CH,==CH) ALKYNE Acetylene CH=CH AROMATIC Benzene C,H6 & @ ” & (d) a0 H on 109. eG sh 154A cf? \ “ H Casta atk Qa Sao A 121A HyCS==C—-H 180° A yi FY Hc cH 7 ea XY HyperChem TABLE 25.1 First Several Members of the Straight-Chain Alkane Series Boiling Molecular Point Formula Condensed Structural Formula Name (°C) CH, CH, Methane -161 CoH, CH3CH; Ethane -89 C3H¢g CH3CH,»CH;3 Propane -44 C419 CH3CH»,CH,»,CH3 Butane -0.5 CsH2 CH3CH»,CH»,CH»,CH3 Pentane 36 CeHy4 CH3CH»,CH»CH»CH»,CH3 Hexane 68 CryH46 CH3CH»CH»,CH»CH»CH»CH3 Heptane 98 CgHig CH3CH»,CH»,CH»,CH,»,CH»,CH»CH3 Octane 125 CoH 9 CH3CH,CH»,CH,CH,»,CH»,CH»CH»,CH3 Nonane 151 CioH 22 CH3CH»,CH»,CH»CH»,CH»CH»CH»CH»CH3, Decane 174 CH3CH»CH»,CH»CH3 Pentane mp ~—130°C bp +36°C H— TT i CH iq — i —rt i—n— —H —A | H H a se CH;— CH—CH,—CH; Isopentane (2-methylbutane) mp —160°C bp +28°C Structural Isomers | Neopentane CH3—C—CH3 (2,2-dimethylpropane) | mp —20°C CH3 bp +9°C CH» CH, ~CH, | | CH) CH) CH — Cyclohexane Ry CH, CH) \ | O Cyclopentane Cycloalkanes CH, CH»,—CH) L\ Cyclopropane Reactions of Alkanes • The C-C and C-H bonds are very strong. Therefore, alkanes are very unreactive. • At room temperature alkanes do not react with acids, bases, or strong oxidizing agents. • Alkanes do combust in air (making them good fuels): 2C2H6(g) + 7O2(g)  4CO2(g) + 6H2O(l) H = -2855 kJ Alkanes Alkenes • Geometrical isomers are possible since there is no rotation about a C=C  bond. • Note the overlap between orbitals is above and below the plane of the  bonds. – As the C-C bond begins to rotate (moving from cis to trans) the overlap decreases. Unsaturated Hydrocarbons Addition Reactions of Alkenes and Alkynes • The most dominant reaction for alkenes and alkynes involves the addition of something to the two atoms which form the double bond: • Note that the C-C  bond has been replaced by two C-Br  bonds. Unsaturated Hydrocarbons H2C CH2 + Br2 H2C CH2 Br Br Aromatic Hydrocarbons • Aromatic structures are formally related to benzene. • Benzene is not reactive because of the stability associated with the delocalized  electrons. Unsaturated Hydrocarbons TABLE 25.4 Common Functional Groups in Organic Compounds Systematic Functional Type of Suffix Name Group Compound or Prefix Example (common name) S 7 a 7 . C=C Alkene ene C=C Ethene va XS ai’ Ne (Ethylene) —Cc=c— Alkyne -yne H—C=c—H Ethyne (Acetylene) | i —C —O—H Alcohol -ol H—& —O—H Methanol | | (Methyl alcohol) H ) La! Le oh Ether ether AG —o —C—H Dimethyl ether H | i he —X: Haloalkane halo- H-—¢ —Ci: Chloromethane | | (Methy! (X = halogen) H chloride) | ie a i Amine -amine — Ethylamine H H H  Carboxylic Acids O O O 0 0 Hod boon Alon CH;—CH— b OH O HO t — CH)— bd, One bu A OH bu | Lactic acid Methanoic acid Citric acid Acetylsalicylic acid Formic acid Aspirin O oO oO O ea, toe Ho—t—t_on (O)-\on Ethanoic acid Oxalic acid Phenyl methanoic acid Acetic acid Benzoic acid  • A molecule that exists as a pair of nonsuperimposable mirror images is called chiral. • Organic compounds that contain one carbon atom that is attached to four different atoms or groups are chiral. • The carbon atom attached to the four different moieties is called a stereogenic carbon. Chirality in Organic Chemistry \ \ ~ oa oy = S-ibuprofen: CH; CH Protein Structure • Pitch is the distance between coils. • The pitch and diameter ensure no bond angles are strained and the N-H and carbonyl functional groups are optimized for H-bonding. • Tertiary structure is the three dimensional structure of the protein. Video Summary Carbohydrates • Carbohydrates have empirical formula Cx(H2O)y. • Carbohydrate means hydrate of carbon. • Most abundant carbohydrate is glucose, C6H12O6. • Carbohydrates are polyhydroxy aldehydes and ketones. • Glucose is a 6 carbon aldehyde sugar and fructose 6 carbon ketone sugar. • The alcohol side of glucose can react with the aldehyde side to form a six-membered ring. O i H—c H—C—OH HO—C—H H—C—OH H—C—OH H—C—OH H Glucose H H—C—OH *C=O HO—C—H H—C—OH H—C—OH H—C—OH H Fructose Polysaccharides • Bacteria in the stomach of animals contain cellulases, which are enzymes that enable animals to use cellulose for food. Carbohydrates • Nucleic acids carry genetic information. • DNA (deoxyribonucleic acids) have molecular weights around 6 - 16  106 amu and are found inside the nucleus of the cell. • RNA (ribonucleic acids) have molecular weights around 20,000 to 40,000 amu and are found in the cytoplasm outside the nucleus of the cell. • Nucleic acids are made up of nucleotides. Nucleic Acids Sugar, phosphate backbone