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Molecular Structure

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Molecules are considered as a simple assemblage of atoms. Molecular structure specifies the relative position of all atoms in a molecule. Structural formulas are a key tool for describing both structure and reactivity. There are a number of experimental means for precise determination of molecular structure primarily based on spectroscopic and diffraction methods.


The earliest chemists who thought about molecular structure worried only about the numbers and kinds of atoms that were present in the molecule. The number of kinds of atoms, connectivity of the atoms, the stereo chemistry, internal coordinates of the molecule determines the molecular structure of the molecule.

Molecular Structure Definition

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"Molecular geometry or molecular structure is the three dimensional arrangement of the atoms that constitute a molecule inferred from the spectroscopic studies of the compound." Molecular structure is the most basic information about a substance determining most of its properties.

It determines several properties of the substance including its reactivity, color, phase of activity, magnetism and biological activity. The molecular geometry can be described by the positions of these atoms in space, evoking bond lengths of two joined atoms, bond angles of connected atoms.

Molecular Geometry Bond Angles

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If the bonds are considered as straight lines between atoms then any two bonds from the same atom intersect to form a bond angle. Molecular geometry can be described by designating bond angles. Molecular geometry can also be described by indicating an overall arrangement of some or all of the atoms.

Molecular geometry can be predicted by using number of different models or simplified pictures of molecular structure. In the hybridization model we can calculate the ideal geometry associated with each type of hybridization. The hybridization and the corresponding geometry is tabulated below.

S.No
Hybridization
Ideal geometry
Bond angles
1
sp Linear
180o
2
sp2
Planar
120o
3
sp3
Tetrahedral
109o28'
4
sp3d
Trigonal bi pyramidal
120o and 90o
5
sp3d2
Octahedral
90o

The geometry of a molecule can be described either by specifying bond angles or by giving the overall geometry or shape of the molecule.

Molecular Structure of Water

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The six valence electrons of oxygen in a water molecule are hybridized to four sp3 orbitals that are elongated to the corners of a some what deformed, imaginary tetrahedron. Two hybrid orbitals form O-H covalent bonds with a bond angle of 105o for H-O-H whereas the other 2 orbitals hold the non bonding electron pairs.

Water Molecular StructureMolecular Structure of Water
Each water molecule is tetrahedral coordinated with four other water molecules through hydrogen bonds.The two unshared electron pairs of oxygen act as hydrogen acceptor sites and the H-O bonding orbitals act as hydrogen bond donor sites.

Molecular Structure of Sugar

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The molecular formula for sucrose is C12H22O11. In particular this spatial arrangement involves the use of the alpha form of D-glucose and the beta form of D-fructose which are ligated through the loss of a water molecule. The $\alpha$-D-glucose is in the conventional orientation. However the $\beta$-D-fructose is shown in two orientations. In the standard orientation the 6C is up on the left side and the -2-OH is up on the right.
Molecular Structure of Sugar
The glycosidic bond of the sucrose is termed an $\alpha$-$\beta$-1-2 bond because it involves an alpha-OH from the glucose and a beta-OH from the sucrose.

Molecular Structure of DNA

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The DNA molecule consists of two strands that wrap around each other to form a long, twisted ladder called a double helix. DNA is made up of repeated subunits of nucleotides. Each nucleotide has a five carbon sugar a phosphate and a nitrogenous base. The nucleotide contains a nitrogenous base called adenine.

Molecular Structure of DNA

The name of the pentagon shaped sugar in DNA is deoxyribose. Hence the name deoxyribonucleic acid. Sugar is linked to two things a phosphate and a nitrogenous base.

A nucleotide can have one of four different nitrogenous bases.
  1. Adenine - a purine (double ringed nitrogenous base)
  2. Guanine - a purine (double ringed nitrogenous base)
  3. Cytosine - a pyrimidine (single ringed nitrogenous base)
  4. Thymine - a pyrimidine (single ringed nitrogenous base)

Any of these four bases can attach to the sugar. The nucleotides can link up in a long chain to form a single strand of DNA.

Molecular Structure of Glucose

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Glucose also known as dextrose is found in sweet fruits such as grapes and figs. Carbohydrates must be digested into glucose for circulation in the blood. Glucose is a class of sugar molecules called hexoses, molecules having six carbon atoms. 2-deoxyriblse the sugar in the backbone of the DNA molecules, is a pentose a molecule with five carbon atoms.

The molecular structure of glucose is shown below.

Molecular Structure of Glucose

Glucose is a typical monosaccharide and is also the main sugar of the body. Glucose is so small that it can pass through the villi and capillaries into our bloodstream.

Molecular Structure Chart

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To understand the molecular structure we must know the nature of chemical bonding which hold the atoms in a molecule together. The list of compounds and their molecular structure if tabulated below.

S.No
Compounds
Molecular structure
1
Molecular Structure of Caffeine Molecular Structure of Caffeine
2
Diamond Molecular Structure Diamond Molecular Structure
3
Molecular Structure of Carbohydrates Molecular Structure of Carbohydrates
4
Molecular Structure of Ethanol Molecular Structure of Ethanol
5
Acetone Molecular Structure
Acetone Molecular Structure
6
Molecular Structure of Ice
Molecular Structure of Ice
7
Molecular Structure of Sucrose Molecular Structure of Sucrose
8
Molecular Structure of Starch
Molecular Structure of Starch

Radiation provided an important tool for the study of matter. Rutherford first suggested the use of alpha particles to probe the internal structure of the atom in 1911. As a result of this experiment the nucleus and its protons were discovered.

Rutherford proposed that the only way that the alpha particles could be deflected through large angles was of all the atom's positive charge and nearly all its mass was concentrated in a small dense nucleus with the electrons some distance away.
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Newland's law of octaves states that when elements are arranged in order of increasing atomic weights then every eighth element has properties similar to that of the first element. Law of octaves failed to assign the position to the elements with large atomic weights.
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Bohr's Model of the Atom

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Bohr's model of the atom can explain the observed emission spectrum of hydrogen. However it fails to explain the spectra of atoms more complex than hydrogen. The orbits in the Bohr model are circular. This is where the model is inaccurate. The electrons move in quasi chaotic orbits around the nucleus and the orbits have several different shapes that define them.
The ionization energy is the energy required to remove an electron from an atom. It thus depends on how strongly the electron is bound in the atom. The stronger the binding the higher will be the ionization energy. The smaller the ionization energy the more likely it is that ionization will occur. All elements not just the metals have ionization energy values.
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Cyclic molecules which have the characteristics property called aromaticity. Although aromaticity is not a function of the stability and chemical reactivity, it is a function of the electronic structure and it is the main object of the present essay to define aromaticity with reference to the electronic structure.
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The distribution of electrons in various molecular orbitals in a molecule is called the electronic configuration of molecule. It gives an important information about the molecule. From the electronic configuration of a molecule or a molecular ion it is possible to find out the number of electrons in bonding molecular orbitals and in anti bonding molecular orbitals.
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Cathode ray tube experiment was one of innovative and inspired experiment of J.J Thomson. J.J. Thomson postulating that the rays are negatively charged particles swimming in a set of positive charge, this idea can be an initial idea for understanding of the structure of atom.
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The spectral lines in absorption as well as emission spectroscopy are not exactly sharp lines but appear as broad peaks. The dark spectral lines are called absorption lines because they result from the absorption of light. The emission lines shows that the emission and absorption lines occur at the same wavelength.
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Electromagnetic radiation is a phenomenon of nature that is caused by accelerating charged particles. It is called electromagnetic radiation because a charges particle has an electric filed associated with it. Electromagnetic radiation however is not just the light we see with our eyes. The light we see with our eyes is only a small fraction of what electromagnetic radiation actually is.
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The portion of the electromagnetic spectrum lying between about 400 and 750nm is the visible region. If a substance absorbs a visible light it appears to have a color if not it appears white. Absorption of radiation in the UV and visible regions is associated with changes in the electronic energy of molecules. For this reason UV and visible spectra are sometimes called electronic spectra.
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