Organic Chemistry1 Lec1 PDF

 first semester by Introduction Structure of an Atom  What Is an Atom?  Atoms are often referred to as the building blocks of matter.  Each element on the periodic table is composed of one type of atom and cannot be broken down into a simpler substance. What Is an...

 first semester by Introduction Structure of an Atom  What Is an Atom?  Atoms are often referred to as the building blocks of matter.  Each element on the periodic table is composed of one type of atom and cannot be broken down into a simpler substance. What Is an Atom?  Atoms are composed of smaller subatomic particles such as the proton, neutron, and electron.  Atoms contain a nucleus surrounded by an electron cloud that consists of one or more energy levels.  Inner Structure of an Atom Nucleus - Small, dense, positively charged center of the atom which contains most of the atom’s mass Inner Structure of an Atom The nucleus contains the following subatomic particles: Protons - positively (+) charged particles Neutrons - particles that have no charge (neutral), but contribute to the atom’s mass Outer Structure of an Atom Electron cloud - an area around the nucleus where electrons are likely to be found orbiting the nucleus in several energy levels Outer Structure of an Atom The electron cloud contains several energy levels  Electrons - negatively (-) charged particles located in specific energy levels surrounding the nucleus Outer Structure of an Atom Multiple energy levels in the electron cloud completely surround the nucleus. Electrons follow a specific order to fill the energy levels. Maximum of 2 electrons Maximum Nucleus of 8 electrons Maximum of 8 electrons* *Applies to the first 18 elements only Outer Structure of an Atom The electrons in the outermost energy level are called valence electrons We will go into more detail about the importance of valence electrons in our next unit.  Decoding Atom Information from the Periodic Table Atomic Number 6 C Atom’s Symbol Atom’s Carbon Name Atomic Mass 12.0  Decoding Atom Information from the Periodic Table Atomic number # of protons = # of electrons 6 C Carbon 12.0 Atomic mass = # of protons plus the # of neutrons  Atom Characteristics  The number of protons in the nucleus is the atomic number of that atom. Protons are used to identify elements.  The atomic number represents the number of protons (+) and is equal to the number of electrons (-).  Atom Characteristics  The atomic mass is the mass of the protons plus the mass of the neutrons. Atomic mass is recorded in the SI units: atomic mass units (amu). Protons and neutrons each are given an amu of 1. Electrons have a mass of nearly zero.  Isotopes Atoms with the same number of protons but different numbers of neutrons Another way to say – atoms of the same element with different numbers of neutrons An elements mass number is the number of protons plus the number of neutrons REVIEW: – to determine the number of neutrons subtract the atomic number from the mass number Mass # – atomic # = # of neutrons Valence Electrons  Chemical Bonds – The Octet Rule Lewis & Koessel explained the nature of chemical bonds. Common types of chemical bonds include ionic and covalent bonds. Ionic bond is formed by transfer of electrons, covalent bond is formed by sharing electrons. Ultimately, atoms make bonds in order to produce a noble gas configuration, which is highly stable.  “Octet rule Since most noble gases, except helium, have 8 electrons in valence shells, the tendency of atoms to resemble noble gases is therefore called the “octet rule”.  Electronegativity Electronegativity is a measure of the ability of an atom to attract electrons. In the periodic table, electronegativity is high on the right top, and low on the left bottom. Ionic substance (salts) have very high melting points, are soluble in polar solvents (like water), and conduct electric current. The square of a wave function (ψ2) for a particular x,y,z location expresses the probability of finding an electron at that location in space. Therefore, an orbital can be defined as a region in space where the probability of finding an electron is high. Atomic orbitals, s, p, d, ….etc, have distinctive shapes obtained from plots of ψ2.  Electron Configurations The relative energies of atomic orbitals in the first and second principal shells are as follows: (a) Electrons in 1s orbitals have the lowest energy because they are closest to the positive nucleus. (b) Electrons in 2s orbitals are next lowest in energy. (c) Electrons of the three 2p orbitals have equal but higher energy than the 2s orbital. (d) Orbitals of equal energy (such as the three 2p orbitals) are called degenerate orbitals.  We need follow only a few simple rules: Aufbau principle: fill low energy orbitals first. Pauli exclusion principle: a maximum of two paired electrons per orbital (spin up and spin down). Hund's rule: degenerate orbitals are filled with one unpaired electron first and then paired.  Molecular Orbitals (MOs) A molecular orbital (MO) represents the region of space where one or two electrons of a molecule are likely to be found. Bonding MO (ψMolec) happens when two orbitals of same phase overlapped (addition, reinforcement). This indicates that ψ is large between nuclei, better bonding, and stable.  On the other hand, Antibonding MO (ψ* Molec) happens when two orbitals of opposite phase overlapped (subtraction). This indicates that ψ is zero between nuclei, no contribution to bonding and unstable.  Linear Combination of Atomic Orbitals (LCAO) produces MOs. Bonding MOs are substantially more stable than ψ1s AOs. Antibonding MOs are substantially less stable than ψ1s AOs. Electrons in the molecule are placed in bonding MOs to produce the ground state configuration (Aufbau). Excited state is achieved when a photon is absorbed, an electron jumps to the antibonding MO.  The Structure of Methane (sp3 Hybridization) Atomic orbitals (s, p, d...) alone cannot account for bonds in methane. Bonds in methane can be represented via orbital hybridization. Orbital Hybridization means combination of wave functions for atomic orbitals in various proportions to produce hybrid atomic orbitals. Hybrid atomic orbitals have, in various proportions, properties of the original atomic orbitals.  E.g: sp3 hybridization has 25% s-character and 75% p-character. For instance, for methane, the Ground state configuration of C is: One of the 2s electrons goes to 2pz. Wave functions of 2s, 2px, 2py and 2pz mix to form four equivalent 2sp3 hybrid orbital.  Overlap of 1s atomic orbital of H and an sp3 atomic orbital from C produces MOs for C-H bonds. Only bonding MOs are shown here. Very strong sigma (σ) bonds are formed due to complete overlap of (+) lobes. All purely single bonds are sigma bonds.  Another example can be shown for the ethane (below): When two π atomic orbitals combine to form a π bond, two molecular orbitals form: One is a bonding molecular orbital and the other is an antibonding molecular orbital. The bonding π molecular orbital results when π-orbital lobes of like signs overlap; the antibonding π molecular orbital results when opposite signs overlap (diagram below).  Organic structures Organic structures can be written with several formats. Following is an example of propyl alcohol: 58  Geometry Also, the structural formula can inform about the geometry of the organic structures (in three dimensions), for instance, the bonds of the tetrahedral structure of methane can be drawn as 1. a dashed wedge: bond behind plane, 2. solid wedge: bond in front of plane 3. and ordinary line: bond in plane. 59  Other examples include ethylene which represents the geometry of a carbon with double bond that has a trigonal planar geometry. This indicates that all bonds are in one plane, with angle of 120o. In case of acetylene (ethyne), the geometry is linear which indicates that all bonds are in the same plane with angle of 180o. 61  Restricted Rotation & Double Bond Optimum overlap between p orbitals of a π bond occurs when they are parallel. Rotation around the π bond is thus energetically expensive as it breaks the bond (264 kJ/mol). 62  Carbons joined by single bonds (σ bonds) have low energy barrier to rotation (13-26 kJ/mol) and thus rotate freely. 63  stereoisomers Restricted rotation around double bonds introduces a new type of isomerism of cis- trans isomerism. The two compounds are not constitutional isomers because the connectivity is the same. They are classified as stereoisomers and are often called cis-trans isomers. 64  Cis indicates substituents on the same side, while Trans indicates substituents on opposite sides. They are not superposable. 65  Bond Lengths The greater the s-character, the shorter the bond – because – s-orbital is spherical and close to nucleus. The greater the p-character the longer the bond, – because – p-orbital is lobe-shaped and extended away from nucleus. 66  How to Predict Molecular Geometry? Molecular geometry is predicted based on the Valence Shell Electron Pair Repulsion (VSEPR) model: 1. Consider a molecule in which central atom is covalently bonded to two or more groups 2. Consider all electron pairs; bonding pairs and lone pairs. 3. Electron pairs in valence shell repel one another and stay as far apart as possible. Lone pairs are generally more repulsive than bonding pairs. 4. Describe the geometry of the molecule by considering nuclei positions only (disregard lone pairs). 67 Ex Nu of pairs Geometry Angle Structure methane has four pairs tetrahedral of bonding 109.5o. electrons. ammonia (NH3) three bonding trigonal pairs of pyramid 107° electrons and one nonbonding pair water two bonding angular or 104.5°, pairs of bent shape electrons and the two nonbonding electron