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BMS1011 W1L1

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59 views39 pages

BMS1011 W1L1

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BMS1011

Structure of Biological
Macromolecules
Atoms and Atomic Structures

Prof. Tanja Junkers


School of Chemistry
Email: tanja.junkers@monash.edu
Warning
This material has been reproduced and communicated to you by
or on behalf of Monash University in accordance with s113P of
the Copyright Act 1968 (the Act).

The material in this communication may be subject to copyright


under the Act.

Any further reproduction or communication of this material by you


may be the subject of copyright protection under the Act.

Do not remove this notice.


Your lecturer

Prof. Tanja Junkers


School of Chemistry
220A, Building 19
tanja.junkers@monash.edu

Questions?
Drop-in Zoom sessions:
Tuesdays between 3 and 4pm
https://monash.zoom.us/j/81840218776?pwd=TDVvYVQ0TVpFdlNub05tZ01ZaEFQZz09
Or via email
Structure of Biological Macromolecules
Structure of this part of the unit

7 lectures + 3 Workshops + MCQs + SAQ

Lecture 1: Atoms and Atomic Structures


Lecture 2: Chemical equilibria

Lecture 3: Functional Groups


Lecture 4: Chirality

Lecture 5: Lipids
Lecture 6: Carbohydrates

Lecture 7: Amino Acids


Study material
• Brown and Poon – Introduction to Organic Chemistry
• Blackman – Chemistry
• Crowe & Bradshaw – Chemistry for Biosciences

You will be getting…


• Lecture slides
• Online content on moodle
• Your own notes
Study material
What we learn:
Introduction
Medicine Biomedical
Science

Psychology
Introduction
Motivation
Learning outcomes
At the end of this session, you should be able to:

• Understand the electronic structure of atoms


• Understand Lewis Model and able to write Lewis structures
• Understand resonance structures
• Understand parent and molecular geometry using VSEPR
• Predict the polarity of bonds and compounds
Introduction
It all starts with chemistry…

Chemistry The study of the nature, properties


and transformations of matter.

Matter Anything that has mass and occupies space,


that is, things you can see, touch, taste, or
smell.
Introduction
It all starts with chemistry…

All of chemistry (+biochemistry etc.) ultimately boils down


to molecular electronic structure.

Reason: electronic structure governs bonding and thus


molecular structure and reactivity

Before we can understand molecular electronic


structures we need to introduce a number of concepts
which are more easily demonstrated in atoms.

atomic structure → molecular structure → chemistry


Atoms
Mass Number (A)

C
12
Symbol of element
6

Atomic Number (Z)

The mass number (A) of an atom is the total number of


protons plus neutrons in that atom.

The number of protons in the nucleus of an atom of any


particular element is called that element’s atomic number (Z).

There are as many electrons as there are protons (Z).


Electrons
• Electrons are confined to regions of space called principle
energy levels (shells) – each shell can hold 2n2 electrons
(n = 1, 2, 3…)
• Each shell is divided into subshells, which are designated
by the letter s, p, d,….. and further divided to orbitals
Valence electrons
Focusing on the outer shell…
• Valence electrons are the electrons in the
outer shell that bond with other atoms.
• Core electrons – other electrons closer to the
nucleus
Carbon, C = 1s2 2s22p2
• Columns on the periodic
table are called GROUPS
• Elements in the same
group have similar
chemical properties
• Reason: Each group
member has the same
number of valence
electrons
Molecular bonding
Share or divide
Weak interactions
Van-der-Waals, H-bonds

Hydrogen-bonding and dipol-dipol bonding


Molecular bonding
Share or divide

covalent
ionic
Molecular bonding
Electronegativity and polarity

Electronegativity table
Molecular bonding Electronegativity table
Electronegativity and polarity

3.5 – 2.1 = 1.1


(polar covalent)

4.0 – 2.1 = 1.9


(polar covalent)

2.5 – 2.1 = 0.4


(nonpolar covalent)

3.0 – 0.9 = 2.1


(ionic covalent)
Molecular bonding
Covalent bonds

• A covalent bond forms when a portion of an atomic orbital of


one atom overlaps a portion of an atomic orbital of another
atom.
In forming the covalent bond in H–H, for example, there is
overlap of the 1s orbitals of each hydrogen.
Molecular bonding
Covalent bonds
A Problem
• Overlap of a 2s atomic orbitals of one atom and 2p atomic
orbitals of another would give bond angles of 90°.
• Instead, we observe bond angles of approximately 109.5°, 120°,
and 180°.
A Solution
• Hybridization of atomic orbitals.
• 2nd row elements use sp3, sp2, and sp hybrid orbitals for
bonding.
Lewis structures
Drawing molecules
Covalent bonding:
• Involves the sharing of one or more electrons between
these atoms
• Satisfy The Octet Rule
• Multiple bonds may be formed
• Start with Lewis structures (electron dot diagrams)

methane water
Lewis structures
Drawing molecules

Water

1) Draw skeleton: H cannot be central atom, so O must be


H O H

2) Number of valence electrons: H: 2x1 = 2; O: 1x6 = 6; 2 + 6 = 8 valence e-

3) 2 e- for each pair of bonded atoms H:O:H

4) Total e- - e- put into structure = leftover e- : 8 - 4 = 4 leftover

5) e- needed to fill octets: H needs zero, O needs 4; 0 + 4 = 4 needed

6) e- needed – e- leftover = e- in multiple bonds : 4 – 4 = 0, so all 4 leftover


electrons go in as lone pairs (non-bonding)
Lewis structures
Formal charges
Assign electrons in the molecule to individual atoms
according to the following rules:

1. Nonbonding electrons are assigned to the atom on


which they are located
2. Bonding electrons are divided equally between the
bonded atoms
3. For each atom, the formal charge is computed by
the following equation:

formal charge = valence e - nonbonding e - (bonding e)


2
Resonance structures
Resonance - electron pair delocalisation

More than one possible Lewis structure exists for structures


with alternate single-double bond arrangements.

e.g. ozone

I and II are Resonance structures – resonance


contributors, not different types of molecules, i.e not real
bonding depictions
Resonance structures
Resonance hybrids

resonance contributors

The above Lewis structures are based on a localised bonding picture.


In resonance hybrids, however, the density of some electron pairs are
considered delocalised, i.e. spread over entire molecule.

resonance hybrid
Resonance structures
Example for resonance hybrid

resonance contributors

resonance hybrid
Molecular shapes – Parent geometries
Molecular shapes – Parent geometries
Examples:
Lewis Structure Parent Geometry

SO3 Trigonal planar

H2O Tetrahedral

NO2-
Trigonal planar
VSEPR
Molecular geometry

Valence Shell Electron Pair Repulsion (VSEPR) is a model


used to predict the shape of molecules. The basic premise is:

“Each group of valence electrons around a central


atom is located as far away from the others as
possible in order to minimise repulsions”

Question: Why is BF3 planar


while NH3 is pyramidal?
VSEPR
Molecular geometry

Answer: Nitrogen has an extra lone pair of valence


electrons. Lone pairs also influence molecular shape,
and must be included as one of the “group of valence
electrons”.
VSEPR
Molecular geometry

Applying the VSEPR model

STEP 1: Draw a Lewis structure of the molecule, and identify


the atom whose geometry is of interest. This is usually the
central atom.

STEP 2: Count the number of electron charge clouds


surrounding the atom of interest. This is the total number
of lone pairs plus connections to other atoms

STEP 3: Predict molecular shape by assuming that the


charge clouds orient in space so that they are as far away
from one another as possible
VSEPR
Molecular geometry
Polar and Non-polar Molecules
Summary and learning outcomes
After this lecture you should be able to:

• Understand what atoms and their atomic structures are

• Understand Lewis Model and able to write Lewis structures far


various molecules

• Able to draw resonance structures

• Able to predict parent and molecular geometry using VSEPR

• Predict the polarity of bonds and compounds


PACKUP AND EXIT

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