User:LorneSeeley/sandbox

Biogeochemical Cycles: General Definitions[edit]
Biogeochemical cycle, also known as substance turnover or cycling of substances, is a pathway where a chemical substance moves through biotic [1](biosphere) and abiotic [2] (lithosphere, atmosphere, and hydrosphere) compartments of the Earth.

In simpler words, continual recycling of nutrients through the air, water, rock and soil, and living organisms

All of these nutrients are essential to life.

No new molecules are being lost and replenished – what we have is what was here at the beginning (a closed system)

The 5 spheres of the environments are:


 * Biotic:
 * Biosphere: Life (All the living organisms)
 * Abiotic:
 * Hydrosphere: Water
 * Lithosphere (or Geosphere): Soil, sediments, rocks, etc. (The Earth’s body)
 * Atmosphere: Air
 * Anthrosphere: Those parts of the environment consisting of human activities and constructs

Elemental cycles include Calcium (Ca), Carbon (C), Hydrogen (H), Mercury (Hg), Nitrogen (N), Oxygen (O), Phosphorus (P), Selenium (Se), Sulfur (S).

Molecular cycles include Water and Silica.

Macroscopic cycles include Rock and Human-induced cycles for synthetic compounds (e.g. polychlorinated biphenyl (PCB))

Energy cycle - The flow of energy in an ecosystem is an open system; Sunlight constantly gives the planet energy while it is eventually used and lost in the form of heat throughout the trophic levels of a food web (energy flow). Carbon is used to make carbohydrates, fats, and proteins, the major sources of food energy. These compounds are oxidized to release carbon dioxide, which can be captured by plants to make organic compounds. The chemical reaction is powered by the light energy of the sun. Sunlight is required to combine carbon with hydrogen and oxygen into an energy source ( – organic or biological carbon, contained in energy-bearing molecules), but ecosystems in the deep sea, where no sunlight can penetrate, obtain energy from sulfur.

Pools of materials on earth


 * Reservoir: holding materials for long periods of time (long residence time)
 * e.g., coal deposits storing carbon for long periods of time
 * Mainly abiotic components of biogeochemical cycles
 * Main reservoirs: oceans, sediments, and the atmosphere
 * Exchange pools: holding materials for short periods of time (short residence time)
 * e.g., animal and plants utilize carbon to produce carbohydrates, fats, and proteins (to build their internal structures) or to obtain energy.
 * Mainly biotic factors of biogeochemical cycles

Cycles of matter


 * Exogenic cycles: Earth’s surface and the atmosphere
 * in oxygen cycle
 * in nitrogen cycle
 * in carbon cycle
 * Endogenic cycles: Involve sub-surface rocks of various kinds
 * Sulfur cycle
 * Interface: Sediments and soil

General scheme of ‘cycle of matter’


 * Hydrosphere: Conveyor + reservoir (ocean, lakes, etc.)
 * Anthroposphere: reservoir, relatively much rapid in discharging the matter into the environment
 * Atmosphere: Reservoir
 * Biosphere: Exchange pools
 * Geosphere: Reservoir (e.g. sediments and rocks)

Water Cycle[edit]
Solar energy drives the water cycle in the following processes:


 * 1) Solar energy heats Earth and causes evaporation from water bodies and soil, and evapotranspiration from plants.
 * 2) Evaporated water condenses into clouds.
 * 3) Water returns to Earth as precipitation (rain, snow, hail).
 * 4) Precipitation falling on land is taken up by plants, runs off along the land surface, or percolates into the soil and enters the groundwater.

Groundwater is water that sinks into the soil and is stored in aquifers. An aquifer is a groundwater storage area.

Five Components of Earth's Water Supply:


 * Groundwater (located in the aquifers)
 * Clouds (water vapour)
 * Ice and snow (snowpacks, glaciers, polar ice caps)
 * Surface water (lakes, steams, reservoirs, etc.)
 * Oceans (97% of Earth's water)Water turnover


 * Precipitation
 * Over land: 304 TL/d
 * Over ocean: 1055 TL/d
 * Evapo-transpiration (ET): 195 TL/d
 * Evaporation from oceans: 1164 TL/d
 * Runoff: 110 TL/d
 * Move of water vapor to land (clouds): 110 TL/d
 * Infiltration: 109 TL/d

How do humans alter the water cycle?


 * Altering hydrosphere:
 * Withdrawing large quantities of freshwater for agriculture leading to groundwater depletion.
 * Altering water quality by the addition of nutrients from chemicals and pollutants.
 * Altering lithosphere:
 * Part of geosphere accessible to water and closely interacting with water cycle
 * Clearing vegetation for agriculture, roads, building, and mining.
 * Covering land with buildings and concrete which increases impervious areas and thus runoff, and prevents water from becoming ground water.

Carbon Cycle[edit]
The carbon cycle is the biogeochemical cycle by which carbon is exchanged among the biosphere, pedosphere, geosphere, hydrosphere, and atmosphere of the Earth. Carbon is the main component of biological compounds as well as a major component of many minerals such as limestone. Along with the nitrogen cycle and the water cycle, the carbon cycle comprises a sequence of events that are key to make Earth capable of sustaining life. It describes the movement of carbon as it is recycled and reused throughout the biosphere, as well as long-term processes of carbon sequestration to and release from carbon sinks.


 * 1) Photosynthesis: Producers convert  into sugars.
 * 2) Respiration: Sugars are converted back into.
 * 3) Burial and Sedimentation: Some carbon can be buried or sedimented.
 * 4) Extraction: Human extraction of fossil fuels bring carbon to Earth's surface, where it can be combusted.
 * 5) Exchange:  in the atmosphere and  dissolved in water are constantly exchanged.
 * 6) Combustion: Combustion converts fossil fuels and plant material into.

Major components:


 * 1) Gaseous atmospheric  (small portion (0.04% of Earth’s atmosphere) but significantly important)
 * 2) Dissolved in surface- and groundwater ( or  (aq))
 * 3) Present in minerals, such as  (solids) (a very large amount)

Most important feature of C-cycle


 * C-cycle carries the solar energy through life:
 * is contained in energy-rich molecules. It can react with  or can be reformed when  and water react.
 * In natural systems, this ‘energy’ is solar energy when biologically-bound carbon is produced (photosynthesis) and is heat when it is decomposed (via aerobic respiration in cells).
 * In anthropogenic systems, destruction of biologically-bound carbon (heat generation) is performed through combustion (wood or fossil fuels).
 * Solar energy + C-Cycle --> Biological systems --> Fossil carbon + fossil fuels.
 * Solar energy + C-Cycle --> Biological systems --> Fossil carbon + fossil fuels.

Key players in C-cycle:


 * Microorganisms:
 * Examples:
 * Photosynthetic algae:
 * Carbon fixing agent in water
 * Consume  and produce biomass
 * consumption increase pH, making a conducive environment for  and  precipitation
 * Heterotrophic microorganisms:
 * Convert organic-C fixed by many microorganisms to fossil petroleum, kerogen, coal, and lignite.
 * Degrade organic-C (biomass, petroleum, and xenobiotic sources) and return the inorganic-C to atmosphere.
 * Biodegradation of C-containing compounds in hazardous wastes and hydrocarbons (those in crude oil and synthetic ones) à fundamental of bioremediation technique

Human interferences in C-cycle


 * Deforestation (trees are photosynthetic agents in the lithosphere)
 * Burning fossil fuels which quickly releases large amounts of carbon into the air, causing a major imbalance in the C-turnover

Nitrogen Cycle[edit]
5 major components of the Nitrogen cycle:


 * 1) Nitrogen fixation: Nitrogen fixation converts  from the atmosphere. Biotic processes convert  to ammonia, whereas abiotic processes convert  to nitrate.
 * 2) Assimilation: Producers take up either ammonium  or nitrate . Consumers assimilate nitrogen by eating producers.
 * 3) Ammonification: Decomposers in soil and water break down biological nitrogen compounds into ammonium.
 * 4) Nitrification (Aerobic): Nitrifying bacteria convert ammonium  into nitrite  and then into nitrate.
 * 5) Denitrification (Needs C usage): In a series of steps, denitrifying bacteria in oxygen-poor soil and stagnant water convert nitrate  into oxide  and eventually nitrogen gas.

A new pathway was identified in 1999:


 * Anammox
 * Anaerobic ammonium oxidation
 * Converts ammonium and nitrate anaerobically to  without any  required
 * A shortcut in N-cycle

N-cycle


 * N occurs in all spheres
 * Atmosphere: The major reservoir (78% elemental nitrogen N2 by volume)
 * An essential constituent of life
 * Building block of proteins and genetic materials (DNA)
 * Plants need nitrogen in the form of nitrates to make nucleic acids (DNA) and amino acids
 * is very stable: The rate-limiting step

Again, the microorganisms …


 * Are key players!
 * Entrance from atmosphere into other spheres:
 * Fixation can happen under high-temperature and high-pressure conditions:
 * Lightening and biochemical reactions mediated by microorganisms
 * Exit from different spheres back to atmosphere:
 * Biologically-bound  is mineralized (converted to inorganic, such as , , ) by microorganisms during biomass decay
 * Biologically-bound  is mineralized (converted to inorganic, such as , , ) by microorganisms during biomass decay

Human interferences in N-cycle


 * Burning fuel (anthrosphere): Release of nitric oxide which converts to  in the atmosphere and falls back to the earth as acid rain
 * Using inorganic fertilizers (lithosphere): Releases  (nitrous oxide) into the atmosphere which depletes the ozone layer
 * Destroy forests, grasslands, and wetlands (lithosphere and biosphere): producers are destroyed
 * Agricultural runoff and sewage (hydrosphere and lithosphere): Enter waterways and release of nitrates disrupt the aquatic ecosystems
 * Altering land to croplands (lithosphere): When working with crops (irrigating, harvest, burn to create room for crops) nitrogen is taken from the topsoil.

Phosphorus Cycle[edit]
P-cycle Phosphorus Cycle


 * Eutrophication: Dense growth of aquatic plants
 * Deteriorates the balance of aquatic ecosystems and
 * Loss of biodiversityPhosphorus Cycle


 * P is limiting nutrient in ecosystems


 * Thus, crucial cycle in nourishing life – if it is limiting, life barely flourish!
 * Plants need it to produce nucleic acids (DNA & RNA)
 * Microbial decay returns biological P to the salt solution from which P precipitates.
 * No stable gaseous form of P in nature
 * Stable form in nature: Poorly-soluble minerals
 * So, P-cycle is endogenic (occurs in geosphere)
 * Two major reservoir:
 * Lithosphere: Deposits of hydroxyapatite in rocks, a calcium salt
 * Anthrosphere: Large quantities of phosphate extracted for fertilizer, chemicals, and food additives. Constituent of some toxic compounds, such as the insecticide organophosphate and military poison nerve gases (Sarin)

How do we harm P-cycle?


 * Lithosphere: Mining for phosphate rock to make inorganic fertilizers
 * Biosphere and lithosphere: Cutting down tropical trees reduces the amount of phosphorus in the tropical soil
 * Hydrosphere: Runoff from animal wastes, fertilizers, and sewage add phosphorus to aquatic systems (eutrophication – the major environmental consequent)

Classification of aquatic environments based on their trophic conditions Classification of aquatic environment based on their trophic conditions

Sulfur Cycle[edit]
Sulfur Cycle S-cycle


 * Relatively complex, because S can be:
 * Several gaseous species
 * Poorly-soluble minerals (solid)
 * Several species in solution (dissolved)
 * It closely tie to O-cycle:
 * Gaseous sulfur oxide - a somewhat- toxic atmospheric pollutant, released from combustion of sulfur-bearing fossil fuels
 * Soluble sulfate ion - the main constituent of acid rain
 * Significant species involved:
 * Gaseous hydrogen sulfide
 * Volatile dimethyl sulfide  which is released to the atmosphere by biological processes in the ocean
 * Mineral sulfides, such
 * Sulfuric acid,, the major constituent of
 * Biologically-bound sulfur in sulfur-containing proteins

How do Humans interfere in S-cycle?


 * Atmosphere: Burning coal and oil to create electricity, which releases sulfur into the air
 * Anthrosphere: Refining petroleum to create gasoline
 * Lithosphere and anthrosphere: Creating metals from ores (smelting)
 * Hydrosphere and anthrosphere: Some pesticides

Oxygen Cycle[edit]
In the Oxygen Cycle there are chemically bounded, such as , , minerals and organic matter, and gaseous , such as the huge reservoir: atmosphere. Oxygen Cycle O-cycle


 * Tangled with other cycles, especially with C-cycle
 * The major reservoir: atmosphere
 * Atmosphere: 20%  by volume
 * Major constituents after
 * Oxygen enters biosphere by respiration, microbial decay, and anthropogenic activities (combustion)
 * It returns to atmosphere via photosynthesis:

Sunlight

Oxygen contribution in energy yielding

Oxygen exchange among the atmosphere, geosphere, hydrosphere, and biosphere. A major component of O-cycle
 * Elemental oxygen becomes chemically bound by various energy-yielding processes
 * More importantly:
 * Combustion:
 * Metabolic (biochemical) processes in organisms:
 * Can oxidize inorganic substances (in oxidative weathering):
 * Can oxidize inorganic substances (in oxidative weathering):
 * Can oxidize inorganic substances (in oxidative weathering):


 * Stratospheric ozone
 * A relatively small concentration (~ 10 km high in atmosphere)
 * Filters ultraviolet (UV) with wavelengths of 220-330 nm
 * Protects the life on the Earth from the severe damages of this radiation

How do humans alter O-cycle?


 * Combustion is the biggest consumer of
 * Deforestation: Prevents photosynthesis which replenish  resources

Anthropogenic disturbances: The consequences & remedies[edit]
Lifelong balance on Earth


 * Before the industrial evolution
 * The surface of planet Earth evolved over billions of years as a balanced biogeochemical system
 * This balance was sustained by:
 * Sun power
 * A large-scale cycling of elements largely run by the global environmental microbiomes

Natural geochemical & biological element cycling


 * They overlap in a balanced fashion to maintain the homeostasis of carbon, nitrogen, and phosphorus

Impact of mankind on the Earth


 * Mankind has had little impact on plant Earth during most of its time on it:
 * Simple huts or tents for dwellings
 * Narrow trails worn across the land for movement
 * The food gathered largely from natural sources
 * There are evidences that prehistoric humans – who were gradually becoming technologically developed – were beginning to have impact on earth:
 * e.g., drove some species to extinction by excessive hunting
 * e.g., burning forests to provide grazing land for attracting animals

Consequences[edit]
Anthrosphere


 * With industrial revolution and fast technological advancement in the last century, defining a new ‘sphere’ became important
 * Definition: Part of the environment made or modified by humans and used for their activities
 * Pronounced, sometimes overwhelming influence on the environment as a whole
 * Has altered all other spheres of the environment, especially geosphere
 * The main source of most environmental pollutions

Anthrosphere is the result of Technology


 * Prehistory
 * Primitive tools of stone, wood, and bone
 * Pre-dating the Roman era
 * Metallurgy
 * Domestication of the horse
 * Discovery of the wheel
 * Architecture
 * Control of water for canals and irrigation
 * Writing to communicate
 * The Greek and Roman era
 * Development of machines (e.g. pulley, windlass, inclined plane, catapult, water screw for moving water, etc.)
 * Invention of water wheel (for power transmission by wooden gears)
 * 740
 * Printing with wood blocks
 * 1700
 * Gunpowder
 * 1800s
 * Explosion of technology
 * Steam power
 * Telegraph
 * Electricity
 * Cement
 * Photography
 * Internal combustion engines
 * 1900s and onward
 * Vast increase in energy use
 * High speed in:
 * Manufacturing
 * Transportation
 * Communication
 * Information transfer
 * Computation
 * Vast new variety of chemicals
 * New or improved materials for new applications (e.g. nanotechnology)
 * Widespread of application of computation for:
 * Manufacturing
 * Communication
 * Transportation
 * Passenger- and freight-carrying airplanes
 * Rapid advances in biotechnology

Anthropogenic changes: human impact


 * Started in the last century
 * Exacerbated in the last 20 years

Anthropocene

Key components of the anthrosphere Components of Anthrosphere
 * There is a new theory which says:
 * ‘The influence of anthropogenic activities is so great which assert a transition is under way to a new era, the Anthropocene, in which the nature of the Earth’s environment is largely determined by human activities in the anthrosphere.’ – Stanley E. Manahan. Environmental Chemistry. 9th edition, 2010.


 * Different infrastructures:
 * Transportation systems (railroads, highways, and air transport systems)
 * Energy-generating and transmission systems
 * Buildings (for dwellings and other activities, such as education, commerce, manufacturing, etc.)
 * Telecommunication systems
 * Water supply and distribution systems
 * Wastewater treatment and disposal systems (for municipal wastewater, industrial wastes, and municipal solid refuse)
 * Croplands and the irrigation systems (modified lands and the altered associated environment for food production)

Infrastructure is made up of the physical component (e.g. roads, bridges, pipelines) and the instructions to operate (e.g. laws, regulations, operational procedures).

Why is industry disruptive?

The anthrosphere is a respiratory of many of the pollutant by-products of human activities Effects of the anthrosphere on earth
 * An artificial metabolic system
 * Where: Abiotic feedstocks are converted to products
 * Intercepts with natural cycles in several adverse ways:
 * One directional with little or no recycling
 * Emissions of  and other greenhouse gases
 * Spreading of nonbiodegradable polymers and xenobiotics
 * Demand of nitrogen and phosphorus for intensive agriculture
 * Surplus of lignocellulosic waste (plant dry matter – biomass)


 * Anthrosphere is severely contaminated.
 * Chemicals which are persistent, bio-accumulative (in lipid tissues), and toxic (PBT)
 * Database of U. S. EPA for BPTs:  here & here
 * They can leak into other sphere
 * e.g., chlorofluorocarbons (CFCs) (Freons – refrigerants used from the late 1920s to 1990). It depletes ozone.  Due to such long-term usage and its stability, it is a ‘normal’ constituent of atmosphere now, even if its usage is banned!

Remedies[edit]
The survival of mankind and the planet Earth requires to change our mindset from: ‘a two-way interaction between science and technology’

To: ‘a three-way one where environmental consideration and sustainable development play key roles’

Gaia hypothesis:

Evolution of anthrosphere
 * Advanced by Lames Lovelock
 * In slow-pace changes throughout the history, ‘organisms on the Earth have modified the Earth’s climate and other environmental conditions in a manner conducive to the existence and reproduction of the organisms’ -- Stanley E. Manahan. Environmental Chemistry. 9th edition, 2010.
 * Why not we artificially induce such beneficial integration at this era, to prevent the catastrophic consequences of recent human impacts!Steps in evolution of the anthrosphere to a more environmentally compatible form

Industry ecology: Integration of anthrosphere into the total environment


 * The motto: ‘closing the loop’
 * Definition: when industry attempts to produce with maximum efficiency + minimal impact – recycle as much as possible!
 * Modern practice of this approach roots in an article by Frosch & Gallopoulos (1989).
 * Industrial ecosystems should work analogous to natural ecosystems.
 * Industrial metabolism: processing of energy and matter through industrial ecosystems

Green chemistry: Integration of anthrosphere into the total environment


 * Command and control
 * Before 1970
 * With laws and regulations
 * 'End-of-pipe' measures
 * Most of easy measures and minimal reduction in pollution
 * Continuous, expensive, and litigious
 * Based of reduction of exposure
 * Green chemistry
 * Started as 1990s
 * Based on the concept of industrial ecology
 * Based on reduction of hazard

Green chemistry


 * Definition: Sustainable (safe and nonpolluting) practice of chemical science and manufacturing, while it consumes minimum energy and materials and produces little or no waste.
 * Mostly applied to synthetic chemistry (production of new and existing chemicals)
 * A key concept of green synthetic chemistry is high atom economy
 * Atom economy: The fraction of all reagents that goes into the final product
 * Conventional synthesis chemistry
 * Even with 100% yield, by-product(s) may be generated
 * Yield ≠ atom economy
 * Green synthetic chemistry
 * 100% yield should be accompanied with 100% atom economy, leaving no residues behind
 * Yield = atom economy

Example 1


 * In synthesizing a chemical, the following reaction occurs. The mass in kilogram of each material participating in the reaction is given in parentheses. Determine percent yield and percent atom economy.
 * Unused-A (28.8) Unused-B (23.0) By-product (108)
 * Solution:
 * Yield will be:
 * Atom economy will be:
 * Atom economy will be:

Principles of green chemistry


 * Based on The Three R’s concept:
 * Reduce
 * Auxiliary substances (solvents)
 * raw materials
 * Waste production
 * Energy consumption
 * Hazard usage abd generation
 * Toxicity
 * Reuse
 * Renewable raw materials
 * Biodegradable products
 * Recycle
 * Renewable raw materials
 * Biodegradable products

10 aspects of green chemistry


 * 1) Chemical transformation under mild conditions: Harsh reaction conditions (high pressure and temperature) should be avoided (e.g., enzymatic reactions in microorganisms).
 * 2) Green catalyst: Catalysts with maximum specificity and efficiency which save in use of energy, materials, & toxic reagents and decrease the need of separation (e.g., H2O2,microbial enzymes)
 * 3) Solventless processes: Many hazards and environmental problems roots in processes where solvents are involved.
 * 4) Less polluting solvents: preferably water
 * 5) Supercritical fluids: e.g., CO2 which is a good reaction media and allow easy separation
 * 6) Process intensification: decrease the process footprint (smaller reactors), reducing the hazard posed by reacting large quantities in large containers
 * 7) Electricity: a mass-less, and cheap (only a few cents per mole) reagent and easy to transport which can sometimes be used for oxidation-reduction of chemicals
 * 8) Renewable feedstocks: Use renewable raw materials (e.g., biomass from plants) instead of non-replenishable ones (i.e., petroleum and natural gas)
 * 9) Design for degradability: Products should be degradable by natural processes so that, in case of any leakage/discharge, the contamination is transient.
 * 10) Biodegradable polymers: should be used in textile, plastic bags, etc. to make them prone to degradation by earth’s natural microbiome (e.g., biochemically synthesized polymeric materials such as those taken from carbohydrate feedstock).

Definitions: Differentiating organic and inorganic chemistry[edit]
History

Ammonium cyanate (an inorganic compound) --heat--> Urea (an organic compound
 * ‘Chemistry’ was an undifferentiated field until almost the beginning of 1800s
 * First usage of the terms ‘inorganic’ and ‘organic’ was in year 1685:
 * Distinguished the origin of substances: mineral (nonliving sources) vs. animals/plants
 * Originated from the publication of Nicolas Lémery, the French physician and chemist
 * First usage of the terms ‘organic chemistry’ and ‘inorganic chemistry’ in the 1830s
 * Until 1828, it was believed that organic compounds cannot be synthesized except by living plants and animals (vital-force theory).
 * Friedrich Wöhler accidently discovered (1828):Urea


 * By 1850, the modern organic chemistry was well established.
 * Today, about a million organic compounds are synthesized which do not naturally exist.

Definitions


 * Organic chemistry
 * The chemistry of life
 * The chemistry of hydrocarbons
 * The chemistry of C, H, O (major elements) and N, P, S (minor elements)
 * Inorganic chemistry
 * The chemistry of everything else
 * The chemistry of the whole periodic table (including carbon)

Organic chemistry[edit]
Organic compounds differ from inorganic compounds in 7 ways:


 * 1) Combustable
 * 2) Lower melting/boiling points
 * 3) Less soluble in water
 * 4) Isomerism (i.e. several organic compounds may share the same formula.)
 * 5) Molecular reactions, not ionic - slow
 * 6) Very high MW (Often >> 1000)
 * 7) Source of food for bacteria

Sources of organic compounds


 * Nature: e.g. fibre, vegetable oils, animals oils and fats, alkaloids cellulose, starch, sugars, etc.
 * Synthesis: A wide variety of compounds and materials prepared by manufacturing processes
 * Fermentation: e.g. alcohols, acetone, glycerol, antibiotics, acid, etc. which are derived from metabolic reactions of micro-organisms on organic matter

Importance of organic chemistry in Environmental Engineering


 * Wastes produced in the following processes:
 * Processing natural organic materials
 * Synthesizing organics (the desired compounds and the by-products)
 * Fermentation industries
 * These are major problems with the industrial and hazardous waste
 * The duty of Environmental Engineers is to deal with them.

Carbon (C) atom: Why are so many compounds of C available/possible?


 * C can have four covalent bonds (four electrons to share)
 * C atoms can link together by covalent binding in a variety of ways

Electron dot diagram of a C-atom


 * Carbon is able to form 4 covalent bonds with other carbon or other elements (4 valence electrons to share).
 * Valence electron is an outer shell electron that can participate in the formation of chemical bond.
 * In a single covalent bond, both atoms in the bond contribute one valence electron in order to form a shared pair.

Overall structure of organic compounds


 * 1) Continuous open chain
 * 2) A chain with branches
 * 3) Ring:
 * 4) Aliphatic ring: 2 covalent bonds
 * 5) Aromatic: 1 covalent bond
 * 6) Chains or rings containing other elements

Isomerism


 * In inorganic chemistry, a molecular formula represents just one compound.
 * In organic chemistry, most molecular formula do not represent any particular compound.
 * Compounds which can be represented by the same molecular formula: isomers
 * So, in organic chemistry:
 * Molecular formula: Just shows the elements which compose the compound
 * Structural formula: (1) shows the molecular representation; (2) a 2D model shows bonding patterns and shapes of molecules; (3) the best way to distinguish isomers

Examples of isomerism


 * Glyceraldehyde
 * Molecular formula:
 * Glyceraldehyde Structural formula:
 * Carbon in the center
 * Short lines are electrons
 * Short lines are electrons

General characteristics of organic compounds:


 * They do not dissolve in polar solvents, like water because they are nonpolar compounds. Remember the rule "likes dissolve likes".
 * Low melting points - due to weak intermolecular forces.
 * React slower than ionic compounds - due to strong covalent bonds between atoms.

Types of bonds:


 * Remember: Carbon has 4 bonding sites
 * Single Bond: Single covalent bond in which they share one pair of electrons (2 e-)
 * Double Bond: Carbon atoms may share two pairs of electrons to form a double bond
 * Triple Bond: Carbon atoms may share three pairs of electrons to form a triple bond

Types of compounds:


 * Saturated Compounds: Carbon atoms are linked by Single Bonds. (e.g. ethane: )
 * Unsaturated Compounds: Compounds where carbon atoms have Double or Triple Bonds. (e.g. ethylene: )

3 major types of organic compounds


 * Aliphatic: Characteristics groups are mainly linked to a straight or branched C chain (e.g. butane)
 * Aromatic: The characteristics groups are linked to a particular ring of carbons (six-member C ring with three double bonds) (e.g. benzene)
 * Heterocyclic: Have a ring structure in which one member is an element other than C (e.g. purine, pteridine, phenoxazine, phenothiazine)

Characteristics of functional groups


 * Functional groups are the collections of atoms that attach the carbon skeleton of an organic molecule and confer specific properties.
 * Each type of organic molecule has its own specific type of functional group.
 * Functional groups in biological molecules play an important role in the formation of molecules like DNA, proteins, carbohydrates, and lipids.
 * Examples of functional groups:
 * Hydroxyl (Polar)
 * Methyl (Nonpolar)
 * Carbonyl (Polar)
 * Carboxy (Charged, ionizes to release . Since carboxyl groups can release  ions into solution, they are considered acidic)
 * Amino (Charged, accepts  to form . Since amino groups can remove  from solution, they are considered basic)
 * Phosphate (Charged, ionized to release . Since phosphate groups can release  ions into solution, they are considered acidic)
 * Sulfhydryl (Polar)
 * Polar vs. Nonpolar
 * Polar: Charges are distributed evenly and cancel out each other (e.g. water molecule)
 * Nonpolar: Charges are distributed unevenly (e.g. Carbon dioxide)

Organic compounds of concern in Environmental Engineering:[edit]
Organics of concern:


 * Trace organics
 * Detergents
 * Detergents
 * Soaps
 * Synthetic detergents
 * Aliphatics
 * Hydrocarbons
 * Saturated (e.g. alkanes)
 * Unsaturated (e.g. alkenes, alkynes)
 * Alcohols
 * Aldehydes and ketones
 * Acids
 * Esters
 * Ethers
 * Alkyl halides and others halogenated aliphatic compounds
 * Simple compounds containing nitrogen
 * Cyclic aliphatic compounds
 * Mercaptans or thioalcohols
 * Food-related compounds
 * Carbohydrates
 * Fats, oils and waxes
 * Proteins and amino acids
 * Pesticides
 * Chlorinated
 * Organic phosphate
 * Carbamate
 * S-Triazines
 * Aromatics
 * Hydrocarbons
 * Phenols
 * Alcohol, aldehydes, ketones and acids
 * Simple compounds containing nitrogen

Aliphatics[edit]
Aliphatic hydrocarbons


 * Are compounds of carbon and hydrogen
 * Two types:
 * Saturated hydrocarbons:
 * Adjacent C-atoms are joined with single covalent bonds
 * All other bonds are satisfied with hydrogen
 * Other names: paraffin series, methane series, alkanes
 * The principle source is petroleum
 * e.g. gasoline and diesel fuel are distinct mixtures of saturated hydrocarbons
 * A whole series of compounds
 * Starting with one C-atom, increasing one C-atom at a time
 * General formula:
 * Methane
 * Ethane
 * Propane
 * Butane (2 isomers)
 * Pentane (3 isomers)
 * Hexane (5 isomers)
 * Heptane (9 isomers)
 * Octane (18 isomers)
 * Nonane (35 isomers)
 * Decane (75 possible isomers)
 * Methane :
 * Simplest hydrocarbon
 * Considerable importance in environmental engineering
 * Major end-product of anaerobic treatment
 * A component of march gas and natural gas
 * In a mixture with air (5-15% methane), highly explosive - can be used as fuel for gas engines
 * A greenhouse gas (GHG): its concentration in stratosphere
 * Is a potent GHG
 * About 28 times more powerful than  at warming the Earth, on a 100-year timescale
 * There's not that much  in the atmosphere (~1,800 pub - about as much as two cups of water inside a swimming pool). That's about 200 times less concentrated in the atmosphere than.
 * Methane's chemical shape is remarkably effective at trapping heat
 * ~60% of its emission is due to human activities:
 * Agriculture (livestock and feedlots, rice paddies, etc.)
 * Oil and gas drilling sites
 * Landfills
 * Physical constants of some normal paraffins Characteristics of normal paraffins
 * The term 'normal' refer to those isomers that all C-atoms are arranged in a straight chain
 * Characteristics:
 * Colourless, odourless, quite insoluble in water (especially those with 5 C-atoms or more), dissolve in organic solvents
 * At room temperature:
 * up to 5 C-atoms: gas
 * 6 to 17 C-atoms: liquid
 * More than 17 C-atoms: solid
 * An important feature
 * Quite inert toward most chemical reagents
 * e.g. strong bases, acids, or aqueous solutions of oxidizing agents don't react with saturated hydrocarbons at room temperature
 * At elevated temperature, strong oxidizing agents (e.g. concentrated sulphuric acid ) oxidize the compounds to  and water
 * That's why they are called 'paraffin' (from Latin term 'arum affine', meaning little affinity)
 * Homologous series of hydrocarbons
 * Organic compounds can be classified into groups with related structures and properties
 * Homologous series: When the formula of a series of compounds differ by a common increment
 * In terms of saturated hydrocarbons: this increment is by (methylene group)
 * Unsaturated hydrocarbons:
 * Have at least two C-atoms with double or triple bond
 * All remaining bonds are satisfied with hydrogen
 * Four classes
 * Ethylene series (alkenes)
 * Other names: Olefins, alkenes
 * Each member of saturated hydrocarbons series, except methane, can lose hydrogen to become unsaturated compound
 * This process can start from ethene, where the series took its name from
 * Contain one double (unsaturated) bond in the molecule
 * E.g. Butene
 * Diolefins
 * Contains two double bonds in the molecule
 * e.g. Diene
 * Polyenes
 * Contains more than two double bonds in the molecule
 * e.g. lycopene - a bright red hydrocarbon found in tomato and some red fruits and vegetables (carrot, watermelon, etc.)
 * Of interest in vegetable-canning industrial waste
 * The chlorine demand of such waste is very high
 * Acetylene series (alkynes)
 * Other name: alkynes
 * Contains a triple bond in the molecule
 * Can be found in industrial waste, such as those from manufacturing of some types of synthetic rubber
 * e.g. Acetylene
 * Environmental concerns:
 * Unsaturated hydrocarbons seldom create problem per se
 * However, unsaturated bonds can occur in many organic compounds and exhibit common properties, regardless of the type of compound they exist in
 * Unsaturated compounds can take parts in many reactions:
 * Oxidation (easily oxidizable)
 * Reduction (Under special conditions of temperature, pressure, and catalysis - of special important in the conversion of vegetable oil to solid fats)
 * Addition (halogen acids, hypochlorous acids, halogens - increase the chlorine demand of waste treatment)
 * Polymerization (binding two unsaturated compound to form a polymer - molecules of higher weight)
 * Bacterial oxidation (are more prone to bacterial oxidation rather than saturated compounds)
 * These compounds, particularly ethylene, propylene, and butylene (alkenes), are formed in great quantities during pyrolysis (cracking large molecules to smaller ones under heat) of petroleum
 * Polymerization is used in many industries, such as synthesis of resins, fibres, detergents, etc.
 * Reaction with hypochlorous acid is of great importance, because it increases the chlorine-demand of wastewater (industrial waste) containing appreciable amounts of unsaturated compounds
 * Chlorinated organic compounds → adverse health and environmental effects
 * Parent compounds, because they can be used to produce a wide variety of chemicals
 * Alcohols
 * Primary oxidation producers of hydrocarbons

Methane Methyl alcohol or methanol

Propane n-Propyl alcohol


 * Also known as hydroxy alkyl. Alkyl group is denoted as  and hydroxy group is represented by.
 * Thus general formula of alcohol is
 * e.g. in methyl alcohol,  is alkyl group