Atoms and Elements

• Chemical Activity

• Ions

Chemical Composition of the Earth’s Crust

Crystallinity• The Silicon-Oxygen Tetrahedron  

Minerals

• Crystalline Solids

• Natural and Inorganic Substances

• Definite Chemical Composition

• The Important Minerals

Rocks versus Minerals

Feldspar: NaAlSi3O8 - KAlSi3O8

Quartz: SiO2

Biotite: KMg3AlSi3O10(OH)2 - KFe3AlSi3O10(OH)2

Granite rock type

Rock: an aggregate of one or more minerals; in this case there are three minerals present.

Mineral Structures and Atoms

From: Plummer et al.

Mineral: A naturally occurring inorganic element or compound having orderly internal structure and characteristic chemical composition, crystal form, and physical properties.

1 angstrom = 1.0 × 10-10 meters

Atomic Structure and the Composition of Matter

• The atom is a basic building block of minerals.

• Matter is a special form of energy; it has mass and occupies space. Neither matter nor energy may be created or destroyed - they may only be converted from one form to the other.

• Energy is the ability to do work and it occurs in a number of forms, including:

– Potential; Kinetic; Electrical; Heat; Chemical; Nuclear

– Radiant (the only form in which there is an absence of matter)

• Atoms are the smallest division of matter that retain the characteristics of the elements.

Elements and the Periodic Table

• Approximately 300 different kinds of atoms that are capable of independent, prolonged existence. These are called nuclides.

• If nuclides are grouped by chemical characteristics, about 100 sets result and these are referred to as elements.

• The modern Periodic Table was devised in 1869 by Julius Meyer and Dmitri Mendeleev. It organizes the elements into groups and families with similar chemical and physical properties.

Periodic Table

Groups or Families

Periods

Crustal Abundance

Crustal volume:<1% of EarthMantle volume: 83% of EarthCore volume: 16% of Earth

Crustal mass:<1% of EarthMantle mass: 68% of EarthCore mass: 31% of Earth

What element is most abundant for the entire Earth?

Atomic Particles: Basics

• Atoms are composed of electrons and two large nuclear particles called protons and neutrons.

• Protons and neutrons are approximately equal in mass and are ~1800 times more massive than the electron. Both nuclear particles are composed of quarks, smaller fundamental particles.

• Protons have unit positive charge (+1), while electrons have unit negative charge (-1). Neutrons carry no charge.

• Atoms are electrically neutral and thus the number of electrons must equal the number of protons.

Basic Terminology

• Atomic number (Z): The atomic number represents the number of unit positive charges on the nucleus and is equal to the number of protons within the nucleus, since each proton carries unit positive charge. In electrically neutral atoms, it also represents the number of electrons, which carry unit negative charge.

• Mass number (A): The mass number is equal to the total number of nucleons, which is the sum of the number of protons and neutrons. A does not equal the total mass of the atom; rather, it represents a whole number approximation of the mass, as expressed in amu.

• The number of neutrons is simply defined as the A - Z.

Isotopes and Isobars• A specific type of atom is designated by using its chemical symbol,

which is an abbreviation of its name in German, Latin, or English, with the A, the mass number, placed in the upper left and Z, the atomic number, placed in the lower left corner. For example, 23Na11, has a mass number of 23 and an atomic number of 11.

• Isotopes are atoms of the same element that differ in mass. For example, 87Sr and 86Sr or 238U and 235U. Isotopes have similar chemical characteristics and are studied using a mass spectrograph or spectrometer. Most elements have at least two naturally occurring isotopes.

• Isobars are nuclides that have the same mass number but different atomic numbers. For example, 36S and 36Ar are isobars; they both contain a total of 36 nucleons (protons plus neutrons), but the sulfur isotope has 16 protons and 20 neutrons, while the argon isotope has 18 protons and 18 neutrons. Isobars do not have similar chemical characteristics!

Atomic Weight

• Atomic weight is the weighted average of the atomic masses of the naturally occurring isotopes. For example, a natural sample of the element chlorine contains a mixture of 75.53% 35Cl and 24.47% 37Cl. Thus the atomic weight is obtained by multiplying the mass of each isotope (in amu) times its fractional abundance:

• 0.7553 (34.97 amu) + 0.2447 (36.95 amu) = 35.45 amu

Atomic Models

• Bohr Model– Electron shells

• Quantum Mechanics– Orbitals– Afbau Filling Order– Quantum numbers and superposition of states

Bohr Atomic Model

The Bohr model for the atom envisioned these electrons in stable orbits of specified radius and energy, where we could exactly pinpoint the position of any individual electron. Each energy level was permitted to have a specified number of electrons, and was called a shell. We know now that this simple view is not correct; it is impossible to exactly determine the position

of an electron in space.

Oxygen Atom

The Quantum Mechanical View• Using the theory of quantum or wave mechanics we can calculate the

probabilities of various electron configurations, and thus show that specified regions near the nucleus have higher probabilities for finding an electron than others. Each electron does, however, have a specific energy. Must solve wave equation for specific states!

• The combination of the energy and probability gives rise to the current understanding for electron distributions, which are referred to as electron orbitals; these orbitals are referred to as s (sharp), p (principal), d (diffuse), and f (fundamental).

• With increasing atomic number, each new element has an additional electron also added to it extra-nuclear cloud. From theory and experiment, we know that these electrons are added in a systematic fashion, with the lowest energy orbitals being filled first.

• This process is called aufbau filling (1s -> 2s -> 2p -> 3s -> 3p -> 4s -> 3d -> 4p -> 5s, etc. ). Combine with Pauli exclusion principle to yield filling order.

Quantum Numbers

• n = principal• l = orbital (0 -> (n-1))

• ml = magnetic (± l)

• ms = spin (±1/2)– l = 0 -> s orbital

= 1 -> p orbital

= 2 -> d orbital

= 3 -> f orbitaln = 6; l = 4; m = 1

From: http://www.daugerresearch.com/orbitals/

Animated Orbital Simulations

| 4, 3, 3 | and | 4, 1, 0 | | 3, 2, 2 | and | 3, 1, -1 |

Superposition of States

From: http://www.daugerresearch.com/orbitals/

Water, Ice and Snow

• Most important substance on Earth

• Essential for biological life as we know it

• Unique volumetric property

• Molecular symmetry and its relationship to crystal morphology

• Crystal growth and its effect on crystal morphology

Water Atomic Structure

Chemical Formula: H2O

Snowflake Morphology

1 - 5 mm

From: http://www.its.caltech.edu/~atomic/snowcrystals

Hexagonal Symmetry

Oddly, ice is less dense than liquid water, hence it floats and lakes freeze from the top down!

Snowflake Growth

From: http://www.its.caltech.edu/~atomic/snowcrystals

LT-SEM Images of Snow Crystals

Compounds and Bonding • Chemical compounds• Ionic bonding

– NaCl as a type example– Electron transfer and shell completion

• Covalent bonding– Diamond - pure C example– Electron sharing

• Silicon Tetrahedron– Structure (strong sp3 covalent bonds)– Building block of silicate minerals

Halite Atomic Structure

Chemical Formula: NaCl

Note Cubic Symmetry and Closest Packing

Chemical compound: Two or more elements joined together bya chemical bond. Most minerals are composed of at least twoelements.

Outer Shell Filling

1s2

1s22s22p6

Ionic Bonding and Electron Exchange

1s22s22p63s1

1s22s22p63s23p5

+1e-

17p+ + 18e- = -1

11p+ + 10e- = +1

Ionic Bonding:Electron Transfer

Cations (+) are always smaller than the neutral atom;Anions (-) are always larger than the neutral atom.

Covalent Bonding: Electron Sharing

Diamond Example - Pure Carbon in complex 3D network

Silicon Tetrahedron: SiO4 (net -4 charge)

1.30 Å

0.34 Å

1 angstrom = 1.0 × 10-10 meters

Bridging Oxygen (BO)

Silicate Mineral Structures I

Silcon Tetrahedron:strong sp3 hybrid covalent bonds - 50% ionic; 50% covalent character

These structures are thebasic building blocks ofsilicate minerals.

Silicate structures may beCharacterized by the the number ofBO’s per Si. The higher the BO/SiRatio, the more complex andpolymerized the structure.

Silicate Structures

Olivine Structure: (Mg,Fe)2SiO4

Models of Chain Silicates: Pyroxenes

A

B

OxygenPositive ion

etc. etc.

etc. etc.

etc.

etc.

Silicon+

2+

2+

+

2+

2+

2+

2

2

+

2+

2+

+

2+

2+

2+

2

2

Oxygen

etc. etc.etc.

Silicon

etc. etc.etc.

Silicon

Oxygen

etc. etc.etc.

Silicon

Positive ion

etc. etc.etc.

2+

2+

+

2+

2+

2+

2

2+

2+

2+

+

2+

2+

2+

2

2+

OxygenPositive ion

etc. etc.etc.

2+

2+

+

2+

2+

2+

2

2+

Silicon

2+

2+

+

2+

2+

2+

2

2+