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Chapter 2: Molecular Structure and Bonding Bonding Theories

The study of organic chemistry must at some point extend to the molecular level, for the physical and chemical properties of a substance are ultimately explained in terms of the structure and bonding of molecules. This module introduces some basic facts and principles that are needed for a discussion of organic molecules. Four elements, hydrogen, carbon, oxygen and nitrogen, are the major components of most organic compounds.

Consequently, our understanding of organic chemistry must have, as a foundation, an appreciation of the electronic structure and properties of these elements.

The truncated periodic table shown above provides the orbital electronic structure for the first eighteen elements hydrogen through argon. According to the Aufbau principle , the electrons of an atom occupy quantum levels or orbitals starting from the lowest energy level, and proceeding to the highest, with each orbital holding a maximum of two paired electrons opposite spins.

The periodic table shown here is severely truncated. There are, of course, over eighty other elements. Electron shell 1 has the lowest energy and its s-orbital is the first to be filled. Shell 2 has four higher energy orbitals, the 2s-orbital being lower in energy than the three 2p-orbitals. In the third period of the table, the atoms all have a neon-like core of 10 electrons, and shell 3 is occupied progressively with eight electrons, starting with the 3s-orbital.

The highest occupied electron shell is called the valence shell , and the electrons occupying this shell are called valence electrons.

The chemical properties of the elements reflect their electron configurations. For example, helium, neon and argon are exceptionally stable and unreactive monoatomic gases. Helium is unique since its valence shell consists of a single s-orbital. This group of inert or noble gases also includes krypton Kr: 4s 2 , 4p 6 , xenon Xe: 5s 2 , 5p 6 and radon Rn: 6s 2 , 6p 6. In the periodic table above these elements are colored beige.

The halogens F, Cl, Br etc. In their chemical reactions halogen atoms achieve a valence shell octet by capturing or borrowing the eighth electron from another atom or molecule. The alkali metals Li, Na, K etc.

These atoms have only one electron in the valence shell, and on losing this electron arrive at the lower shell valence octet. As a consequence of this electron loss, these elements are commonly encountered as cations positively charged atoms.

The elements in groups 2 through 7 all exhibit characteristic reactivities and bonding patterns that can in large part be rationalized by their electron configurations. It should be noted that hydrogen is unique. Its location in the periodic table should not suggest a kinship to the chemistry of the alkali metals, and its role in the structure and properties of organic compounds is unlike that of any other element.

As noted earlier, the inert gas elements of group 8 exist as monoatomic gases, and do not in general react with other elements. Some dramatic examples of this reactivity are shown in the following equations. Why do the atoms of many elements interact with each other and with other elements to give stable molecules?

In addressing this question it is instructive to begin with a very simple model for the attraction or bonding of atoms to each other, and then progress to more sophisticated explanations.

When sodium is burned in a chlorine atmosphere, it produces the compound sodium chloride. Sodium chloride is an ionic compound, and the crystalline solid has the structure shown on the right. Transfer of the lone 3s electron of a sodium atom to the half-filled 3p orbital of a chlorine atom generates a sodium cation neon valence shell and a chloride anion argon valence shell.

Electrostatic attraction results in these oppositely charged ions packing together in a lattice. The attractive forces holding the ions in place can be referred to as ionic bonds. The other three reactions shown above give products that are very different from sodium chloride.

Water is a liquid at room temperature; carbon dioxide and carbon tetrafluoride are gases. None of these compounds is composed of ions. A different attractive interaction between atoms, called covalent bonding, is involved here. Covalent bonding occurs by a sharing of valence electrons, rather than an outright electron transfer. Examples of covalent bonding shown below include hydrogen, fluorine, carbon dioxide and carbon tetrafluoride.

These illustrations use a simple Bohr notation, with valence electrons designated by colored dots. Note that in the first case both hydrogen atoms achieve a helium-like pair of 1s-electrons by sharing. In the other examples carbon, oxygen and fluorine achieve neon-like valence octets by a similar sharing of electron pairs.

Carbon dioxide is notable because it is a case in which two pairs of electrons four in all are shared by the same two atoms. This is an example of a double covalent bond.

Non-bonding valence electrons are shown as dots. These formulas are derived from the graphic notations suggested by A. Couper and A.

Some examples of such structural formulas are given in the following table. If the electron pairs in covalent bonds were donated and shared absolutely evenly there would be no fixed local charges within a molecule. A dipole exists when the centers of positive and negative charge distribution do not coincide.

A large local charge separation usually results when a shared electron pair is donated unilaterally. In the formula for ozone the central oxygen atom has three bonds and a full positive charge while the right hand oxygen has a single bond and is negatively charged. The overall charge of the ozone molecule is therefore zero.

Similarly, nitromethane has a positive-charged nitrogen and a negative-charged oxygen, the total molecular charge again being zero. Finally, azide anion has two negative-charged nitrogens and one positive-charged nitrogen, the total charge being minus one.

In general, for covalently bonded atoms having valence shell electron octets , if the number of covalent bonds to an atom is greater than its normal valence it will carry a positive charge.

If the number of covalent bonds to an atom is less than its normal valence it will carry a negative charge. The formal charge on an atom may also be calculated by the following formula:. Because of their differing nuclear charges, and as a result of shielding by inner electron shells, the different atoms of the periodic table have different affinities for nearby electrons.

The ability of an element to attract or hold onto electrons is called electronegativity. A rough quantitative scale of electronegativity values was established by Linus Pauling, and some of these are given in the table to the right.

A larger number on this scale signifies a greater affinity for electrons. Fluorine has the greatest electronegativity of all the elements, and the heavier alkali metals such as potassium, rubidium and cesium have the lowest electronegativities. It should be noted that carbon is about in the middle of the electronegativity range, and is slightly more electronegative than hydrogen.

When two different atoms are bonded covalently, the shared electrons are attracted to the more electronegative atom of the bond, resulting in a shift of electron density toward the more electronegative atom. Such a covalent bond is polar , and will have a dipole one end is positive and the other end negative. The degree of polarity and the magnitude of the bond dipole will be proportional to the difference in electronegativity of the bonded atoms.

Thus a O—H bond is more polar than a C—H bond, with the hydrogen atom of the former being more positive than the hydrogen bonded to carbon. Likewise, C—Cl and C—Li bonds are both polar, but the carbon end is positive in the former and negative in the latter. Although there is a small electronegativity difference between carbon and hydrogen, the C—H bond is regarded as weakly polar at best, and hydrocarbons in general are considered to be non-polar compounds.

The shift of electron density in a covalent bond toward the more electronegative atom or group can be observed in several ways. For bonds to hydrogen, acidity is one criterion. If the bonding electron pair moves away from the hydrogen nucleus the proton will be more easily transferred to a base it will be more acidic.

A comparison of the acidities of methane, water and hydrofluoric acid is instructive. Methane is essentially non-acidic, since the C—H bond is nearly non-polar. As noted above, the O—H bond of water is polar, and it is at least 25 powers of ten more acidic than methane. H—F is over 12 powers of ten more acidic than water as a consequence of the greater electronegativity difference in its atoms.

Electronegativity differences may be transmitted through connecting covalent bonds by an inductive effect. Replacing one of the hydrogens of water by a more electronegative atom increases the acidity of the remaining O—H bond. Thus hydrogen peroxide, HO—O— H , is ten thousand times more acidic than water, and hypochlorous acid, Cl—O— H is one hundred million times more acidic.

This inductive transfer of polarity tapers off as the number of transmitting bonds increases, and the presence of more than one highly electronegative atom has a cumulative effect. Excellent physical evidence for the inductive effect is found in the influence of electronegative atoms on the NMR chemical shifts of nearby hydrogen atoms. Functional groups are atoms or small groups of atoms two to four that exhibit a characteristic reactivity when treated with certain reagents.

A particular functional group will almost always display its characteristic chemical behavior when it is present in a compound. Because of their importance in understanding organic chemistry, functional groups have characteristic names that often carry over in the naming of individual compounds incorporating specific groups.

In the following table the atoms of each functional group are colored red and the characteristic IUPAC nomenclature suffix that denotes some but not all functional groups is also colored.

Organic Chemistry With a Biological Emphasis. Electronic Configurations Four elements, hydrogen, carbon, oxygen and nitrogen, are the major components of most organic compounds. Ionic Bonding When sodium is burned in a chlorine atmosphere, it produces the compound sodium chloride. Covalent Bonding The other three reactions shown above give products that are very different from sodium chloride. Charge Distribution If the electron pairs in covalent bonds were donated and shared absolutely evenly there would be no fixed local charges within a molecule.

Formal Charges A large local charge separation usually results when a shared electron pair is donated unilaterally. Polar Covalent Bonds H 2. Functional Groups Functional groups are atoms or small groups of atoms two to four that exhibit a characteristic reactivity when treated with certain reagents.

Functional Groups with Multiple Bonds to Heteroatoms.

Unit: Chemical bonding and molecular structure

Part 1 What is a chemical bond? Ionic Bond Normally between a metal and a non-metal: They exchange electrons and become ions charged atoms which attract each other by electrostatic force. A pair of ions does not stay alone but form crystals 4. Covalent Bond Two non-metals share valence electrons: Remark: Transition metals can form covalent bonds also! Polar Covalent Bond Two non-metals share electrons unevenly because of electronegativity difference.

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Click the button below to download the full Chemistry Form 2 Notes pdf document, with all the topics. They are soluble in polar solvents like water, ethanol and acetone propanone. They are insoluble in non-polar organic solvents like tetrachloromethane, benzene and hexane. Diagram: Illustration of Van der Waals forces. Sodium and magnesium chlorides. Diagram: Formation of a dimer in aluminium chloride. Phosphorus III chloride and phosphorus V chloride.

molecules;. • explain the concept of hydrogen bond. CHEMICAL BONDING AND. MOLECULAR STRUCTURE. Matter is made up of one or different type of.

Chapter 2: Molecular Structure and Bonding Bonding Theories

Chemical bonding describes a variety of interactions that hold atoms together in chemical compounds. Chemical bonds are the connections between atoms in a molecule. These bonds include both strong intramolecular interactions, such as covalent and ionic bonds. They are related to weaker intermolecular forces, such as dipole-dipole interactions, the London dispersion forces, and hydrogen bonding.

Structure and Bonding covers introductory atomic and molecular theory as given in first and second year undergraduate courses at university level. This book explains in non-mathematical terms where possible, the factors that govern covalent bond formation, the lengths and strengths of bonds and molecular shapes. Throughout the book, theoretical concepts and experimental evidence are integrated. An introductory chapter summarizes the principles on which the Periodic Table is established, and describes the periodicity of various atomic properties which are relevant to chemical bonding. Symmetry and group theory are introduced to serve as the basis of all molecular orbital treatments of molecules.

Chapter 2: Molecular Structure and Bonding Bonding Theories

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3 Response
  1. Sinforoso V.

    A chemical bond is a lasting attraction between atoms , ions or molecules that enables the formation of chemical compounds.

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