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    1 Atomic Structure and Bonding

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    John E. McMurry is the author of the organic chemistry textbook Organic Chemistry. The document provides an overview of the origins and foundations of organic chemistry. It discusses how organic chemistry emerged from the study of carbon compounds derived from biological sources. A key development was Wohler's successful synthesis of urea in 1828, demonstrating that organic compounds could be synthesized in the lab. The document then reviews some fundamental concepts from general chemistry that are important for organic chemistry, including atomic structure, bonding theories, and how hybridized atomic orbitals like sp3 and sp2 influence the structures of molecules like methane and ethylene.

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    1 Atomic Structure and Bonding

    Uploaded by

    Melvin Pogi138
    61 views54 pages
    John E. McMurry is the author of the organic chemistry textbook Organic Chemistry. The document provides an overview of the origins and foundations of organic chemistry. It discusses how organic chemistry emerged from the study of carbon compounds derived from biological sources. A key development was Wohler's successful synthesis of urea in 1828, demonstrating that organic compounds could be synthesized in the lab. The document then reviews some fundamental concepts from general chemistry that are important for organic chemistry, including atomic structure, bonding theories, and how hybridized atomic orbitals like sp3 and sp2 influence the structures of molecules like methane and ethylene.

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    John E. McMurry is the author of the organic chemistry textbook Organic Chemistry. The document provides an overview of the origins and foundations of organic chemistry. It discusses how organic chemistry emerged from the study of carbon compounds derived from biological sources. A key development was Wohler's successful synthesis of urea in 1828, demonstrating that organic compounds could be synthesized in the lab. The document then reviews some fundamental concepts from general chemistry that are important for organic chemistry, including atomic structure, bonding theories, and how hybridized atomic orbitals like sp3 and sp2 influence the structures of molecules like methane and ethylene.

    Copyright:

    © All Rights Reserved
    Download as PPTX, PDF, TXT or read online from Scribd
    Download as pptx, pdf, or txt
    61 views54 pages

    1 Atomic Structure and Bonding

    Uploaded by

    Melvin Pogi138
    John E. McMurry is the author of the organic chemistry textbook Organic Chemistry. The document provides an overview of the origins and foundations of organic chemistry. It discusses how organic chemistry emerged from the study of carbon compounds derived from biological sources. A key development was Wohler's successful synthesis of urea in 1828, demonstrating that organic compounds could be synthesized in the lab. The document then reviews some fundamental concepts from general chemistry that are important for organic chemistry, including atomic structure, bonding theories, and how hybridized atomic orbitals like sp3 and sp2 influence the structures of molecules like methane and ethylene.

    Copyright:

    © All Rights Reserved
    Download as PPTX, PDF, TXT or read online from Scribd
    Download as pptx, pdf, or txt
    of 54

    John E.

    McMurry

    www.cengage.com/chemistry/mcmurry

    Chapter 1
    Structure and Bonding

    Paul D. Adams • University of


    Origins of Organic Chemistry
     Organic chemistry is study of carbon
    compounds.
     Organic chemistry focuses on carbon
    compounds and following movement of the
    electrons in carbon chains and rings, and also
    how electrons are shared with other carbon
    atoms and heteroatoms.
     Organic chemistry is primarily concerned with
    the properties of covalent bonds and non-
    metallic elements, though ions and metals do
    play critical roles in some reactions.
    Origins of Organic Chemistry

    Jöns Jacob Berzelius,first


    coined the term “organic
    chemistry” in 1806 for the
    study of compounds derived
    from biological sources. (VITAL
    FORCES THEORY)
    Origins of Organic Chemistry

    In 1828, Friedrich Wöhler (widely regarded as a pioneer in


    organic chemistry) successfully completed an organic synthesis
    by heating ammonium cyanate and synthesizing of the
    biological compound urea (a component of urine in many
    animals) in what is now called “the Wöhler synthesis.”
    Origins of Organic Chemistry

     The ability to manipulate organic


    compounds includes fermentation to create
    wine and the making of soap, both of which
    have been a part of society so long their
    discovery has been lost in antiquity.

     SAPONIFICATION
     FERMENTATION
    Origins of Organic Chemistry
     Why is it so special?
     carbon's special ability to bond with itself.
     Carbon is unique in its ability to form a wide variety of
    compounds from simple to complex.
     90% of more than 30 million chemical compounds
    contain carbon. Carbon is group 4A element, it can
    share 4 valence electrons and form 4 covalent bonds.
    Why This Chapter?
     Review ideas from general chemistry: atoms, bonds,
    molecular geometry
    1.1 Atomic Structure
     Structure of an atom: small diameter (2  10-10 m = 200 pm)
     Nucleus very dense
     protons (positively charged)
     neutrons (neutral)
     small (10-15 m)

     Electrons
     negatively charged
     located in space remindful of a cloud (10-10 m) around nucleus

    [ångström (Å) is 10-10 m = 100 pm]


    Atomic Number
    and Atomic Mass
     The atomic number (Z): number of protons in nucleus
     The mass number (A): number of protons plus neutrons
     The atomic mass (atomic weight) of an element is
    weighted average mass in atomic mass units (amu) of
    an element’s naturally occurring isotopes.

    Atomic Number= #protons and electrons


    Atomic Mass–Atomic Number =Neutrons
    Atomic Number
    and Atomic Mass
    Atomic Number= #protons and electrons
    Atomic Mass–Atomic Number =Neutrons
    Shapes of Atomic Orbitals for
    Electrons
     Four different kinds of orbitals for electrons based on
    those derived for a hydrogen atom
     Denoted s, p, d, and f
     s and p orbitals most important in organic and biological
    chemistry
     s orbitals: spherical, nucleus at center
     p orbitals: dumbbell-shaped, nucleus at middle
     d orbitals: elongated dumbbell-shaped, nucleus at
    center
    Orbitals and Shells
    (Continued)
     Orbitals are grouped in shells of increasing size and
    energy
     Different shells contain different numbers and kinds of
    orbitals
     Each orbital can be occupied by two electrons
    Orbitals and Shells
    (Continued)
     First shell contains one s orbital, denoted 1s, holds only
    two electrons
     Second shell contains one s orbital (2s) and three p
    orbitals (2p), eight electrons
     Third shell contains an s orbital (3s), three p orbitals
    (3p), and five d orbitals (3d), 18 electrons
    Orbitals and Shells
    (Continued)
    P-Orbitals
     In each shell there are three perpendicular p orbitals,
    px, py, and pz, of equal energy

     Lobes of a p orbital are separated by region of zero


    electron density, a node
    1.3 Atomic Structure: Electron
    Configurations
     Ground-state electron configuration (i.e., lowest
    energy arrangement) of atom
     lists orbitals occupied by its electrons.
     Rules:
     1. Lowest-energy orbitals fill first: 1s  2s  2p 
    3s 
    3p  4s  3d (Aufbau (“build-up”) principle)
    1.3 Atomic Structure: Electron
    Configurations
    1.3 Atomic Structure: Electron
    Configurations
     Ground-state electron configuration (i.e., lowest
    energy arrangement) of atom
     lists orbitals occupied by its electrons.
     Rules:
     2. Electrons act as if they were spinning around an axis.
    Electron spin can have only two orientations, up  and
    down . Only two electrons can occupy an orbital, and
    they must be of opposite spin (Pauli exclusion
    principle) to have unique wave equations
    1.3 Atomic Structure: Electron
    Configurations
     Ground-state electron configuration (i.e., lowest
    energy arrangement) of atom
     lists orbitals occupied by its electrons.
     Rules:
     3. If two or more empty orbitals of equal energy are
    available, electrons occupy each with spins parallel until
    all orbitals have one electron (Hund's rule).
     To the chalkboard (p-orbital filling as example)
    1.4 Development of Chemical
    Bonding Theory
     Atoms form bonds because the resulting
    compound is more stable than the
    separate atoms
     Ionic bonds in salts form by electron
    transfers.
     Organic compounds have covalent
    bonds from sharing electrons (G. N.
    Lewis, 1916)
    Development of Chemical
    Bonding Theory
     Lewis structures (electron dot) show valence electrons of an atom as dots
     Hydrogen has one dot, representing its 1s electron
     Carbon has four dots (2s2 2p2) due to 4 e- in valence shell

     Kekulé structures (line-bond structures) have a line drawn between two atoms
    indicating a 2 e- covalent bond.
     Stable molecule results at completed shell, octet (eight dots) for main-group
    atoms (two for hydrogen)
    Development of Chemical
    Bonding Theory
     Atoms with one, two, or three valence electrons form
    one, two, or three bonds.

    valence e- valence e-
    Development of Chemical
    Bonding Theory
     Atoms with four or more valence electrons form as
    many bonds as electrons needed to fill the s and p
    levels of their valence shells to reach a stable octet.
     Carbon has four valence electrons (2s2 2p2), forming
    four bonds (CH4).
    valence e-
    Development of Chemical
    Bonding Theory
     Nitrogen has five valence electrons (2s2 2p3) but forms
    only three bonds (NH3).

    valence e-
    Development of Chemical
    Bonding Theory
     Oxygen has six valence electrons (2s2 2p4) but forms
    two bonds (H2O)

    valence e-
    Development of Chemical
    Bonding Theory
    Non-Bonding Electrons
     Valence electrons not used in bonding are called nonbonding
    electrons, or lone-pair electrons
     Nitrogen atom in ammonia (NH3)
     Shares six valence electrons in three covalent bonds
    and remaining two valence electrons are
    nonbonding lone pair
    1.5 Describing Chemical Bonds:
    Valence Bond Theory
     Covalent bond forms when two atoms approach
    each other closely so that a singly occupied orbital
    on one atom overlaps a singly occupied orbital on
    the other atom

     Two models to describe covalent bonding.


     Valence bond theory
     Molecular orbital theory
    1.5 Describing Chemical Bonds:
    Valence Bond Theory
    Valence Bond Theory:
     Electrons are paired in the overlapping orbitals and are attracted to
    nuclei of both atoms
     H–H bond results from the overlap of two singly
    occupied hydrogen 1s orbitals
     H-H bond is cylindrically symmetrical, sigma () bond

    cylindrically symmetrical
    Bond Energy
     Reaction 2 H·  H2 releases 436 kJ/mol
     i.e., product has 436 kJ/mol less energy than two atoms:
    H–H has bond strength of 436 kJ/mol
    Bond Energy
     Distance between
    nuclei that leads to
    maximum stability
     If too close, they
    repel because both
    are positively
    charged
     If too far apart,
    bonding is weak
    Describing Chemical Bonding
    Theory
     Kekulé and Couper independently observed that
    carbon always has four bonds
     van't Hoff and Le Bel proposed that the four bonds of
    carbon have specific spatial directions
     Atoms surround carbon as corners of a
    tetrahedron
    1.6 sp3 Orbitals and
    the Structure of
    Methane
    Carbon has 4 valence electrons (2s 2p2) 2

     In CH4, all C–H bonds are identical (tetrahedral)


     sp3 hybrid orbitals: an s orbital and three p orbitals
    combine: form four equivalent, unsymmetrical,
    tetrahedral orbitals (s + ppp = sp3)

    Linus Pauling (1931): his picture near men’s bathroom across from elevators
    The Structure of Methane
     sp3 orbitals on C overlap with 1s orbitals on 4 H atoms
    to form four identical C-H bonds
     Each C–H bond has a strength of 439 kJ/mol and
    length of 109 pm
     Bond angle: each H–C–H is 109.5°: the tetrahedral
    angle.
    1.7 sp3 Orbital-based
    Structure of Hexane
    1.8 sp2 Orbitals and
    the Structure of
    Ethylene
    Some Representations of Ethylene are given
     To explain planar geometry and trigonal shape about C’s in
    ethylene

    H H H H
    C C H 2 C CH 2
    H H C C
    H H
    1.8 sp2 Orbitals and
    the Structure of
    Ethylene
    sp hybrid orbitals: 2s orbital combines with two 2p
    2

    orbitals, giving 3 orbitals (s + pp = sp2). This results in a


    double bond.
     sp2 orbitals are in a plane with120° angles
     Remaining p orbital is perpendicular to the plane
    Bonds From sp2
    Hybrid Orbitals
     Two sp2-hybridized orbitals overlap to form a  bond
     p orbitals overlap side-to-side to formation a pi ()
    bond

     sp2–sp2  bond and 2p–2p  bond result in sharing four


    electrons and formation of C-C double bond
    Bonds From sp2
    Hybrid Orbitals
     Electrons in the  bond are centered between nuclei
     Electrons in the  bond occupy regions are on either
    side of a line between nuclei
    Structure of Ethylene
     H atoms form  bonds with four sp2 orbitals
     H–C–H and H–C–C bond angles of about 120°
     C–C double bond in ethylene shorter and stronger than
    single bond in ethane
     Ethylene C=C bond length 134 pm (C–C 154 pm)
    1.9 sp Orbitals and the
    Structure of Acetylene
     Sharing of six electrons forms C C

     Two sp orbitals form  bonds with hydrogens


    sp Orbitals and the Structure of
    Acetylene
     C-C a triple bond sharing six electrons
     Carbon 2s orbital hybridizes with a single p orbital
    giving two sp hybrids
     two p orbitals remain unchanged
     sp orbitals are linear, 180° apart on x-axis
     Two p orbitals are perpendicular on the y-axis and
    the
    z-axis
    Orbitals of Acetylene
     Two sp hybrid orbitals from each C form sp–sp  bond
     pz orbitals from each C form a pz–pz  bond by
    sideways overlap and py orbitals overlap similarly
    1.10 Hybridization of Nitrogen
    and Oxygen
     Elements other than C can have hybridized orbitals
     H–N–H bond angle in ammonia (NH3) 107.3°
     C-N-H bond angle is 110.3 °
     N’s orbitals (sppp) hybridize to form four sp3 orbitals
     One sp3 orbital is occupied by two nonbonding
    electrons, and three sp3 orbitals have one electron
    each, forming bonds to H and CH3.
    1.10 Hybridization of Sulfur
    1.11 Describing Chemical Bonds:
    Molecular Orbital Theory
     A molecular orbital (MO): where electrons are most likely
    to be found (specific energy and general shape) in a
    molecule
     Additive combination (bonding) MO is lower in energy
     Subtractive combination (antibonding) MO is higher
    energy
    Molecular Orbitals in
    Ethylene
     The  bonding MO is from combining p orbital lobes
    with the same algebraic sign
     The  antibonding MO is from combining lobes with
    opposite signs
     Only bonding MO is occupied

    https://www.youtube.com/watch?
    v=r2XmaiEC0Vw
    1.12 Drawing Structures
    (Avoided in this Class)
     Drawing every bond in organic molecule can
    become tedious.
     Several shorthand methods have been
    developed to write structures.
     Condensed structures don’t have C-H or C-C
    single bonds shown. They are understood.
    e.g.
    Drawing Skeletal Structures
    (Commonly Used)
    General Rules:
    1) Carbon atoms aren’t usually shown
    Drawing Skeletal Structures
    (Commonly Used)
    General Rules:
    2) Instead a carbon atom is assumed to be at each
    intersection of two lines (bonds) and at the end of
    each line.
    Drawing Skeletal Structures
    (Commonly Used)
    General Rules:

    3) Hydrogen atoms bonded to carbon aren’t shown.


    Drawing Skeletal Structures
    (Commonly Used)
    General Rules:
    4) Atoms other than carbon and hydrogen ARE shown
    Summary
     Organic chemistry – chemistry of carbon compounds
     Atom: charged nucleus containing positively charged protons
    and netrually charged neutrons surrounded by negatively
    charged electrons
     Electronic structure of an atom described by wave equation
     Electrons occupy orbitals around the nucleus.
     Different orbitals have different energy levels and
    different shapes
     s orbitals are spherical, p orbitals are
    dumbbell-shaped
     Covalent bonds - electron pair is shared between atoms
     Valence bond theory - electron sharing occurs by overlap of two
    atomic orbitals
     Molecular orbital (MO) theory - bonds result from combination
    of atomic orbitals to give molecular orbitals, which belong to the
    entire molecule
    Summary (Continued)
     Sigma () bonds - Circular cross-section and are formed by
    head- on interaction
     Pi () bonds - “dumbbell” shape from sideways interaction of p
    orbitals
     Carbon uses hybrid orbitals to form bonds in organic molecules.
     In single bonds with tetrahedral geometry, carbon has four sp3
    hybrid orbitals
     In double bonds with planar geometry, carbon uses three
    equivalent sp2 hybrid orbitals and one unhybridized p orbital
     Carbon uses two equivalent sp hybrid orbitals to form a triple
    bond with linear geometry, with two unhybridized p orbitals
     Atoms such as nitrogen and oxygen hybridize to form strong,
    oriented bonds
     The nitrogen atom in ammonia and the oxygen atom
    in water are sp3-hybridized

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