Chapter 5: Carbon Chemistry

1. Chapter 5: Carbon Chemistry A Dioxin Molecule

2. Organic Chemistry 101: Single bonds: formed when one pair of electrons is shared between two carbon atoms. Double bonds: involve the sharing of two pairs of electrons. Triple bonds: The sharing of three pairs of electrons. Unsaturated carbon compound: when multiple bonds occur between carbon atoms. Saturated carbon compound: when there are only single bonds between the carbon atoms. Functional group: an atom or group of atoms that can be attached to the carbon atoms.

3. Hydrocarbons Hydrocarbon: the most common organic compound and contains just hydrogen and carbon. Alkanes: the C atoms have single bonds and occur as straight or branched chains and as rings. Alkenes: have a double bond between two of the carbons. Alkynes: have a triple bond between two of the carbons. Substitution reactions: one or more hydrogens are replaced by atoms of another element. (CH4 + Cl2 CH3Cl + HCl) Addition reaction: some of the electrons in the unsaturated bonds are used to bind with additional atoms. (C2H4 + H2 C2H6.)

4. Structural formula: shows the orientation of the atoms in either two or three dimensions. Condensed structural formula: used to save space and are written in terms of carbon units. Molecular formula: gives the numbers of each type of atom in the molecule. (i.e. Butane’s molecular formula: C4H10.

5. Isomers: compound with the same molecular formula, but different structural formulas. Geometric isomers: compounds with double carbon bonds preventing the free rotation between the two carbon atoms.

6. Another common way to abbreviate structure in organic compounds includes the following: https://www.chemgapedia.de/vsengine/vlu/vsc/en/ch/2/vlu/alkane/alkane_struktur.vlu/Page/vsc/en/ch/2/oc/stoffklassen/systematik_struktur/acyclische_verbindungen/gesaettigte_kohlenwasserstoffe/alkane/strukturvielfalt.vscml.html

7. Naming and Types of Hydrocarbon Compounds Alkanes:

8. Steps to follow carbon-chemistry nomenclature • Name of the compound is based on the longest continuous chain of carbon atoms. The root name indicates the number of carbon atoms in the chain, and the ane (for a single bond) is added to the root name. • The carbon atoms in the longest continuous chain are numbered sequentially from one end. If substituent groups are added to the chain, the numbering starts at the end of the chain that will give the lowest number of the substituent groups. • All groups attached to the longest continuous chain are identified by the number of the carbon atom to which they are attached and the name of the substituent group. If the substituent group is derived from an alkane, it is named by removing the ane and replacing it with yl. If two or more groups are present, they are listed in alphabetical order.

9. Steps to follow carbon-chemistry nomenclature, cont. 4) A prefix is used to denote multiple substitutions by the same kind of group. This prefix is ignored when deciding the alphabetical order rule. Let’s examine the following molecule and name it. CH3—C—CH2—CH—CH2—CH2—CH3. CH3 CH2—CH3 CH3 4-ethyl-2,2-dimethylheptane

10. Alkene and Alkyne nomenclature • Find the longest chain containing the double and/or triple bond. The stem name is based on the number of carbon atoms, as is the case for alkanes. A prefix number is used to indicate the position of the carbon atom immediately before the double or triple bond, and a suffix (ene or yne) is used to indicate whether the compound is an alkene or an alkyne. • The chain is numbered so that the double/triple bond will have the lowest location. If both types of bonds are present, the double bond takes precedence in establishing the start of the numbering sequence.

11. Alkene and Alkyne nomenclature, cont. 3) If more than one double bond is present, the location numbers are indicated first and the ending is given as diene, triene, etc. If a triple bond is also present, the double bonds are designated as the main stem, dropping the e, and the triple bond is designated by an extra suffix. 4) Unsaturated subtituents are named by using the prefix of the chain after replacing the terminal e with yl. For example, propene becomes propenyl. Name that molecule… CH3—C==CH—C C—CH2—CH3 — — — C==CH2 3-methyl-1,3-octdien-5-yne

12. Cyclic Hydrocarbons: the carbon atoms are arranged in a ring. The cyclic hydrocarbons do not form flat structures like aromatic hydrocarbons and are thus distinguished from them. For simple rings, without attached substituent groups, the prefix cyclo is used to distinguish a ring structure. For example, cyclohexane would consist of six singly-bonded carbon atoms in a ring structure. Cyclohexene would consist of six atoms with one double bond in a ring structure and cyclohexyne would consist of six carbon atoms with one triple bond in a ring structure.

13. Aromatic (Aryl) Hydrocarbons: built upon a benzene ring of six hydrogen atoms and 6 carbon atoms. It was originally thought that benzene consisted of alternating single and double bonds, but it was eventually realized that the ring has six identical bonds, neither single or double. Modern representation of the benzene ring show it as a hexagon enclosing a circle, indicating that it consists of a ring of delocalized (p) electrons.

14. Aromatic hydrocarbons nomenclature

15. Polycyclic Aromatic Hydrocarbons (PAH) PAHs consist of two or more benzene rings which form a planar structure. They are formed from the incomplete combustion of other hydrocarbons.

16. Functional Groups: consist of specific bonding configurations of atoms in organic molecules and usually, but not always, contain at least one element other than carbon or hydrogen.

17. Organohalide compound: a hydrocarbon that contains at least one atom of F, Cl, Br or I. Nomenclature is simple using prefixes such as fluoro (for F), Chloro (for Cl), Bromo (for Br) and Iodo (for I). Polychlorinated biphenyls (PCBs)consist of two benzene rings joined by a single bond with attached chlorine atoms. Chlorinated phenols: These can be significantly hazardous wastes. They have been used a wood preservativesa benzene ring that has an attached OH functional group and at least one Cl atom attached. Esters: special group of compounds formed by a condensation reaction involving carboxylic acids and alcohols.

18. Figure 5-15. Structure of DDT. The molecule consists of two benzene rings joined by a chlorinated ethane group. Each ring has a Cl atom substituting for a H atom. The IUPAC name for this molecule would be dichlorodiphenlytrichloroethane.

19. http://southernersjournal.com/?tag=running-behind-ddt-truck http://www.whale.to/vaccines/ddt_spraying.html

20. http://grossmontcuyamaca.blogspot.com/2012/06/grossmont-college-students-to-study.htmlhttp://grossmontcuyamaca.blogspot.com/2012/06/grossmont-college-students-to-study.html

21. Structure of 2,3,7,8-tetrachlorodibenzo-p-dioxin (TCDD). The rings are numbered as shown. Note that the chlorine atoms occur in positions 2, 3, 7, and 8. The tetra prefix indicates that there are four chlorine atoms.

22. http://frogstorm.com/?p=2915 http://burningissues.org/car-www/medical_effects/yushchenko-dioxin-poisen.htm

23. Organooxygen Compounds: hydrocarbons that have at least one oxygen-containing functional group. Alcohols: contain a hydroxyl functional group attached to an alkane. i.e. ethanol Phenols: benzene rings in which one hydrogen is replaced with an OH functional group. i.e. poison ivy toxin and ascorbic acid. Ketones: contain a carbonyl group (C=O) that occurs in the alkane molecule bonded to two other carbon atoms. i.e. acetone Carboxyl acids: organic acids that contain a hydroxyl group attached to a carbonyl group. (-COOH). i.e. acetic acid Ethers: consist of two carbon groups connected by an oxygen. i.e. dimethyl ether

24. Organonitrogen Compounds Nitrogen is an important component of several functional groups, most notably amino acids and amines. Amino acid: characterized by the presence of an amino group (NH2). Amines: derivatives of ammonia (NH3), in which one or more of the hydrogen atoms are replaced by alkyl groups (functional groups derived from alkanes) or an aromatic ring. Aminocarboxyl acids: (-CH2CO2H) groups bonded to nitrogen atoms. Carbamates: derived from carbamic acid--Often used as pesticide or herbacide.

25. Organosulfur compounds • There are three major organosulfur compounds: • Compounds that contain the functional group in which oxygen is replaced by sulfur. (Thiols, sulfides, disulfides, thiourea –both N & S) i.e.1-napthylthiourea—a rodenticide. • Compounds that contain a functional group consisting of sulfur and oxygen. (Sulfoxides, sulfones). • Sulfur heterocyclics: where sulfur is attached at one of the points in a cyclic carbon molecule.

26. Examples of Organosulfur compounds

27. Organophosphorus compounds Phosphorus can occur in organic compounds in either a 3+ (PH3 –Phosphine) or 5+ (PH5 –Phosphane) oxidation state. Organophosphorus compounds are also distinguished on the basis of their P–C to P–O–C linkages.

28. Polymers: high-molecular-weight compounds that are composed of a large number of simple repeating units called monomers. The conversion process from monomer to polymer is known as polymerization.

29. polyethylene terephthalate http://blog.heritage-enviro.com/Blog/?Tag=plastic%20recycling http://www.speciation.net/News/Toxic-antimony-species-found-in-beverages-stored-in-PET-containers-;~/2006/08/16/2316.html http://www.sustainableisgood.com/blog/2009/02/preservegimme5.html http://earth911.com/recycling/construction/pvc/ Figure 5-21. Examples of monomers used to build the common synthetic polymers. See text for examples of the uses of each synthetic polymer. http://green514.com/2008/03/29/polystyrene-6/

30. Carbon Compounds in the Environment

31. Natural Sources of Carbon Compounds…

32. Humic Substances: a general category of naturally occurring, biogenic, heterogeneous organic substances that can generally be characterized as being yellow to black in color, of high molecular weight, and refractory. • Humin: that fraction of the humic material that is insoluble in water at all pH values. • Humic acid: that fraction of the humic material that is soluble in water at pH values greater than 2. • Fulvic acid: that fraction of the humic material that is soluble in water at all pH values. • Humic and Fulvic acids are the major components of both freshwater and marine DOC. (although there are significant differences in the types of humic substances that occur in these 2 environments.)

35. Soil Organic Matter Soil: a complex system of air, water, decomposing organic matter, living plants, and animals, in addition to the residues of rock weathering, organized into definite structural patterns as dictated by the environmental conditions.

36. http://esask.uregina.ca/entry/soils.html http://www.extension.org/pages/33600/management-recommendations-for-soil-carbon-storage

37. Gelisols - soils with permafrost within 2m of the surface. Histosols - organic soils. Spodosols - acid forest soils w/ a subsurface accumulation of metal-humus complexes. Andisols - soils formed in volcanic ash. Oxisols - intensely weathered soils of tropical and subtropical environments. Vertisols - clayey soils with high shrink/swell capacity. Aridisols - CaCO3-containing soils of arid environments with subsurface horizon development. Ultisols - strongly leached soils with a subsurface zone of clay accumulation and <35% base saturation. Mollisols - grassland soils with high base status. Alfisols - moderately leached soils with a subsurface zone of clay accumulation and >35% base saturation. Inceptisols - soils with weakly developed subsurface horizons. Entisols - soils with little or no morphological development.

39. Marine Organic Matter Marine and terrestrial sedimentary environments differ in a number of important ways. Marine sediments have a greater porosity and a narrower range (7-8 versus 4.0 – 8.5) of pH than terrestrial sediments. Different environments contain different organisms and as a result have different C/N ratios and d13C values.

40. Coal: carbonaceous sediment composed most often of the remains of spores, algae, fine plant debris and noncarbonaceous ash. Humic coals: derived from humic substances via a peat stage. Sapropelic coals: formed from fairly fine-grained organic muds in quiet, oxygen-deficient shallow waters. Peat: Unconsolidated, semicarbonized plant remains with high moisture content. Not true coal.

41. Lignite: (brown coal) coal with high moisture content and commonly retain many of the structures of the original woody plant fragments. Bituminous: coals that are hard, black coals with a higher carbon content than lignite and commonly display alternating bright and dull bands.

42. Anthracite: hard, black, dense coal commonly containing more than 90% carbon. Anthracite is hard and shiny and breaks with conchoidal fracture.

43. Petroleum: any hydrocarbon-rich fluid (liquid or gas) derived from kerogen by increases in pressure and temperature. Kerogen: a polymeric organic material that occurs in sedimentary rocks in the form of finely disseminated organic macerals—the preserved remains of plant material. Diagenetic environment: the environment in which processes occur at pressures and temperatures greater that those of the weathering environment, but below those required to produce metamorphism.

44. Cracking: the process whereby complex organic molecules such as kerogens or heavy hydrocarbons are broken down into simpler molecules (e.g. light hydrocarbons) by the breaking of carbon-carbon bonds in the precursors. The rate of cracking and the end products are strongly dependent on the temperature and presence of any catalysts.

45. Sweet crude oil has a low sulfur content. Sour crude oil has a high sulfur content. Why would the percentage of S and N be important?

46. Natural carbon inputs to surface and ground waters. TOC is the total organic carbon and is composed of the DOC and the POC. DOC is dissolved organic carbon—can pass through a 0.45mm filter. POC is particulate organic carbon—carbon particulate matter retained by a 0.45mm filter. Sources of carbon can either be allochthonous (from outside the aquatic system) or autochthonous (from within the aquatic system).

47. The concentrations of organic carbon vary greatly with differing aquatic systems, as does DOC / POC. In general: Surface waters have higher TOC than deep waters, because of photosynthetic organisms. Coastal waters have a higher TOC than open ocean waters, because of land inputs. Groundwater has a low carbon content, because organic carbon is used as a food supply by heterotrophic microbes.

48. Anthropogenic Carbon inputs to surface and ground waters Organic carbon: Think waters overrun by septic systems… If these effluents contain nutrients (N, K, P) which are often limited in the natural environment, it can lead to eutrophication. BOD: (biological oxygen demand) the capacity of the organic matter in a sample of natural water to consume oxygen. The BOD should be much lower than 8.7 mgO2/L (O2 saturation value at 25°C).The median BOD for unpolluted waters in the United States is 0.7 mgO2 / L

49. Pesticides: chemicals used to control the growth of unwanted organisms. Insecticides: a pesticide used to control insects. Herbicide: a pesticide used to control plant growth. Fungicide: a pesticide used to control the growth of various types of fungus. Hard pesticides: typically organochlorine compounds that are persistent in the environment, but have low toxicity in mammalian systems. Soft pesticides: Typically organophosphorus compounds and carbamates that have short residence times in the environment, but are often highly toxic. LD50: the amount of the chemical per unit of body mass required to produce death in 50% of an exposed animal population.

50. Bioconcentration factor: (BCF) the expression of the tendency of a particular organic chemical in water to concentrate in fatty tissue. log BCF = 0.935*log KOW – 1.495 Where KOW = [S]octanol / [S]water and [S]octanol is the concentration of the chemical in the alcohol: 1-octanol and [S]water is the concentration of the chemical in water. The higher the KOW value, the more strongly a chemical is partitioned into the fatty tissue. Chemicals with log KOW values of 7 to 8 or greater tend to be strongly adsorbed to sediments and are unlikely to enter living tissue.