Video: Elements and Compounds

Not all elements have their outermost shells filled with electrons. To become more
stable, they form molecules, two or more atoms chemically bonded together.

For instance, elemental oxygen has six valence electrons, and needs two more. It could
join join with another atom of oxygen to form one molecule, or find two hydrogens with
one electron each to create H2O, water, which is a compound, an atomic combination
of more than one type of element.
Pure substances consist of only one type of matter. A pure substance can be an
element or a compound. An element consists of only one type of atom, while a
compound consists of two or more types of atoms held together by a chemical bond.

Elements

Elements are classified as atomic or molecular based on the nature of their basic units.
They are unique forms of matter with specific chemical and physical properties that
cannot break down into smaller substances by ordinary chemical reactions. There are
118 elements, but only 98 occur naturally. The remaining elements are unstable and
require scientists to synthesize them in laboratories. The four elements common to all
living organisms are oxygen (O), carbon (C), hydrogen (H), and nitrogen (N). In the
nonliving world, elements are found in different proportions, and some elements
common to living organisms are relatively rare on the earth as a whole. For example,
the atmosphere is rich in nitrogen and oxygen but contains little carbon and hydrogen,
while the earth's crust has little nitrogen and carbon, although it contains oxygen and a
small amount of hydrogen. In spite of their differences in abundance, all elements and
the chemical reactions between them obey the same chemical and physical laws
regardless of whether they are a part of the living or nonliving world.

Compounds
Compounds are pure substances composed of two or more elements in fixed, definite
proportions. Compounds are classified as molecular (covalent) or ionic based on the
bonds present in them.

Molecular compounds (or covalent compounds) result when two or more different
nonmetal atoms share electrons to form covalent bonds. The basic units of molecular
compounds are discrete neutral molecules composed of different constituent atoms. For
example, methanol contains CH3OH molecules as base units, consisting of one carbon
atom, one oxygen atom, and four hydrogen atoms, all of which are covalently
connected.

A compound that contains ions and is held together by ionic bonds is called an ionic
compound. When an element composed of atoms that readily lose electrons (a metal)
reacts with an element composed of atoms that readily gain electrons (a nonmetal), a
transfer of electrons usually occurs, producing ions. The compound formed by this
transfer is stabilized by the electrostatic attractions (ionic bonds) between the ions of
opposite charge present in the compound. For example, when each sodium atom gives
up one electron to form a sodium cation (Na+) and each chlorine atom accepts one
electron to form a chloride anion (Cl−), the resulting compound NaCl is composed of
sodium ions and chloride ions in the ratio of one Na+ ion for each Cl− ion.

This text is adapted from Openstax, Biology 2e, Section 2.1: Atoms, Isotopes, Ions and
Molecules: The Building Blocks and Openstax, Chemistry 2e, Section 2.6: Molecular
and Ionic Compounds.

Reference

Clark, M. A., Douglas, M., Choi, J. Section 2.1: Atoms, Isotopes, Ions and Molecules:
The Building Blocks. In Biology 2e. OpenStax. Houston, TX (2018).
Clark, M. A., Douglas, M., Choi, J. Section 2.6: Molecular and Ionic Compounds. In
Chemistry 2e. OpenStax. Houston, TX (2018).

Video: Molecular Shapes

The same molecule can be depicted in a number of structural arrangements to highlight
specific functions.

The most common model is called a Lewis Dot structure, a 2D representation which
notes atoms with their chemical symbol and electron bonds between them as lines.
Dots represent any unshared pairs of electrons.

Bond line structures are simplified by removing carbons and hydrogens. Their presence
is implied at the angles of the bonds. It can be helpful in organic chemistry, where many
molecules have long carbon backbones or ring structures.<

A more accurate arrangement is the ball and stick model, a 3D interpretation that
highlights atoms as colored spheres and their bonds using sticks. In this case, the bond
angles and their relative positions in space are easily visualized. Similarly, in space-
filled models, the color coding of atoms is maintained, but the 3D size of individual
atoms now represents their relative atomic radii.

The bonds between atoms are indicated by closeness of one molecule to one another.
Molecules have characteristic shapes that are crucial for their function. The
arrangement of various electron groups around the central atom dictates their molecular
geometry. Electron pairs in the valence shell of a central atom will adopt an
arrangement that minimizes repulsions between the electron pairs by maximizing the
distance between them. The valence electrons form either bonding pairs, located
primarily between bonded atoms, or lone pairs.

Two regions of electron density in a diatomic molecule are oriented linearly on opposite
sides of the central atom to minimize repulsions, and three electron groups are
arranged in a trigonal planar geometry. Four electron groups form a tetrahedron, five
electron groups have trigonal bipyramidal geometry, and six groups are oriented
octahedrally.
It is important to note that the electron-pair geometry around a central atom is not
always the same as its molecular structure. The electron-pair geometry describes all the
regions where electrons are located in a molecule, in bonds and lone pairs. The
molecular structure describes the location of the atoms in a molecule, not the electrons.
This means that the electron-pair geometry is the same as the molecular structure only
when there are no lone electron pairs around the central atom.

A lone pair of electrons occupies a larger space than a bonding pair because a lone pair
is bound to only one nucleus, but two nuclei share a bonding electron group. Because
of this, lone pair–lone pair repulsions are greater than lone pair–bonding pair and
bonding pair–bonding pair repulsions.

Part of this text is adapted from Openstax, Chemistry 2e, Section 7.6: Molecular
Structure and Polarity.

Reference:

Flowers, P., Theopold, K., Langley, R., Robinson, W. R., Clark, M. A., Douglas, M.,
Choi, J. Section 7.6: Molecular Structures. In Chemistry 2e. OpenStax. Houston, TX
(2019).

Video: Carbon Skeleton

Organic compounds contain a structural backbone of carbon atoms, referred to as the
carbon skeleton. The element can form up to four bonds, which contributes to its
flexibility.

For instance, methane with only one carbon and single bonds is the simplest
hydrocarbon.

As more carbons are added, the chain lengthens forming new molecules.

With each addition, the skeleton can form branched side chains as is the case in
isohexane, or continue being straight and unbranched, like in hexane. Furthermore,
these structures can contain double bonds at varying positions, forming hexenes and
even be arranged in rings, for example, in cyclohexene.
Life on Earth is carbon-based, as all macromolecules that make up living organisms
contain carbon atoms. All organic compounds have a carbon backbone. Each carbon
atom is tetravalent and can bond with four other atoms, making it an extraordinarily
flexible component of biological molecules. Because carbon’s valence electrons are
stable, it rarely becomes an ion. As the carbon chain increases in length, structural
modifications such as ring structures, double bonds, and branching side chains become
possible.

Carbon-carbon bonds form the basis of the carbon skeleton. Hydrogen atoms readily
bond to the carbon atom. Molecules that contain only hydrogen and carbon are called
hydrocarbons. Hydrocarbons usually form long chains or have branches protruding at
various points. Changing the number of bonds changes the properties of the molecule.
For example, a fatty acid with a long hydrocarbon tail with one or more double bonds
will behave differently than a fatty acid with no double bonds.

Isomers

Molecules having the same chemical formula but different structural arrangements are
called isomers. One example of isomers can be seen in two different molecules that
share the chemical formula C6H14. Hexane has a single linear chain of carbon atoms,
while isohexane has a branch point on the second carbon atom. Some isomers are
mirror images of each other, which are called enantiomers.

Functional Groups Build on Carbon Skeletons

The unique properties of biological molecules are conferred by functional groups
bonded to the carbon skeleton, such as amino (–NH2) or methyl groups (–CH3).
Functional groups can alter the structural and chemical properties of the molecule. The
properties of functional groups influence many fields of study, such as synthetic drug
design.

Video: Covalent Bond

A covalent bond is formed when two atoms share valence electrons, completing each of
their outer shells to create one stable molecule with a single bond.
The number of covalent bonds can increase depending on how many electrons are
shared. For instance, when two oxygen atoms, each with six valence electrons, share
two pairs of electrons, a double bond is formed. These bonds are nonpolar covalent,
because the electrons are shared evenly between the atoms. They have the same
attraction for the electrons in the covalent bonds. That is to say, the atoms have the
same electronegativity. The more strongly an atom attracts the electrons of a covalent
bond, the more electronegative the atom is.

If two different elements have similar electronegativity, like carbon and hydrogen, they
will also share electrons equally in a nonpolar covalent bond. But when two different
elements with very different electronegativity are bound together, they have unequal
sharing of electrons, a polar covalent bond.

For example, water has one strong oxygen and two weak hydrogens. The oxygen atom
holds all of the negatively charged electrons most of the time, giving it a partial negative
charge. This situation leaves the hydrogens with a partial positive charge, making the
compound polar.
Overview
When two atoms share electrons to complete their valence shells they create a covalent
bond. An atom’s electronegativity—the force with which shared electrons are pulled
towards an atom—determines how the electrons are shared. Molecules formed with
covalent bonds can be either polar or nonpolar. Atoms with similar electronegativities
form nonpolar covalent bonds; the electrons are shared equally. Atoms with different
electronegativities share electrons unequally, creating polar bonds.

A Covalent Bond Is Formed by Two Shared Electrons

The number of covalent bonds that an atom can form is dictated by how many valence
electrons it has. Oxygen, for example, has six out of eight possible valence electrons,
meaning that each oxygen atom needs two more electrons to become stable. Oxygen
can form single bonds with two other atoms, as it does when it forms water with two
hydrogen atoms (chemical formula H2O). Oxygen can also form a double bond with just
one other atom that also needs two more electrons to complete its octet (e.g., another
oxygen atom). Carbon has four valence electrons and therefore can form four covalent
bonds, as it does in methane (CH4).

When a covalent bond is made, both atoms share a pair of electrons in a hybrid orbital
that differs in shape from a normal orbital. The electrons participating in the bond thus
orbit in a modified path around the nuclei of both atoms. Covalent bonds are strong and,
once formed, cannot be broken by physical forces.

Electronegativity Determines Whether a Molecule Is Polar or Nonpolar

Electronegativity is the tendency of an atom to attract electrons in a bond. The most
electronegative atom is fluorine. Starting with fluorine at the top right corner of the
periodic table (omitting the noble gases in the rightmost column), the electronegativity of
atoms tends to decrease with diagonal leftward movement down the periodic table,
such that atoms with the lowest electronegativities are at the bottom left corner (e.g.,
francium, or Fr). If atoms have extremely different electronegativities, they will likely
form ions instead of covalent bonds. However, for atoms that form covalent bonds with
one another, their electronegativity values determine whether the bond will be polar or
nonpolar.

A nonpolar bond is one in which the electrons are shared equally, and there is no
charge across the molecule. A polar bond, by contrast, occurs when one atom is more
electronegative than another and pulls the electrons toward it. Polar bonds have a
partial negative charge on one side and a partial positive charge on the other, which is
important because it causes polar molecules to behave differently than nonpolar ones.

Polar molecules are hydrophilic because their partial charges attract them to other
charged molecules, which also means they are soluble in water. Nonpolar molecules—
those containing long stretches of hydrocarbons, such as fats—are said to be
hydrophobic. Unlike polar molecules, nonpolar molecules will not dissolve in water.
Cells are often surrounded by fluid and have cytoplasms that contain water. Thus, the
way a molecule interacts with water and other charged molecules impact how it is
transported and used by cells.

Video: Ionic Bonds

An ionic bond is the noncovalent attraction that holds two charged atoms, ions together.
Like the cation of potassium, potassium plus, and the anion of chloride, chlorine
[Link] this case a valence electron from potassium was given to chlorine to create
more stable atoms.

With both of their outer shells completely filled. The strength of the bond is dependent
upon the environment.
If surrounded by oxygen the bond is difficult to break, but in an aqueous solution the
compound dissolves into its ionic components.
Overview
When atoms gain or lose electrons to achieve a more stable electron configuration they
form ions. Ionic bonds are electrostatic attractions between ions with opposite charges.
Ionic compounds are rigid and brittle when solid and may dissociate into their
constituent ions in water. Covalent compounds, by contrast, remain intact unless a
chemical reaction breaks them.

Opposing Charges Hold Ions Together in Ionic Compounds

Ionic bonds are reversible electrostatic interactions between ions with opposing
charges. Elements that are the most reactive (i.e., have a higher tendency to undergo
chemical reactions) include those that only have one valence electron, (e.g., potassium)
and those that need one more valence electron (e.g., chlorine).

Ions that lose electrons have a positive charge and are referred to as cations. Ions that
gain electrons have a negative charge and are called anions. Cations and anions
combine in ratios that result in a net charge of 0 for the compound they form. For
example, the compound potassium chloride (KCl) contains one chloride ion for each
potassium ion, because the charge of potassium is +1 and the charge of chloride is -1.
The compound magnesium chloride (MgCl2) contains two chloride ions for each
magnesium ion because magnesium’s charge is +2.

Ions Can Dissociate from One Another in Water

The electrostatic forces holding ionic compounds together are strong when the
compounds are in solid form. Since the melting points of ionic compounds tend to be
very high, they are generally found as solids on the Earth’s surface. Howeverionic
bonds are not as strong as covalent bondsbecause the ions can be pulled apartor
dissolvedin a chemical reaction liquids like water. Ions dissolved in water are said to be
in a chemical reaction, and many ions are capable of conducting electric currents when
in this form.

Electrolytes Are Important for Biological Systems

Electrolytes are ions that can conduct electricity when dissolved in water. In biological
systems, electrolytes are essential for osmotic regulation—the balance of water across
cellular membranes. Electrolytes also contribute to critical biological processes that rely
upon electrical charges across the cell membrane, such as muscle contractions and
nerve impulses. Common biological electrolytes include the calcium ion (Ca2+), the
sodium ion (Na+), the magnesium ion (Mg2+), the potassium ion (K+), the phosphate
ion (PO43-) and the chloride ion (Cl-).

Electrolyte imbalances can cause severe physical symptoms and even death. One of
the most commonly-encountered electrolyte imbalances is hyponatremia, insufficient
sodium levels in the blood. Hyponatremia can be a symptom of another medical
condition or caused by ingesting too much water without adequately replacing sodium.
Treatments for this serious condition aim to restore the balance of sodium in the body
so that the brain, heart, and other organs can function properly.

Video: Hydrogen Bonds

Hydrogen bonds are very weak attractions between one atom with a partial negative
charge, an electronegative atom like oxygen and a hydrogen atom with a partial positive
charge.

While these bonds, most commonly found between H2O molecules in water, are weak
individually, cumulatively they are very strong.
Hydrogen bonds are weak attractions between atoms that have formed other chemical
bonds. One of these atoms is electronegative, like oxygen, and has a partial negative
charge. The other is a hydrogen atom that has bonded with another electronegative
atom and has a partial positive charge.

Hydrogen Bonds Control the World!

Because hydrogen has very weak electronegativity when it binds with a strongly
electronegative atom, such as oxygen or nitrogen, electrons in the bond are unequally
shared. The other atom pulls the electrons to itself, sharing them with the hydrogen
atom a smaller amount of the time. This gives the hydrogen atom a partial positive
charge, causing it to be attracted to atoms with a partial negative charge. The
cumulative effect of these weak attractionsis life-altering, endowing water with high heat
capacity, high heat of vaporization, ability to dissolve polar molecules, adhesion,
cohesion, and strong surface tension.

Video: Van der Waals Interactions

Van der Walls interactions are nonspecific attractions created when one atom comes
close enough to another one to disturb its electrons, inducing temporary dipoles that are
cohesive.

Such activity contributes to the three-dimensional structure of DNA.

Atoms and molecules interact with each other through intermolecular forces. These
electrostatic forces arise from attractive or repulsive interactions between particles with
permanent, partial, or temporary charges. The intermolecular forces between neutral
atoms and molecules are ion–dipole, dipole–dipole, and dispersion forces, collectively
known as van der Waals forces.

Polar molecules have a partial positive charge on one end and a partial negative charge
on the other end of the molecule, creating a dipole. In a polar molecule like water, the
more electronegative oxygen atom bears the partial negative charge, and the less
electronegative hydrogen atom carries the partial positive charge. The water molecules
are attracted to each other because of the positive end of one water molecule and the
negative end of another. This attractive force is called a dipole–dipole attraction.

An ion–dipole force is the electrostatic attraction between an ion and a dipole. These
forces are common in solutions and play an important role in the dissolution of ionic
compounds in water. When an ionic compound like KCl is added to a polar solvent like
water, the ions in the solid separate and disperse uniformly. Ion–dipole forces attract the
positive end of the polar water molecules to the negative chloride ions at the surface of
the solid, and they attract the negative ends to the positive potassium ions. The water
molecules surround individual K+ and Cl- ions, reducing the strong interionic forces that
bind them together in a solid and dissolving them. The strength of ion–dipole
interactions is directly proportional to i) the charge on the ion and ii) the magnitude of
the dipole of polar molecules.

Dispersion forces are present in all condensed phases, regardless of the nature of the
atoms or molecules composing the substance. These attractive forces are also called
London dispersion forces in honor of German-born American physicist Fritz London who
first explained them in 1928. The electrons of an atom or molecule are in constant
motion at any moment in time, and an atom or molecule can develop a temporary,
instantaneous dipole if its electrons are distributed asymmetrically. The presence of this
dipole can, in turn, distort the electrons of a neighboring atom or molecule, producing an
induced dipole. These rapidly fluctuating, temporary dipoles result in a relatively weak
electrostatic attraction between the species—a so-called dispersion force. Dispersion
forces are relatively weak and become significant only when the molecules come very
close. Larger and heavier atoms and molecules exhibit stronger dispersion forces than
smaller and lighter ones.

This text is adapted from Openstax, Chemistry 2e, Chapter 10: Liquids and Solids.

Video: States of Water

Many substances, like water, can be found in one of three states, solid, liquid, or gas,
depending on the relationship between the molecular attractive forces and the kinetic
energy.

For example, the solid phase, ice, occurs when the temperature drops to 0 degrees
Celsius or lower, reducing the kinetic energy. Hydrogen bonds form between
molecules, creating a lattice structure.

By increasing the temperature, kinetic energy is reintroduced and many of the bonds
can now separate, the melting point between solids and liquids. In this phase molecules
are constantly forming and breaking bonds with each other.

Raising the temperature to 100 degrees Celsius or higher causes vaporization of water,
which disrupts all of the bonds, allowing free movement in a gaseous state. If the
temperature drops, the gas can return to a liquid, a process known as condensation.

Gasses can also phase directly into a solid, skipping the liquid state in a process called
deposition, which is how snowflakes are created. The reverse, sublimation, describes
how solids transition directly into their gaseous state, as is the case in the freeze drying
of many foods.
Water exists in any one of the three classical states: solid (ice), liquid (water), and gas
(steam or water vapor). The state of water depends on i) the intermolecular forces that
draw molecules together and ii) the kinetic energy that leads to movements that pull
them apart.

Water freezes when the intermolecular forces are greater than the kinetic energy. Unlike
most other substances, water is less dense in its solid state than in its liquid state. This
is because each water molecule can form hydrogen bonds with four molecules, forming
a tetrahedral structure. This property allows ice to float on liquid water. Without the
floating ice, bodies of water would freeze from the bottom up, killing aquatic life.

When kinetic energy is applied to ice in the form of heat, ice melts into liquid water. In
this state, hydrogen bonds between water molecules constantly break and form again.
When ice melts, the temperature of the water remains at the melting point until all the
water is liquid. Only then will the water temperature increase.

As kinetic energy exceeds intermolecular forces, water becomes vapor. The process of
generating steam from liquid water is called vaporization. Increases in kinetic energy
can occur within the sample, as with boiling, or at the surface when water evaporates.
Sublimation is the process by which a gas is generated directly from a solid without first
going through a liquid phase. This transition depends on low atmospheric pressure,
augmenting the effects of kinetic energy.

When kinetic energy decreases, steam can transition into a liquid in a process called
condensation or directly into a solid in a process called deposition. Condensation leads
to for rain and deposition for snow.

In the search for other biocompatible planets, the presence of water is a crucial feature,
especially in liquid form, because life on Earth began in water. Enceladus is an ice-
covered moon of Saturn that has water plumes or geysers on its southern pole. This
initially generated much debate over whether Enceladus had liquid water under the ice,
as the plumes were found to carry both steam and ice. However, the moon's orbit
around Saturn and other clues suggest the presence of a vast liquid ocean in
Enceladus, making it potentially hospitable for life.