Structure and Bonding in Organic Molecules | Organic Chemistry 1

Organic compounds contain carbon atoms bonded hydrogen and other carbon atoms. Organic chemistry studies the properties and reactions of organic compounds. The structure and bonding in organic molecules are studied in this chapter: the atomic structure and electron configurations, the ionic and covalent bonds (octet rule), the formal charges, the hybridization types, the different molecular structures and resonance forms.

Atomic Structure

X: Symbol of the element
A: Mass Number = Number of protons + Neutrons
Z: Atomic Number = Number of protons = Number of electrons
A-Z = Number of neutrons

 

Z is always the same for a specific element

A can be different. XZA and XZA' are two isotopes

Electron Configuration

X: Symbol of the element
A: Mass Number = Number of protons + Neutrons
Z: Atomic Number = Number of protons = Number of electrons
A-Z = Number of neutrons

To easily determine the electron configuration of an element, you must draw a table like the one below and use diagonal lines to determine the order of the subshells
 

Oxygen  ⇒ Z=8 ⇒ 8 electrons 1s22s22p4
Iron ⇒Z=26 ⇒ 26 electrons ⇒1s22s22p63s23p64s23d6

 

Ionic and Covalent Bonds

The octet rule: Atoms tend to form molecules in such a way as to reach an octet in the valence shell and attain a noble-gas configuration

 

An ionic bond is based on the electrostatic attraction of two ions with opposite charges (formed by the loss or the gain of electrons by an element in order to follow the octet rule).

 

Sodium: Z=11 ⇒ 11 electrons  ⇒ 1s2 2s2 2p6 3s1
Nearest noble gas is Ne (1s2 2s2 2p6) ⇒Na needs to lose 1 electron to get Ne's configuration
The most stable ion of sodium is Na+


 

Covalent bonds result from electron sharing between two atoms (especially those in the middle of the periodic table). Electrons are shared to allow the atoms to attain noble-gas configurations.

 

Carbon: Z=6 ⇒6 electrons ⇒ 1s2 2s2 2p2  ⇒4 electrons in its valence shell
C needs 4 additional electrons to get Ne's configuration
C will form 4 covalent bonds with other atoms in order to get 4 additional electrons ⇒ C is tetravalent
 

Nitrogen: Z=7⇒7 electrons ⇒ 1s2 2s2 2p3 ⇒ 5 electrons in its valence shell
N needs 3 additional electrons to get Ne's configuration
N will form 3 covalent bonds with other atoms in order to get 3 additional electrons and will keep 2 electrons unpaired to form a lone-pair electrons N is trivalent

Formal Charges

Formal Charge = (nb of valence electrons in free atom) - (nb of valence electrons in bound atom)

 

What are the formal charges of CH3NO2?
 

N: nb of valence electrons (VE) in free atom = 5 (Z =5)
nb of valence electrons in bound atom = 4 (4 covalent bonds)
Formal charge = 5-4 = +1

O: nb of VE in free atom = 6 (Z =6) 
nb of VE in bound atom = 6 (2 covalent bonds + 2 lone pairs)
Formal charge = 6-6 = 0

O: nb of VE in free atom = 6 (Z =6) 
nb of VE in bound atom = 7 (1 covalent bond + 3 lone pairs)
Formal charge = 6-7 = -1

 

 

 

Hybridization

sp3: Hybridization of 1 s-orbital and 3 p-orbitals to form 4 equivalent sp3 atomic orbitals
⇒4 neighbors (atoms or lone pairs) ⇒ tetrahedral

sp2: Hybridization of 1 s-orbital and 2 p-orbitals to form 3 equivalent sp2 atomic orbitals
⇒3 neighbors (atoms or lone pairs) ⇒trigonal planar

sp: Hybridization of 1 s-orbital and 1 p-orbitals to form 2 equivalent sp atomic orbitals
⇒2 neighbors (atoms or lone pairs) ⇒linear

 

Resonance Forms

Resonance forms differ only in the placement of their π or non-bonding electrons and obey rules of valency.
Different resonance forms of a substance are not equivalent.

 

Structures

Kekulé structure: straight-line notation to represente covalent bond. Lone pairs are shown as 2 dots.

Condensed structure: the main carbon chain is written horizontally, the attached H to the right of the associated C atom. Other substituents are added through connecting vertical lines.

Skeletal structure: C atoms are not shown. Instead, a C is assumed to be at each intersection of 2 lines and at the end of each line. 
H atoms bonded to C are not shown.
Atoms other than C and H are shown as well as H bonded to atoms other than C.

 

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