Organic Chemistry I (CHEM 2201) Fall 2024 Lecture Notes PDF

Organic Chemistry I CHEM 2201 FALL 2024  Chapter 1 Structure and Bonding © 2017 Pearson Education, Inc.  In this chapter we will consider:  What kinds of atoms make up organic molecules  The principles th...

Organic Chemistry I CHEM 2201 FALL 2024  Chapter 1 Structure and Bonding © 2017 Pearson Education, Inc.  In this chapter we will consider:  What kinds of atoms make up organic molecules  The principles that determine how the atoms in organic molecules are bound together  How best to depict organic molecules Copyright © 2016 by John Wiley & Sons, Inc. All rights reserved. Life & the Chemistry of Carbon Compounds  Organic chemistry is the chemistry of compounds that contain the element carbon. Carbon, atomic number 6, is a second-row element  If a compound does not contain the element carbon, it is said to be Copyright © 2016 by John Wiley & Sons, Inc. All rights reserved.  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  Although carbon is the principal element in organic compounds, most also contain hydrogen, and many contain nitrogen, oxygen, phosphorus, sulfur, chlorine, or Copyright © 2016 by John Wiley & Sons, Inc. All rights reserved.  There are two important reasons why carbon is the element that nature has chosen for living organisms: Carbon atoms can form strong bonds to other carbon atoms to form rings and chains of carbon atoms Carbon atoms can also form Copyright © 2016 by John Wiley & Sons, Inc. All rights reserved.  Because of these bond-forming properties, carbon can be the basis for the huge diversity of compounds necessary for the emergence of living organisms Copyright © 2016 by John Wiley & Sons, Inc. All rights reserved.  Atomic Structure  Compounds made up of elements combined in different proportions  Elements made up of atoms  Atoms positively charged nucleus containing protons and neutrons with a surrounding cloud of negatively charged electrons Copyright © 2016 by John Wiley & Sons, Inc. All rights reserved.  Each element is distinguished by its atomic number (Z)  Atomic number = number of protons in nucleus Copyright © 2016 by John Wiley & Sons, Inc. All rights reserved.  Isotopes  The nuclei of all atoms of the same element will have the same number of protons  Some atoms of the same element may have different masses because they have different numbers of neutrons. Such atoms are called isotopes Copyright © 2016 by John Wiley & Sons, Inc. All rights reserved.  Examples 12 C 13 C 14 C (6 protons (6 protons (6 protons 6 neutrons) 7 neutrons) 8 neutrons) (6 electrons) (6 electrons) (6 electrons) 1 H 2 H H 3 Hydrogen Deuterium Tritium (1 proton (1 proton (1 proton 0 neutrons) 1 neutron) 2 neutrons) (1 electron) (1 electron) (1 electron) Copyright © 2016 by John Wiley & Sons, Inc. All rights reserved.  Valence Electrons  Electrons that surround the nucleus exist in shells of increasing energy and at increasing distances from the nucleus.  The valence shell - the outermost shell  Valence electrons - electrons in the valence shell which are equal to the group number of the atom Copyright © 2016 by John Wiley & Sons, Inc. All rights reserved.  Carbon is in group IVA It has 4 valence electrons  Nitrogen is in group VA It has 5 valence electrons  Halogens are in group VIIA F, Cl, Br, I all have 7 valence electrons Copyright © 2016 by John Wiley & Sons, Inc. All rights reserved.  Chemical Bonds: The Octet Rule  Ionic bonds are formed by the transfer of one or more electrons from one atom to another to create ions  Covalent bonds result when atoms share electrons Copyright © 2016 by John Wiley & Sons, Inc. All rights reserved.  Octet Rule In forming compounds, they gain, lose, or share electrons to give a stable electron configuration characterized by 8 valence electrons When the octet rule is satisfied for C, N, O and F, they have an electron configuration analogous to the noble gas Ne Copyright © 2016 by John Wiley & Sons, Inc. All rights reserved.  Recall: electron configuration of noble (inert) gas # of e-s in outer shell He [1s2] 2 Ne 1s2[2s22p6] 8 Ar 1s22s22p6[3s23p6] 8 Copyright © 2016 by John Wiley & Sons, Inc. All rights reserved.  Ionic Bonds  Atoms may gain or lose electrons and form charged particles called ions Anionic bond is an attractive force between oppositely charged ions Copyright © 2016 by John Wiley & Sons, Inc. All rights reserved.  Electronegativity (EN) The intrinsic ability of an atom to attract the shared electrons in a covalent bond Electronegativitiesare based on an arbitrary scale, with F the most electronegative (EN = 4.0) and Cs the least (EN = 0.7) Copyright © 2016 by John Wiley & Sons, Inc. All rights reserved.  element H (EN) (2.1) Li Be B C N O F ……..……… (1.0) (1.6) (2.0) (2.5) (3.0) (3.5) (4.0) Na Mg Si P S Cl ………………...…… (0.9) (1.2) (1.8) (2.1) (2.5) (3.0) K Br ………………………..………………………………… (0.8) (2.8) Rb I ………………………………………………..………… (0.8) (2.5) Cs …………………………………………………………………… (0.7) Copyright © 2016 by John Wiley & Sons, Inc. All rights reserved.  give 1 e- to Na Cl 1s2 2s2 2p6 3s1 1s 2s 2p 3s 3p 2 2 6 2 5 1 e- in outermost shell) (7 e- in outermost shell) ionic bonding + – Na Cl 1s2 2s2 2p6 1s2 2s2 2p6 3s2 3p6 8 8 Copyright © 2016 by John Wiley & Sons, Inc. All rights reserved. Covalent Bonds & 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 Copyright © 2016 by John Wiley & Sons, Inc. All rights reserved.  Example :.Cl Cl. : : : : : [Ne] 3s 3p 2 5 [Ne] 3s 3p 2 5 covalent bonding : : : : : Cl—Cl : Copyright © 2016 by John Wiley & Sons, Inc. All rights reserved.  Ions, themselves, may contain covalent bonds. Consider, as an example, the ammonium ion H H+ N H N H H H H H (ammonia) (ammonium cation) (3 bonds on N) (4 bonds on N with a positive charge on N) Copyright © 2016 by John Wiley & Sons, Inc. All rights reserved.  How to Write Lewis Structures  Lewis structures show the connections between atoms in a molecule or ion using only the valence electrons of the atoms involved  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 Copyright © 2016 by John Wiley & Sons, Inc. All rights reserved.  If the structure that is being drawn 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  In drawing Lewis structures we try to give each atom the electron configuration of a noble gas  Examples Lewis structure of CH3Br Totalnumber of all valence electrons: C H Br 4 + 1 x 3 + 7 = 14 Copyright © 2016 by John Wiley & Sons, Inc. All rights reserved.  H H C Br H H : H C Br: 8H : remainin valence g6 electrons valence electrons Copyright © 2016 by John Wiley & Sons, Inc. All rights reserved. Lewis structure of methylamine (CH5N) Total number of all valence electrons: C H N 4 + 1 x 5 + 5 = 14 Copyright © 2016 by John Wiley & Sons, Inc. All rights reserved.  H H C N H H H 2 valence H electrons left : H C N H 12 H H valence electrons  Drawing Organic Molecules — Condensed Structures All atoms are drawn in, but the bond lines are generally omitted. Atoms are usually drawn next to the atoms to which they are bonded. Parentheses are used around similar groups bonded to the same atom. Lone pairs are omitted. H3C CH2 CH2 CH3 H H H H Partially Condensed structure H C C C C H CH3(CH2)2CH3 C4H1 H H H H Fully Condensed structure CH3CH2CH2CH3 Lewis structure (expanded) 0 Condensed structure  Examples of Condensed Structures H H H H H CH3CH2CHCH2CH3 CH3CH2CH(CH3)CH2CH3 CH3CH(CH2CH3)2 H C C C C C H CH3 H H H H H C H H H H C H H C C H CH3CH CHCH3 H C H H H H H H C C C O H (CH3)2CHCH2OH H H H C H H Cl H H CH3 Cl C C C O C CH3 (Cl)2CH(CH2)2OC(CH3)3 H H H CH3  Skeletal or Bond-Line Structures Assume there is a carbon atom at the junction of any two lines or at the end of any line. Assume there are enough hydrogens around each carbon to make it tetravalent. Draw in all heteroatoms and the hydrogens directly bonded to them. H H H H H C C C C H H H H H C4H1 Lewis structure (expanded) Skeletal or Bond-Line structure 0 H H H H H C C C O H (CH3)2CHCH2OH O OH H H H C H H  Isomerism  Molecules that have the same molecular formula but differ in the arrangement of their atoms are called isomers.  Constitutional (or structural) isomers differ in their bonding sequence (different connectivity).  Stereoisomers differ only in the arrangement of the atoms in space (same connectivity).  Constitutional Isomers  Constitutional isomers have the same chemical formula, but the atoms are connected in a different order.  Constitutional isomers have different properties. Therefore, they must have different names.  Geometric Isomers: Cis and Trans  Stereoisomers are compounds with the atoms bonded in the same order, but their atoms have different orientations in space.  Cis and trans are examples of geometric stereoisomers; they occur when there is a double bond in the compound.  Since there is no free rotation along the carbon–carbon double bond, the groups on these carbons can point to different places in space.  Exceptions to the Octet Rule  Elements in the 2nd row in the periodic table usually obey the Octet Rule (Li, Be, B, C, N, O, F) since they have one 2s and three 2p orbitals available for bonding  Elements in the 3rd row in the periodic table have d orbitals that can be used for bonding and may not obey the Octet Rule Copyright © 2016 by John Wiley & Sons, Inc. All rights reserved.  Examples Cl 2- F Cl Cl P F F Si Cl F F Cl F PCl5 (SiF62-) Copyright © 2016 by John Wiley & Sons, Inc. All rights reserved.  Some highly reactive molecules or ions have atoms with fewer than eight electrons in their outer shell F B F F Copyright © 2016 by John Wiley & Sons, Inc. All rights reserved.  Formal Charges and How to Calculate Them F.C. = # valence electrons - # bonding electrons - # nonbonding electrons 2 A Summary of Formal Charges C C C Copyright © 2016 by John Wiley & Sons, Inc. All rights reserved.  Resonance Forms  The structures of some compounds are not adequately represented by a single Lewis structure.  Resonance forms are Lewis structures that can be interconverted by moving electrons only.  The true structure will be a hybrid between the contributing resonance forms.  Resonance Forms Resonance forms can be compared using the following criteria, beginning with the most important: 1. Has as many octets as possible 2. Has as many bonds as possible 3. Has the negative charge on the most electronegative atom 4. Has as little charge separation as possible  Major & Minor Contributors  The major contributor is the one in which all the atoms have a complete octet of electrons.  Major & Minor Contributors  (Cont’d) When both resonance forms obey the octet rule, the major contributor is the one with the negative charge on the most electronegative atom. The oxygen is more electronegative, so it should have the negative charge. N C O N C O  Non-Equivalent Resonance  Opposite charges should be on adjacent atoms. The most stable one is the one with the smallest separation of oppositely charged atoms.  Quantum Mechanics & Atomic Structure  Wave mechanics & quantum mechanics Each wave function (y) corresponds to a different energy state for an electron Each energy state is a sublevel where one or two electrons can Copyright © 2016 by John Wiley & Sons, Inc. All rights reserved.  From the wave functions (y): The energy associated with the state of an electron can be calculated The relative probability of finding an electron in a given region of space can be calculated Copyright © 2016 by John Wiley & Sons, Inc. All rights reserved.  The phase sign, (+) or (-) of a wave equation indicates whether the solution is positive or negative when calculated for a given point in space relative to the nucleus  Wave functions, whether they are for sound waves, lake waves, or the energy of an electron, have the possibility of constructive interference and destructive interference Copyright © 2016 by John Wiley & Sons, Inc. All rights reserved. Constructive interference occurs when wave functions with the same phase sign interact. There is a reinforcing effect, and the amplitude of the wave function increases Copyright © 2016 by John Wiley & Sons, Inc. All rights reserved. Destructive interference occurs when wave functions with opposite phase signs interact. There is a subtractive effect, and the amplitude of the wave function goes to zero or changes sign Copyright © 2016 by John Wiley & Sons, Inc. All rights reserved. Atomic Orbitals and Electron Configuration Copyright © 2016 by John Wiley & Sons, Inc. All rights reserved.  Electron Configurations  The relative energies of atomic orbitals in the 1st & 2nd principal shells are as follows: Electrons in 1s orbitals have the lowest energy because they are closest to the positive nucleus Electrons in 2s orbitals are next lowest in energy Electrons of the three 2p orbitals have equal but higher energy than the Copyright © 2016 by John Wiley & Sons, Inc. All rights reserved.  Aufbau principle Orbitals are filled so that those of lowest energy are filled first  Pauli exclusion principle Each orbital can accommodate a maximum of two electrons with opposite spin.  Hund’s rule When dealing with degenerate orbitals, such as p-orbitals, one electron is placed in each orbital first , before electrons are paired up. Copyright © 2016 by John Wiley & Sons, Inc. All rights reserved. Copyright © 2016 by John Wiley & Sons, Inc. All rights reserved.  Molecular Orbitals Copyright © 2016 by John Wiley & Sons, Inc. All rights reserved.  We cannot simultaneously know the position and momentum of an electron  An atomic orbital (AO) represents the region of space where one or two electrons of an isolated atom are likely to be found  A molecular orbital (MO) represents the region of space Copyright © 2016 by John Wiley & Sons, Inc. All rights reserved.  An orbital (atomic or molecular) can contain a maximum of two paired electrons with opposite spin (Pauli exclusion principle)  When atomic orbitals combine to form molecular orbitals, the number of molecular orbitals that result always equals the number of atomic orbitals that combine Copyright © 2016 by John Wiley & Sons, Inc. All rights reserved.  A bonding molecular orbital (ymolec) results when two atomic orbitals of the same phase overlap Copyright © 2016 by John Wiley & Sons, Inc. All rights reserved.  An antibonding molecular orbital (y*molec) results when two orbitals of opposite phase combine Copyright © 2016 by John Wiley & Sons, Inc. All rights reserved. Copyright © 2016 by John Wiley & Sons, Inc. All rights reserved. The Structure of Methane: sp3 Hyb H H H H Copyright © 2016 by John Wiley & Sons, Inc. All rights reserved. The Structure of Methane: sp3 Hyb H H H H Copyright © 2016 by John Wiley & Sons, Inc. All rights reserved.  The Structure of Methane: sp3 Hyb  The carbon must undergo hybridization to form 4 equal atomic orbitals  The atomic orbitals must be equal in energy to form four equal-energy symmetrical C-H bonds H H H H The Structure of Methane: sp3 Hyb Copyright © 2016 by John Wiley & Sons, Inc. All rights reserved. The Structure of Methane: sp3 Hyb Copyright © 2016 by John Wiley & Sons, Inc. All rights reserved. The Structure of Methane: sp3 Hyb Copyright © 2016 by John Wiley & Sons, Inc. All rights reserved. Copyright © 2016 by John Wiley & Sons, Inc. All rights reserved. The Structure of Ethane H H C C H H H H Copyright © 2016 by John Wiley & Sons, Inc. All rights reserved. The Structure of Ethane Copyright © 2016 by John Wiley & Sons, Inc. All rights reserved.  The Structure of Ethene (Ethylene): sp2 Hybridization Copyright © 2016 by John Wiley & Sons, Inc. All rights reserved.  The Structure of Ethene (Ethylene): sp2 Hybridization Copyright © 2016 by John Wiley & Sons, Inc. All rights reserved.  The Structure of Ethene (Ethylene): sp2 Hybridization Copyright © 2016 by John Wiley & Sons, Inc. All rights reserved. Copyright © 2016 by John Wiley & Sons, Inc. All rights reserved. An sp2-hybridized carbon atom Copyright © 2016 by John Wiley & Sons, Inc. All rights reserved. A model for the bonding molecular orbitals of ethene formed from two sp2-hybridized carbon atoms and four hydrogen atoms Copyright © 2016 by John Wiley & Sons, Inc. All rights reserved. Copyright © 2016 by John Wiley & Sons, Inc. All rights reserved. Copyright © 2016 by John Wiley & Sons, Inc. All rights reserved.  The Structure of Ethyne (Acetylene): sp Hybridization 1  bond+ 2  bond H C C H 180o sp hybridizedcarbon Linearstructure Carbonwith (2 + 2 ) bonds Copyright © 2016 by John Wiley & Sons, Inc. All rights reserved.  The Structure of Ethyne (Acetylene): sp Hybridization Copyright © 2016 by John Wiley & Sons, Inc. All rights reserved. Copyright © 2016 by John Wiley & Sons, Inc. All rights reserved.  H C C H Copyright © 2016 by John Wiley & Sons, Inc. All rights reserved.  sp orbital 50% s character, 50% p character  sp2 orbital 33% s character, 66% p character  sp3 orbital 25% s character, 75% p Copyright © 2016 by John Wiley & Sons, Inc. All rights reserved. d Lengths of Ethyne, Ethene & Et  The carbon–carbon triple bond of ethyne is shorter than the carbon–carbon double bond of ethene, which in turn is shorter than the carbon–carbon single bond of ethane Copyright © 2016 by John Wiley & Sons, Inc. All rights reserved.  Reasons: The greater the s orbital character in one or both atoms, the shorter is the bond. This is because s orbitals are spherical and have more electron density closer to the nucleus than do p orbitals The greater the p orbital character in one or both atoms, the longer is the bond. This is because p orbitals are lobe-shaped with electron density extending away from the Copyright © 2016 by John Wiley & Sons, Inc. All rights reserved. d Lengths of Ethyne, Ethene & Et Ethane Ethene Ethyne Copyright © 2016 by John Wiley & Sons, Inc. All rights reserved.  END OF CHAPTER 1  Copyright © 2016 by John Wiley & Sons, Inc. All rights reserved.