3. Organic Geochemisty Organic Chemistry is the chemistry... of Carbon -Morrison and Boyd

Transcription

1 3. Organic Geochemisty Organic Chemistry is the chemistry... of Carbon -Morrison and Boyd Definitions, Nomenclature Organic Compound Solubility Octanol-Water Partition Coefficient Organic Compound Sorption Organic Compound Reactions Microbial-Mediated Reactions

2 Classes of Organic Compounds Name Structure Example (aliphatic) R = Alkyl group (-C n H 2n+1 ) #Carbon Prefix 1 methyl 2 ethyl 3 propyl 4 butyl 5 pentyl 6 hexyl 7 heptyl 8 octonyl

3 Classes of Organic Compounds Name Structure Example

4 Classes of Organic Compounds Name Structure Example

5 Example Organic Compound methyl: tert-butyl: Note: tert is short-hand for tertiary ether: Resulting Name: MTBE

6 Aromatic Compounds Contain a Benzene Ring Benzene has a six-carbon ring structure, with 6 hydrogens (one bonded to each carbon); each carbon has both a double and single bond to its neighbor, creating a complex (and stable) p (pi) electron structure; example:

7 Isomers: molecules with identical elemental composition and different structures Example 1: C 2 H 6 O Boiling point: 78 o C (liquid) -24 o C (gas) One of my favorite organic compounds Dentists pass this gas

8 Isomers Example 2: C 2 H 2 Cl 2 cis- and trans- 1,2 dichloroethylene Boiling point: 60 o C (cis-) 48 o C (trans-)

9 Ranges of Organic Compound Water Solubilities Schwarzenbach et.al.

10 Water Solubility vs Molecular Size (Total Surface Area) Schwarzenbach et.al.

11 Octanol-Water Partition Cefficient (K ow ) Octanol: C 8 H 17 OH - The Octanol Water Partition Coefficient (K ow ) is the ratio of the concentration of a compound in a mixture of octanol (an eight-carbon alcohol) and water at equilibrium. - Hence this coefficient is a measure of the difference in solubility of the compound in these two phases. - Hence, K ow measures how hydrophilic ("water-loving") or hydrophobic ("water-fearing") a chemical substance is. - In the field of hydrogeology K ow is often used to predict and model the migration of dissolved hydrophobic organic compounds in soil and groundwater.

12 Octanol-Water Partition Coefficient values for various compounds K ow = Solubility in Octanol/Solubility in Water Moles/L solvent Schwarzenbach et.al. Octanol: C 8 H 17 OH

13 Ranges of K ow for Classes of Organic Compounds Schwarzenbach et.al.

14 Water Solubility vs K ow Tinsley

15 Regression Equations for Estimating Solubility using K ow Lyman, et.al.

16 Estimating K ow using Fragment The addition of a methyl group to each of the base compounds has the effect of increasing the base K ow by about a half a log unit, decreasing its solubility by about 3. Schwarzenbach et.al. Effects

17 Example of K ow Estimation using Fragment Substitution Compound name: Nitrobenzene Compound Structure: Observed K ow : 1.84 Schwarzenbach et.al.

18 Example of K ow Estimation: Tetrachloroethylene (PCE) Fragments Intramolecular Schwarzenbach et.al.

19 Adsorption of Organic Compounds - Adsorption of non-polar organic compounds from water on soil consists primarily of partition (sorption) into the soil organic phase - Adsorption by the soil mineral fraction is relatively unimportant in wet soils due to the strong dipole interaction between soil minerals and water, which excludes non-polar organic solutes from this component of the soil.

20 Inverse Relationship between Solubility and Adsorption of Organic Compounds Solubility in Organic Matter Water Solubility Schwarzenbach et.al.

21 Soil-Water Adsorption Isotherms for various organic compounds K d = slope = Dsoil uptake/dwater conc K d = f om K om K om = C om /C w f om = soil organic 25 o C Chiou et.al., 1979

22 Organic Matter Adsorption (K om ) vs K ow Schwarzenbach et.al.

23 Regression Equations for Soil Adsorption Coefficient K oc = mg adsorbed/g organic carbon mg/ml solution S = water solubility; K ow = octanol-water partition coefficient Lyman, et.al.

24 Example of estimating K oc for Trichloroethylene log K oc = 2.29 K oc = 195 Lyman et.al.

25 Organic Compound Reactions: Microbial Metabolism - All living cells require energy to function - The process of extracting energy and then utilizing that energy is metabolism - Metabolic functions include extracting energy from compounds, storing energy, and using that stored energy to make cellular components, along with other associated life functions (e.g. movement, reproduction) - Many organic compounds are affected by microbially-mediated metabolic reactions.

26 Ex: Oxidation of Glucose Creates Stored Energy in Cellular ATP Ex: C 6 H 12 O 6 + 8O 2 6CO H 2 O kcal Cellular Energy Generation by Oxidation of Glucose via Glycolysis, the Krebs Cycle, and Electron Transfer

27 Nicotinamide adenine dinucleotide (NAD) is a coenzyme found in all living cells. The compound is a dinucleotide, because it consists of two nucleotides joined through their phosphate groups. Nicotinamide adenine dinucleotide exists in two forms, an oxidized and reduced form abbreviated as NAD+ and NADH respectively. In metabolism, NAD is involved in redox reactions, carrying electrons from one reaction to another. The coenzyme is, therefore, found in two forms in cells: NAD+ is an oxidizing agent it accepts electrons from other molecules and becomes reduced. This reaction forms NADH, which can then be used as a reducing agent to donate electrons. (modified f/wikipedia 3/28/16)

28 ATP - ADP Cellular Energy Storage and Release ATP ADP Structure and Hydrolysis

29 Redox Reactions: Energy Released Decreasing Energy Anaerobic Respiration via alternate TEAs

30 Example of Substrate Degradation: Aerobic Oxidation of Methane Catalyzed by Methane Monooxygenase and Formate dehydrogenase Methanol Formaldehyde 3 Methane Nicotinamide adenine dinucleotide, used for electron transfer Formate Chapelle

31 Monooxygenases are enzymes that incorporate one hydroxyl group into substrates in many metabolic pathways. In this reaction, the two atoms of molecular oxygen are reduced to one hydroxyl group and one H 2 O molecule by the concomitant oxidation of NAD(P)H. (Wikipedia, 3/28/16)

32 Electron Transfer in Nitrate Reduction to N 2 (g) nitrate nitrite Nitrogen gas Nitrous oxide Chapelle

33 Electron Transfer in Iron (III) Reduction with Acetic acid Krebs Cycle Acetic acid, vinegar Chapelle

34 Sulfate Reduction using Lactate as a Carbon Source Chapelle cell interior space between the inner cytoplasm membrane and the bacterial outer membrane

35 Methane Production (methanogenesis) from the reduction of (a) CO 2 and (b) Acetate (a) (b) Chapelle

36 Examples of Biodegradation Reactions b-oxidation Removal of ethyl groups via oxidation producing acetyl-coa Lyman et.al.

37 Ex: Oxidation of n-alkanes (a) Terminal Methyl Oxidation Production of organic acids (b)subterminal Methyl Oxidation Chapelle

38 Aerobic Oxidation of Benzene to Cathenol Chapelle

39 Degradation of Toluene under Fe (III) Reducing Conditions Chapelle, after Lovely and Lonergan

40 Degradation Pathways for Benzene (a) and Toluene (b) under Methanogenic Conditions Chapelle

41 Examples of Biodegradation Reactions Reaction contd. Example Removal of halogen group (Cl) via reduction: Lyman et.al.

42 Degradation of Tetrachloroethylene and Trichloroethylene under Methanogenic Conditions, Accumulation of Vinyl Chloride Chapelle?

43 Kinetic Rates of Degradation Reactions Michaelis-Menton equation First-order eq. solution Where: V is the rate of substrate uptake (moles per time), vmax is the maximum rate of substrate uptake, Ks is the substrate concentration at which v = ½ vmax S is substrate concentration (moles per liter), B is the amount of cells (grams). -At low substrate concentrations where S << K, and when the microbial population is steady, the Michaelis-Menton equation is approximated by first-order kinetics: V ~ ks where k is a rate constant (units of 1/time). Chapelle, 2003

44 Benzene, Toluene, and Xylene Degradation under Aerobic and Anaerobic Conditions (Percent remaining after 62 days) Chapelle

45 Summary - K ow (the octanol-water partition coeffcient) is often used to predict and model the solubility, adsorption, and rates of migration of dissolved hydrophobic organic compounds in soil and groundwater. - Microbial degradation can and often does transform and remove many organic contaminants from the subsurface. - Biodegradation occurs through metabolic reactions catalyzed by enzymes, that can support microbial growth. - Biodegradation can and does occur in oxic and anoxic conditions, including nitrate, iron, and sulfate reduction, and methanogenesis.

46 Next Groundwater Geochemistry