TOA Glossary

Activation energy: The activation energy is the amount of energy which must be placed into a system before the given chemical reaction will occur. On an energy diagram, this is the difference in energy between the reactants and the transition state. The activation energy is often perceived as an energy barrier which must be overcome for the reaction to proceed.

Active site: Enzymes are biological materials which catalyze reactions by binding into the active site of the starting material. Many poisons prevent normal enzyme funciton because they have the right structure to bind to particular enzymes in place of the normal reactants. Some drugs are designed to do this to stop unwanted reactions from occurring. When some molecule other than the starting material is bound into the active site, then the reaction cannot occur.

Allotrope: Atoms can be connected differently, even if they are all atoms of the same element. These different bonding arrangements allow for different forms of matter to be made from a single type of atom. Different forms of matter made in this way are called allotropes. For example, ozone (O3) and dioxygen (O2) are allotropes of the element oxygen. Also, diamond, buckyball, and graphite are allotropes of carbon.

Amorphous: Amorphous substances have no definite repeating pattern in their atomic structures. There may be small regions of order, but, overall there is considerable disorder. Most substances we contact on a day to day basis are amorphous.

Atom: All matter is comprised of tiny particles called atoms. An atom is the smallest piece of an element that still retains all the properties of the element. Atoms themselves are made up of smaller particles called protons, electrons, and neutrons. The protons and neutrons reside in the nucleus of the atom and make up most of the mass of an atom. The electrons which surround the nucleus contribute only a small amount to the mass of the atom, but comprise most of the volume.

Atomic mass: The atomic mass is found on the periodic table below the symbol of the element in each box and represents the average mass of an atom. For elements with only one isotope, this mass is the same as the mass of each atom. However, for elements with more than one isotope, not all atoms will have the same mass. Then, the atomic mass is the average mass for all the isotopes of the element.

Atomic mass unit (amu): Protons and neutrons each weigh about one atomic mass unit. The atomic mass unit is defined as exactly 1/12th the mass of a carbon-12 atom, or 1.66057 x 10 -24 g. Atomic mass units allow for determination of relative atomic masses of atoms for different elements.

Atomic number: The atomic number is the total number of protons in an atom. Each element has a unique atomic number, which is written on the periodic table above the symbol of each element.

Ball-and-stick model: One way to represent molecules is the ball-and-stick representation. Each atom is represented by a ball, and each bond between atoms is represented by a stick. Hydrogen atoms are not shown. Although the atoms are proportionally too small compared to the bondlengths shown in this model, the bonding pattern is clearly visible.

Bond dissociation energy: The bond dissociation energy is the amount of energy required to break a bond between two atoms. Higher bond dissociation energies correspond to stronger bonds.

Catalyst: Chemicals which are not consumed in a reaction, but, which speed up the reaction rate are called catalysts. Catalysts aid to form a transition state which is lower in energy than the transition state without the catalyst. Since the barrier to the reaction is lower, the reaction rate increases in the presence of catalysts.

Cation: An atom that loses an electron becomes a positively charged ion called a cation.

Chemical bond: A chemical bond is a strong attractive force between two atoms. This force holds the two atoms close together in space.

Chemical equation: A chemical equation is a method of expressing chemical reactions in a succinct way. The reactants involved are placed on the left, and the products are placed on the right. Usually an arrow seperates the reactants and products. Oftentimes, specific reaction conditions (temperature, pressure, catalyst, etc.) are placed above or below the arrow symbol.

Chemical vapor deposition: Chemical vapor deposition (CVD) is a method for growing solids in which a gaseous precursor (containing fragments of the desired solid) is decomposed and deposited onto a desired surface. CVD is one of the most powerful synthetic methods in material science due to its remarkable flexibility. A variety of surfaces can be coated, and very thin layers can be applied if necessary.

Combustion: Combustion reactions involve elements or compounds burning in the presence of dioxygen. The burning of the octane in gasoline is an example of combustion.

Constructive interference: Constructive interference occurs when two waves overlap such that they are in phase (the troughs and peaks of the two waves coincide). Note, for this to occur down the entire wave, the two waves must have the same wavelength. When constructive interference occurs, the amplitude of the resulting wave is the sum of the two waves. So, if the original two waves had the same amplitude, the resulting wave would have twice their amplitude.

Covalent network solid: Covalent network solids are structures in which the atoms are held together by the sharing of electrons between atoms (called covalent bonds). Network solids have an undefined number of atoms in their structure, and often extend into huge macromolecules.

Crystalline solid: Crystalline solids have the same repeating unit throughout their entire structure. Crystalline solids can be composed of individual molecules, or an extending network of atoms.

Derivative: A derivative of a compound resembles the original compound, except that some modifications in atomic structure are evident. Usually, derivatization of a molecule involves altering part of it slightly or adding a new part to the original compound.

Destructive interference: Destructive interference occurs when two waves overlap such that they are completely out of phase (the troughs and peaks of the two waves are opposed to each other). Note, for this to occur down the entire wave, the two waves must have the same wavelength. When destructive interference occurs, the two waves are subtracted from each other. If the two waves have equal amplitude before colliding they will completely cancel each other.

Diffraction pattern: When light is scattered by a regular array the resulting combinations of constructive and destructive wave interference leads to a diffraction pattern. In x-ray crystallography, an analysis of the diffraction patterns can lead to a determination of the exact positioning of atoms in the repeating unit of the given crystal.

Double bonds: Two pairs of electrons are shared between two atoms in a double bond. In many molecular representations, double bonds are drawn as two lines between the bonded atoms. Double bonds are shorter and stronger than double bonds.

Electromagnetic radiation: Energy that travels through space is electromagnetic radiation. Electromagnetic radiation exhibits both wave and particulate properties (often called the dual nature of light). All electromagnetic radiation consists of oscillating electric and magnetic fields moving at the speed of light, but the wavelength of the radiation can vary widely. The wavelength is inversely proportional to its energy . Radio waves have long frequencies (and low energy) while x-rays have short frequencies (and high energy).

Electron: Electrons are subatomic particles. They are located outside the nucleus and comprise a vast majority of an atom's volume. Electrons are negatively charged, so they are opposite in sign to protons. The magnitude of the two charges, however, is the same. Electrons are the lightest subatomic particles and have a mass of about 1/2000th the mass of a proton or neutron.

Electronic structure: The electronic structure or configuration of an atom is a cataloging of the distribution of electrons about the nuclei. Electrons are located around the atom's nucleus, and the electronic structure describes where these electrons are most likely to be found.

Element: An element is matter that is made of only one type of building block or atom. An element cannot be decomposed into simpler substances by ordinary chemical means. Only a small number of elements exist; 110 different elements are known at this time. Examples of elements include carbon, iron, hydrogen, sodium, and uranium.

Endothermic: Reactions in which heat flows from the surroundings into the system are called endothermic. Since we observe the "surroundings," endothermic reactions are often detected by noting a decrease in temperature.

Energy diagram: An energy diagram is a convenient way of depicting the thermodynamics of reactions. Typically, the y-axis is given in units of energy, and the x-axis is defined as the reaction coordinate. The reaction coordinate is a very general entity which you can think of as the progress of the reaction. It is similar to time, but, the reaction coordinate has no units and no scale. We simply use it to show different stages of the reaction. Usually, the reactants are drawn at a certain level on the left side of the reaction coordinate, and the products are given on the right. A curved line connects the reactants and the products and shows the energies of any intermediates and/or transition states present in the reaction.

Exothermic: Reactions in which heat flows from the system to the surroundings are called exothermic. We can often detect exothermic reactions by observing an increase in temperature.

Heat of reaction: The heat of reaction describes the 'enthalpy' which is given off or absorbed during a reaction. If the pressure of the reaction remains constant, you can think of enthalpy as simply being heat.

In phase: When the peaks and troughs of two waves directly match each other they are said to be in phase. When "in phase" waves of the same amplitude collide, the result is a new wave with twice the amplitude of the original two. This kind of behavior is often called constructive interference.

Inert gases: The last column of the periodic table lists the inert or noble gases. In these gases, the outer shell of electrons in each atom is completely filled. This makes these elements very unreactive. This is why these gases are called inert or noble gases.

Ion: An ion is an electrically charged atom or group of atoms. An atom that gains an electron becomes a negatively charged ion called an anion. An atom that loses an electron becomes a positively charged ion or a cation.

Ionize: An atom is ionized when one of its electrons is ejected. This can occur when the atom is bombarded with other small particles (even other electrons) and one electron is expelled from the atom. This leaves the atom as a charged particle called an ion.

Isotope: Isotopes are atoms of the same element that have different masses. This is because these atoms have different numbers of neutrons in their nuclei, although the atomic number (the number of protons in each atom) for isotopes remains the same.

Joule: A joule is the standard unit for energy. Another common energy unit is the calorie. When we think of dietary calories, we are really thinking of Calories with a capital "C" which contain 1000 calories. Each Calorie contains 4,184 joules.

Kinetic: The study of the rates of chemical reactions is termed kinetics. The product which is formed the quickest is referred to as the kinetic product. The kinetic product need not be the most thermodynamically stable product. When a kinetic product is not the thermodynamic product, it will eventually convert to the more stable form.

Lattice: The positioning of atoms in crystalline solids is referred to as the lattice. The smallest division of the lattice which can still be used to represent the entire structure is called the unit cell.

Lewis dot: Lewis dot structures of atoms use dots to represent valence electrons. The first four dots are arranged on the four sides of the elemental symbol, and any remaining dots are arranged pairwise with those already present. Lewis dot structures of molecules also use dots to represent valence electrons. With molecules, the dots between molecules represent bonds. All of the atoms in a molecule are arranged so that eight dots or electrons surround each atom (except for hydrogen which only needs two electrons and boron which only needs six electrons).

Macromolecules: Macromolecule is a general term to describe a "huge molecule." Although there is no set criteria for macromolecules, they are generally considered to be structures with over 1000 atoms. DNA and proteins are common examples of macromolecules.

Magnetic Resonance Imaging (MRI): MRI gives physiological information by showing images of regions with contrasting water content, such as different areas of the brain. MRI is a form of Nuclear Magnetic Resonance spectroscopy and uses the same basic principles.

Mass spectrometer: A mass spectrometer measures the masses of molecules and atoms by volatilizing and then ionizing them. The ions are then separated according to their mass-to-charge ratio.

Mass-to-charge ratio: The mass-to-charge ratio, denoted m/e, is the unit used by mass spectrometers to separate ions. It is simply a ratio of the mass to the size of the electronic charge for any given molecular ion or fragment. Since the charge is usually +1, the mass and the mass-to-charge ratio are often the same.

Melting Point: The temperature at which a solid changes to a liquid is called the melting point. A completely pure crystalline substance would have an exact temperature at which it melts. Impure substances and amorphous substances will begin melting at one temperature and end at another. For these substances the term "melting range" is more appropriate.

Molecular: Molecular substances are composed of discrete molecules. An exact molecular formula can be written for such substances since each molecule must be composed of the same number and type of atoms (for example, water is H20). Network solids can not have an exact molecular formula since an undefined number of atoms are involved in each structure.

Molecular extended lattice: Many crystalline solids are composed of individual molecules which are packed together in a regular repeating fashion. There are no bonds between the molecules, instead they are held to each other by weaker intermolecular forces.

Molecule: A molecule is a collection of atoms held together by chemical bonds into a discrete, finite structure. One way molecules can be represented is by a chemical formula where symbols for the elements are used to indicate the types of atoms present and subscripts are used to indicate the relative numbers of atoms. For example, buckyball can be written as C60.

Neutron: Like protons, neutrons weigh one atomic mass unit and are housed in the nucleus of an atom. Unlike both protons and electrons, neutrons are neutral (without charge) subatomic particles.

NMR active nuclei: Atoms that have odd numbers of protons (2H, 14N) or odd numbers of protons and neutrons (1H, 15N, 31P, 13C, 19F, 17O) have nuclei that behave like tiny, spinning bar magnets. These atoms have NMR active nuclei.

Noble gases: The last column of the periodic table lists the inert or noble gases. In these gases, the outer shell of electrons in each atom is completely filled, making them very unreactive. Because of their unreactive nature, these gases are often called inert, even "noble" gases.

Nuclear magnetic resonance spectrometer: A nuclear magnetic resonance (NMR) spectrometer measures the energy changes associated with changes of orientation of nuclear spins in a molecule. These changes depend on the electronic environment of the nuceli and are obtained as radio wave frequencies in NMR spectroscopy. NMR spectrometers are very useful in determining the structures of molecules.

Nuclear spins: Nuclei which are NMR active are often called nuclear spins, or spins for short.

Nucleus: The nucleus of an atom is comprised of protons and neutrons. Although the dimensions of the nucleus are very small, most of the mass of an atom comes from the nucleus. If we were to blow up the scale of an atom to an indoor sports arena, the nucleus would have a volume comparable to a marble in the center of the arena, but, its mass would be much greater than the rest of the arena combined!

Octet rule: When atoms form bonds, they do so in a manner that will complete their valence shells. For most elements, a completed valence shell consists of eight electrons. The octet rule is the tendency of atoms in molecules to have eight electrons in their valence shells. Some common elements which do not follow the octet rule are hydrogen (H) which needs only two electrons to complete its shell, and boron (B) which only needs six electrons.

Out of phase: When the peaks from one wave are exactly matched by the troughs of a second wave, the two waves are said to be out of phase. If these two waves collide and have the same amplitude, they will mutually cancel. That is, for every positive point along one wave, the second wave would have a negative counterpart of the same magnitude. When these points are added together, they cancel leaving no net amplitude. This kind of phenomena is often called destructive interference.

Oxidation: Oxidation is a common type of chemical reaction in which electrons are formally transfered between atoms in the reactants and products. When iron rusts it is undergoing an oxidation reaction.

Periodic Table: The periodic table is an arrangement of all the elements. The elements are listed in order of increasing atomic number. Elements listed in the same column on the periodic table have the same number of valence electrons and have similar properties while elements in the same row on the periodic table (called periods) all have the same valence shell. Each box on the periodic table contains information including the elemental symbol, the atomic number, and the average mass in amus of one atom of the element.

Polymer: Molecules which are composed of linked repeating units (called monomers) are refered to as polymers. Polymers are the basis for many plastics and synthetic fibers such as teflon and polyester.

Proton: Protons and neutrons are the building blocks of atomic nuclei. Protons are positively charged particles that weigh one atomic mass unit (amu) or 1.66 x 10E-24 g. The positive charge of the proton is equal in size but opposite in sign to the negative charge of an electron.

Resonance: When a molecule is best described as a superposition of various resonance structures, it is often said that the molecule is in resonance. It is important not to confuse this kind of resonance with the completely different usage in nuclear magnetic resonance (NMR).

Resonance structures: Sometimes a molecule cannot be depicted by any one Lewis structure. Instead, the molecule may be a superposition of two or more structures. In this case, the electron structure of a molecule is described by writing all possible electron-dot formulas. These are called resonance structures, and the actual structure is a combination of all the structures that can be drawn.

Shells: In an atom, shells are distances from the nucleus. The shells that are closest to the nucleus are filled first, and then the higher energy shells farther from the nucleus are filled. In the periodic table, elements in the same row all have the same number of shells of electrons. Hydrogen and helium (H and He) have only one shell of electrons, elements such as lithium in the second row have two shells of electrons, elements such as sodium in the third row have three shells and so forth.

Single bonds: In a single bond, a single pair of electrons is shared between two atoms. A single bond is often represented by a line between two atoms. Single bonds are longer and weaker than double bonds.

Spin flip: Nuclear spins positioned in the field of a large magnet align either with (parallel to) or against (antiparallel to) the external field. Orientation with the external field is slightly lower in energy than orientation against the field, so there are slightly more spins aligned with the field. When the oriented nuclei are irradiated with electromagnetic radiation of the proper frequency, energy absorption occurs, and the lower energy state "spin-flips" to the higher energy state.

Spins: Nuclei which are NMR active are often called nuclear spins, or spins for short.

Subatomic particle: Although an atom is the smallest complete piece of an element, the atom itself is made up of even smaller components known as subatomic particles. The three subatomic particles in atoms are protons, electrons, and neutrons. Elements are defined by the number of protons in their atoms.

Superconductor: A superconductor is a material that conducts electricity with no wasted heat energy. Normal metals such as copper conduct electricity with up to 20% of the total energy wasted in the transmission of a current because of resistance heating of the wires.

Superposition: A hybrid structure is one that is derived from two different parent structures. This structure is not exactly like either of the two structures is came from. Instead, it is a combination of both structures.

Thermodynamic: Thermodynamics is the study of energy and its interconversions. Energy diagrams are often used to describe the thermodynamics of a given chemical reaction.

Thermodynamically favored: When a substance is refered to as the thermodynamically favored product, this means that of the possible products for a reaction, it is energetically the most stable. Sometimes, the thermodynamically favored product is not observed because a less stable product is kinetically favored.

Transition state: On an energy diagram, the maximas (peaks) represent transitions states. A transition state represents the highest energy arrangement of atoms between two more stable forms.

Unit cell: A unit cell is the smallest repeating unit of a crystalline solid which can be used to describe the entire structure. Unit cells are like templates which can be copied to produce an entire crystal.

Valence shell: The valence shell is the outermost shell of electrons in an atom.

Volatile: Substances which have a tendency to enter the gas phase easily (by evaporation, addition of heat, etc.) are called volatile.

Volatilize: Volatilizing liquids converts them into gases. Volatilizing liquids usually involves heating them.

X-ray diffraction: X-ray diffraction is an analytical technique used to determine the structures of crystalline solids. A beam of x-rays is diffracted off of the repeating planes of atoms in crystalline samples to produce a diffraction pattern. Through analysis of the diffraction pattern, atomic structures can often be determined.

Index

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