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Molecular Structure

The three dimensional arrangement of atoms in a molecule is known as molecular structure. Molecular geometry is synonymous with molecular structure. The various types of bonds like the covalent, ionic, metallic or coordination bond usually associate several atoms for a particular molecule..

The type of bonding between atoms and their arrangement with respect to each other decides the molecular structure of the molecule. Molecular structure affects the physical properties like polarity, phase of matter, color, and magnetism as well as biological properties.

Various diffraction methods and spectroscopic methods like Infra-red, microwave and Raman spectroscopy are used to determine the molecular structure of molecules. Mainly six types of molecular structures are possible.

Molecular Structure

  • It has been known for a long time that air and other gases are poor conductors of electricity under ordinary conditions.
  • However, when the pressure is reduced and a high potential is applied, conduction occurs more readily and various luminous effects are observed.
  • In 1645, the German scientist Otto van Guericke was successful in creating the first recognized vacuum tube.
  • In the 18th century, the American inventor and statesman Benjamin Franklin concluded that electricity flowed from the positive terminal (anode) to the negative terminal (cathode); however it is now known that it actually flows from the cathode to the anode.
  • Johann Geisslar in 1854 built a device which could release an electric discharge inside a vacuum tube. When electricity was applied, a green glow appeared directly opposite to the cathode.
  • Later on Eugen Goldstein termed these rays as cathode rays as they emanated from the cathode terminal and named the device as cathode ray tube.

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Molecular Geometry Bond Angles

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Here are examples of molecular structure and bond angle of some molecules.

Shape Ideal bond angle (example bond angle)
Example
Image
Linear 180o CO2 < src="//images.tutorvista.com/cms/images/81/linear.PNG" alt="Linear" title="Linear" />
Bent
120° (119°) SO2
Bent
Angular
104.5° H2O Angular
Linear
180o
XeF4 Linear
Trigonal pyramidal
107.5° NH3 Trigonal Pyramid
Trigonal planar 120° BF3 Trigonal Planar
T - shaped
90°, 180° (87.5°, < 180°) ClF3 T-Shaped
Tetrahedral
109.5° CH4 Tetrahedral
Seesaw
180°, 120°, 90° (173.1°, 101.6°) SF4 Seesaw
Square planar
90o, 180o XeF4 Square Planar
Trigonal bipyramidal
90°, 120°, 180° PCl5 Trigonal Bipyramidal
Square pyramidal 90° (84.8°), 180° BrF5 Square Pyramidal
Octahedral
90o, 180o SF6 Octahedral
Pentagonal bipyramidal
90o, 72o, 180o IF7 Pentagonal Bipyramidal

The molecular structure can be represented in three dimensional presentations. There are various ways to show three dimensional presentations like Line or stick model, Electron density plot, Ball and stick model, Space filling model, Cartoon model.

Molecular structure gives the idea about the arrangement and geometry of the atom in given molecules. Let's discuss the examples of some molecular structure.

Molecular Structure of Water

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A molecule is an aggregation of atoms, which consists of electrons and nucleus. Electrons of atoms involve in bonding and form molecule. The type of bonding depends on atoms. If there are two metals, they form a metallic bond, but combination of non-metal & metal form through an ionic bond.

Two non-metals attached through a covalent bond. In water molecule there is a bonding between non-metals that is hydrogen (H) and oxygen (O).

In one molecule of water (H2O), hydrogen atom bonded with central oxygen atom through a covalent bond which forms through the equal sharing of electrons between both molecules.
Since hydrogen atom has one electron, by forming a covalent bond, the duplet of hydrogen gets completed and it gets stable configuration.

Oxygen has six electrons in its valence shell (2s2, 2p4), hence for getting the octet configuration, it requires two electrons. So, oxygen forms two covalent bonds, one with each hydrogen atom and form H2O molecule.

According to Valence shell electron pair repulsion theory (VSEPR ), in a molecule all atoms arrange themselves in such a manner that there will be minimum repulsion between bonding and non-bonding electrons. The best arrangement of water molecule is the tetrahedral geometry with 109.5o.
However, the presence of lain pair of electrons on oxygen atom exerts strong repulsion on two covalent bonding electron pairs and effectively pushes both hydrogen atoms closer. Hence, the tetrahedral arrangement gets distorted and the H-O-H bond angle becomes 104.4o. The bond length of O-H bond is 0.95840.

Hence water molecule show distorted tetrahedral or bent geometry with 104.45o bond angle. Due to high electronegativity of oxygen compare to hydrogen, the covalent bond in water becomes polar with partial negative charge on oxygen and partial positive charge on hydrogen. Because of polarity in the molecule, it shows a net dipole moment.

Another type of bonding present in water apart from covalent bonding is “Hydrogen bonding”.
Hydrogen bond is a weak electrostatic attraction force between electronegative elements (O, N, F ) and hydrogen.

If a hydrogen bond is present in between two molecules, it’s known as Intermolecular hydrogen bond, while Intramolecular hydrogen bond is present in between atoms of same molecules.

Water molecules are associated by intermolecular hydrogen bonding between oxygen atom and hydrogen atom. Each water molecule can form four Hydrogen Bonds, two with oxygen atom and one with each hydrogen atom. Hence, it forms an elaborate network of molecules.

In the solid state of water, known as ice, water molecules are closely packed with these hydrogen bonds and forms a cage type cluster which is easily identified in snowflakes. Hydrogen bonds provide the stable arrangement to water molecules in ice and give a beautiful symmetry that reveals itself in a snowflake.

Molecular Structure of Sugar

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Sugar or carbohydrates are organic molecules composed of carbon, hydrogen, and oxygen. They serve as energy sources and structural material for cells (cell wall in plant cell) of all organisms. Sugar is termed as edible crystalline carbohydrates, mainly sucrose, lactose, and fructose. Since it’s an organic molecule, the atoms are bonded with simple covalent bonds.

Mainly carbohydrates are simple sugars or also termed as monosaccharide. When these simple sugars or monosaccharides combine with each other, they form a disaccharide. Two to ten simple sugars combine to form oligosaccharides, and those with a larger number are called polysaccharides.

Molecular Structure of Sugar

Monosaccharide have general formula [CH2O]n where n is a number between 3 and 7. They can be classified based on the number of carbons present in molecule.

Sugar with four carbon atoms termed as tetrose, while for five carbon termed as pentose, hexode, and heptoses and so on.

Number of carbons
Category name Examples
Structures
1 Tetrose Erythrose, Threose Classification of Tetrose
2 Pentose
Arabinose, Ribose,
Ribulose, Xylose,
Xylulose, Lyxose
Classification of Pentose
3
Hexose Allose, Altrose,
Fructose, Galactose
Glucose, Gulose, Idose,
Mannose, Sorbose,
Talose, Tagatose
Classification of Hexose
4
Heptoses
Sedoheptulose,
Mannoheptulose
Classification of Heptoses

Monosaccharides can be represented as chain molecule as well as cyclic molecules. The cyclic representation of sugar molecule is known as Haworth projection.

Let’s take the example of glucose, which is a hexose monosaccharide with aldehyde group (-CHO), hence, also known as aldose. Monosaccharides with ketaonic group (>C=O) are termed as ketose sugar.

For example, fructose is a ketose sugar with six carbon atoms. In glucose there are five alcoholic groups (one primary alcoholic group & four secondary alcoholic groups) with one aldehyde group at the terminal carbon atom.

Haworth Projection

Like other Monosaccharides, glucose can also show open chain as well as cyclic ring structure. The six remembered cyclic ring is known as pyranose, while a five member ring is known as furanose. In pyranose ring the oxygen on fifth carbon atom links with the carbon atom of the carbonyl group at C1. C1 transfers its hydrogen to the carbonyl oxygen to create a hydroxyl group.

This rearrangement creates alpha glucose in which the -CH2OH group is on the opposite side of -OH group. The opposite arrangement of alpha glucose is known as beta-glucose. Alpha & beta form of glucose are known as anomers of each other.

Anomers

Disaccharides like sucrose, maltose and lactose are made up of the combination of two monosaccharide units. For example, Maltose forms by reunion of alpha & beta glucose. Two glucose units are attached by a glycosidic linkage which is formed by elimination of one water molecule.

Sucrose is made up of one alpha-glucose and one beta-fructose unit. Beta-galactose and beta-glucose form beta-lactose.
On the other hand, a polysaccharide is made up of many monosaccharide units. These units attach with glycosidic linkage and show branching with the help of hydrogen bonds. For example, Starch, glycogen.
More topics in Molecular Structure
Rutherford Model of the Atom Law of Octaves
Bohr's Model of the Atom Ionization Energy
Aromaticity Electronic Configuration
Cathode Ray Tube Experiment Spectral Lines
Electromagnetic Radiation Visible Spectrum
Frequency and Wavelength Millikan’s Oil Drop Experiment
Atomic Spectroscopy Atomic Emission Spectroscopy
Atomic Absorption Spectroscopy Hydrogen Emission Spectrum
Hydrogen Spectrum Absorption Spectrum
Spectrometer Hydrogen Absorption Spectrum
Spectrophotometer
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