Most of the Universe consists of matter and energy.
- Energy is the capacity to do work.
- Matter has mass and occupies space.
All matter is composed of basic elements that cannot be broken down to substances with different chemical or physical properties. Elements are substances consisting of one type of atom, for example Carbon atoms make up diamond, and also graphite.
- Atoms are the smallest particle into which an element can be divided.
- Center of the atom (nucleus) is occupied by proton.
- Each atom has at least one proton.
- Protons have a charge of +1, and a mass of approximately 1 atomic mass unit (amu).
- Elements differ from each other in the number of protons they have, e.g. Hydrogen has 1 proton; Helium has 2.
- The neutron is also located in the atomic nucleus (except in Hydrogen).
- The neutron has no charge, and a mass of slightly over 1 amu.
- The electron is a very small particle located outside the nucleus.
- Because they move at speeds near the speed of light the precise location of electrons is hard to pin down.
- Electrons occupy orbitals, or areas where they have a high statistical probability of occurring.
- The charge on an electron is -1.
- Its mass is negligible (approximately 1800 electrons are needed to equal the mass of one proton).
Atomic number is the number of protons an
atom has. It is characteristic and unique for each element. The atomic mass also
referred to as the atomic weight, is the number of protons and neutrons in an
atom. Atoms of an element that have differing numbers of neutrons (but a
constant atomic number) are termed isotopes. Biochemical pathways can be
deciphered by using isotopic tracers. The age of fossils and artifacts can be
determined by using radioactive isotopes, either directly on the fossil or on
the rocks that surround the fossil. Isotopes are also the source of radiation
used in medical diagnostic and treatment procedures. Some isotopes are
radioisotopes, which spontaneously decay, releasing radioactivity. Other isotopes are stable. Examples of
radioisotopes are Carbon-14 (symbol 14C), and deuterium (also
known as Hydrogen-2; 2H). Stable isotopes are 12C
and 1H.
Electrons move very fast and seem to straddle
the fence separating energy from matter. Albert Einstein developed his famous
E=mc2 equation relating matter and energy over a century ago.
An orbital is an area of space in which an electron will be found 90% of the
time. Each orbital has a characteristic energy state and a characteristic
shape. The s orbital is spherical. Since each orbital can hold
a maximum of two electrons, atomic numbers above 2 must fill the other orbitals.
The px, py, and pz orbitals
are dumbbell shaped, along the x, y, and z axes respectively. Energy levels are
known as electron shell located a certain distance from the nucleus. The major
energy levels into which electrons fit are K, L, M, and N. Sometimes these are
numbered, with electron configurations being: 1s22s22p1,
(where the first shell K is indicated with the number 1, the second shell L
with the number 2, etc.).
Molecule
Molecules are compounds
in which atoms are in definite, fixed ratios. Those atoms are held together
usually by covalent bond, ionic bond or hydrogen bond. The word molecule comes
from the Latin molecula meaning a unit of mass. This name was
to encompass its original meaning of "the smallest unit of a substance
that still retains the properties of that substance." In 1873, James
Maxwell defined atom and molecule: "An atom is a body which cannot be cut
in two; a molecule is the smallest possible portion of a particular
substance." Molecule is actually a group of two or more
atoms that form the smallest identifiable unit into which a pure substance can
be divided and still retain the composition and chemical properties of that substance.
When atoms approach one another closely, the electron clouds interact with each
other and with the nuclei. If this interaction is such that the total energy of
the system is lowered, then the atoms bond together to form a molecule. The
simplest molecules are composed of just two atoms, which may be the same or
different. Oxygen gas (O2), hydrogen gas (H2), and
nitrogen gas (N2), are made up of molecules composed of just two
atoms of oxygen, hydrogen, or nitrogen respectively. Since these substances are
composed of only one kind of atom, they are elements. Carbon monoxide (CO) is a
gas with molecules composed of one atom of carbon and one atom of oxygen and
carbon dioxide (CO2) is a gas with molecules composed of one atom of
carbon and two atoms of oxygen. Water molecules (H2O) are composed
of one atom of oxygen and two atoms of hydrogen. These substances are compounds
because the molecules that make it up have two kinds of atoms. Many molecules,
especially those in living things such as sugar, fat, or protein molecules and
molecules of DNA or RNA, are much larger and more complex.
Molecules are represented by molecular formulas or chemical formulas. This is the simplest way of representing molecules. Chemical formulas only tell us how many atoms of each element are present in a molecule, but structural formulas also give information about how the atoms are connected in space. In structural formulas, we actually draw the covalent bonds connecting atoms. Covalent bonds are the bonds in which electron pairs are shared between atoms, on the other hand, an ionic bond is formed when two oppositely charged ions attract one another.
Chemical bonding is defined as any of the interactions that account for the association of atoms into molecules, ions, crystals, and other stable species that make up the familiar substances of the everyday world. When atoms approach one another, their nuclei and electrons interact and tend to distribute them in space in such a way that the total energy is lower than it would be in any alternative arrangement. If the total energy of a group of atoms is lower than the sum of the energies of the component atoms, they then bond together and the energy lowering is the bonding energy.
Ionic bonds
The word “ionic”, is something that is related to ions. Ions are charged atoms or molecules. Ionic bond, also called electrovalent bond, type of linkage formed from the electrostatic attraction between oppositely charged ions in a chemical. Ionic bonds are formed when the valence electrons of one atom are transferred permanently to another atom. The atom that loses the electrons becomes a positively charged ion or cation, while the one that gains them becomes a negatively charged ion or anion. An ionic bond can be formed after two or more atoms loss or gain electrons to form an ion. Ionic bonds occur between metals, losing electrons, and nonmetals, gaining electrons. Ions with opposite charges will attract one another creating an ionic bond. In an ionic bond, the atoms are bound by attraction of opposite ions. Pure ionic bonding does not happen with real atoms. All bonds have a small amount of covalence. The larger the difference in electro negativity the more ionic the bond is. Impression of two ions (for example [Na]+ and [Cl]−) forming an ionic bond. Electron orbital generally does not overlap, because each of the ions reached the lowest energy state, and the bond is based only (ideally) on the electrostatic interactions between positive and negative ions. Many ionic solids are soluble in water, although not all. It depends on whether there are big enough attractions between the water molecules and the ions to overcome the attractions between the ions themselves. Positive ions are attracted to the ion pairs on water molecules and coordinate bonds may form. Water molecules form hydrogen bonds with negative ions.
A covalent bond consists of the simultaneous
attraction of two nuclei for one or more pairs of electrons. The electrons located between
the two nuclei are bonding electrons. Covalent bonds
occur between identical atoms or between different atoms whose difference in
electro negativity is insufficient to allow transfer of electrons to form
ions. For example the covalent bond in the hydrogen molecule forms from two
hydrogen atoms, each with one electron in a 1s orbital. The two hydrogen atoms
are attracted to the same pair of electrons in the covalent bond. The bond is
represented either as a pair of dots or as a solid line. Each hydrogen
atom acquires a helium-like electron configuration.
Energy is released when the electrons
associated with the two hydrogen atoms form a covalent bond. The process
releases heat; therefore, it is exothermic. The heat
released when one molecule of a compound forms at 298 K is
the standard enthalpy change (ΔH°) for the process. ΔH°
for forming a mole of hydrogen from two hydrogen atoms is − 435 kJ
mole−1. Since energy is released in the reaction, the hydrogen
molecule is more stable than the two hydrogen atoms. The reverse process,
pulling the two bonded hydrogen atoms apart, requires 435 kJ mole−1,
a quantity called the bond strength of the H─H bond.
The two hydrogen nuclei are separated
by a distance called the bond length. This distance
results from a balance between attractive and repulsive forces. There is an
attraction between the nuclei and the bonding electrons, but there is also
repulsion between the two nuclei as well as between the two electrons.
A covalent bond forms between two hydrogen atoms when there are two sets of electrostatic repulsions (nuclear–nuclear and electron–electron, red), but four sets of electrostatic attractions (green). The attractive forces are equal in magnitude, but opposite in sign. Each hydrogen nucleus attracts both electrons. The net result is that the energy of the system decreases when the bond forms. In covalent bonding, the geometry around each atom is determined by valence shell electron pair repulsion theory (VSEPR rules), whereas in ionic materials, the geometry follows maximum packing rules. Thus, a compound can be classified as ionic or covalent based on the geometry of the atoms. It only occurs if the overall energy change for the reaction is favorable (the bonded atoms have a lower energy than the free ones). The larger the energy change the stronger the bond.
A
hydrogen bond is an intermolecular force that forms a special type of dipole-dipole
attraction when a hydrogen atom bonded to a strongly electronegative atom
exists in the vicinity of another electronegative atom with a lone pair of
electrons. Intermolecular forces occur between molecules. Other examples
include ordinary dipole-dipole interactions and dispersion forces. Hydrogen
bonds are generally stronger than ordinary dipole-dipole and dispersion forces,
but weaker than true covalent and ionic bonds. These bonds result from the weak electrical attraction
between the positive end of one molecule and the negative end of another.
Individually these bonds are very weak, although taken in a large enough quantity;
the result is strong enough to hold molecules together or in a
three-dimensional shape.
Types of hydrogen bonds
Intramolecular
hydrogen bonds
Intramolecular hydrogen bonds are
those which occur within one
single molecule. This occurs when two functional groups of a molecule can form
hydrogen bonds with each other. In order for this to happen, both a hydrogen
donor a hydrogen acceptor must be present within one molecule, and they must be
within close proximity of each other in the molecule. For example,
intramolecular hydrogen bonding occurs in ethylene glycol (C2H4(OH)2)
between its two hydroxyl groups due to the molecular geometry.
Intermolecular hydrogen bonds
Intermolecular hydrogen bonds
occur between separate
molecules in a substance. They can occur between any number of like or unlike
molecules as long as hydrogen donors and acceptors are present in positions where
they can interact with one another. For example, intermolecular hydrogen bonds
can occur between NH3 molecules alone, between H2O
molecules alone, or between NH3 and H2O molecules.
Hydrogen Bonding in Nature
Hydrogen bonding plays a crucial role
in many biological processes and can account for many natural phenomena In
addition to being present in water, hydrogen bonding is also important in the
water transport system of plants, secondary and tertiary protein structure, and
DNA base pairing.
Plants
The cohesion-adhesion theory of
transport in vascular plants uses hydrogen bonding to explain many key
components of water movement through the plant's xylem and other vessels.
Within a vessel, water molecules hydrogen bond not only to each other, but also
to the cellulose chain which comprises the wall of plant cells. Since the
vessel is relatively small, the attraction of the water to the cellulose wall
creates a sort of capillary tube that allows for capillary action. This
mechanism allows plants to pull water up into their roots. Furthermore,
hydrogen bonding can create a long chain of water molecules which can overcome
the force of gravity and travel up to the high altitudes of leaves.
Proteins
Hydrogen bonding is present abundantly in the secondary structure of proteins, and also sparingly in tertiary conformation. The secondary structure of a protein involves interactions between neighboring polypeptide backbones which contain Nitrogen-Hydrogen bonded pairs and oxygen atoms. Since both N and O are strongly electronegative, the hydrogen atoms bonded to nitrogen in one polypeptide backbone can hydrogen bond to the oxygen atoms in another chain and visa-versa. Though they are relatively weak, these bonds offer substantial stability to secondary protein structure because they repeat many times and work collectively. In tertiary protein structure, interactions are primarily between functional R groups of a polypeptide chain; one such interaction is called a hydrophobic interaction. These interactions occur because of hydrogen bonding between water molecules around the hydrophobe that further reinforces protein conformation.