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Date Created: 09/17/15
ESRP 531 Fundamentals of Environmental Toxicology Chemistry Review Addendum Overview of Important Chemical Concepts Emphasis on valency of atoms and relevance for molecular bonding Emphasis on functional groups and the concept of polarity Emphasis on physicochemical properties Emphasis on phase transfer processes Periodic Table of Elements 11 12 IB IIB IB IIB of Electrons in Shell Name Symbol Atomic Atomic 1 2 3 4 5 Net No of Number Mass K L M N 0 Charge of Covalent Kernel Bonds Hydrogen H 1 1008 1 1 1 Helium He 2 4003 2 0 Carbon C 6 12011 2 4 4 4 Nitrogen N 7 14007 2 5 5 3 4C Oxygen O 8 15999 2 6 6 2 1d Fluorine F 9 18998 2 7 7 1 Neon Ne 10 20180 2 8 0 Phosphorus P 15 30974 2 8 5 5 35 Sulfur S 16 32060 2 8 6 6 2 4 6 1C Chlorine Cl 17 35453 2 8 7 7 1 Argon Ar 18 39948 2 8 8 0 Bromine Br 35 79904 2 8 18 7 7 1 Krypton Kr 36 83800 2 8 18 8 0 Iodine I 53 126905 2 8 18 18 7 7 1 Xenon Xe 54 131290 2 8 18 18 8 0 Number of Covalent Bonds that Elements Can Have Helps Understand Molecular Structure Element Atomic Symbol Hydrogen H Carbon C Nitrogen N Oxygen O Fluorine F Phosphorus P Sulfur S Chlorine CI 354 Bromine 8O llCDQ IlO Q IlgtA Covalent Bonds Formed between atoms by shanng electrons Polarity Polar Bonds Owing to differences in electronegativity sharing of electrons in the bonding orbitals may be unequal le toward one atom or the other n Thus positive electron deficient and negative electron rich poles are set up between atoms in a molecule 5 8 C O Ionic Bonding Na C1quot When atoms of very large differences in EN bond such as between column 7 and column 1 or 2 elements then the electrons may be transferred from the atoms of lowest negativity too the atoms of highest negativity Thus the atoms of highest EN would have a permanent negative charge The atoms of lowest EN would have a permanent positive charge Hydrogen Bonding When hydrogen H is bonded to O or N which are more electronegative then the relatively positive H can be attracted to an electronegative atom on nearby molecules Especially if the more EN atom as an unbonded pair of electrons Forms a hydrogen bond not as strong as covalent or ionic bond but it can form stable molecular interactions 8 5 8 o H N Atoms within molecules actually exist in definite geometric spatial relationships to one another that are characteristic of the type of bond For ex carbon atoms have four valence electrons each oriented toward the corner of a tetrahedron C gtNitrogen often uses three valence electrons with an unpaired electron available for bonding an electron deficient species like H its spatial geometry tends to by trigonal N I Geometry Bond Angles Double bonds will make a molecule more rigid giving the atoms less degrees of freedom to flop around and rotate about each other xix gt lt Geometry Bond Angles Aromatic structures alternating double bonds in ringed systems tend to be planar ie less free rotation of the carbon atoms Characterized by delocalized pi electrons that can impart some electronegative character Aromatic structures also are more stable than noncyclic structures Q Note that double bonds in linear structures also have delocalized pi bonds Dipole Moment The overall polarity of a molecule depends on both the presence of polar bonds and on the geometry of the molecule Planar trigonal tetrahedral The the determinant of overall polarity is the vector sum of the individual polar bonds which is called the dipole moment Carbon dioxide Methanol 1 5 v 3 1 13 quot 39 r M M j 1 L 3939f vw 7 7 7 7 a van der Waals only H H HM 114 HH gm may F 1394 9 H 391 umHHHHHHIH a a H Ca rgx xg39 Attraction between H H H 2 molecules due to instantaneous dipole moments M van cler Waals polar 1 I1 H H 1 H39QMEr39gx 4915 Cx39 H H II 1 E IE1 59 Hiquot lfv39 n 1239 H3 H xix xg H HCH H H fCU H gH H dipole dlpole dipole induced dipole E quot T 739 V vt W r U 1quot a I w 1 3 rquot I r 7U M H V H L vii 7 37 7 7 in van der Waals polar Hbonding r l 1EeiiglLilllf illlltll z 454th4W Substance Molecular Dipole B oiling Mass Moment Point MD K propane CH3CH2CH3 44 01 231 dimethyl ether CH3OCH3 46 13 248 methyl chloride CH3Cl 50 20 249 acetaldehyde CH3CHO 44 27 294 acetonitrile CH3CN 41 39 355 C C C C R OH R SH R1 O R2 R1 S R2 alkyl can be denoted by R hydroxy alcohol if phenol then R Q mercapto thi01mercaptan ether sulfide thioether amino primary amine R2 R3 H secondary amine R3 H tertiary amine R1 R2 R3 C aniline if R Q R1 C R2 0 II R C OH 0 R1 C O R2 0 R1 C S R2 carbonyl ketone aldehyde when R 2 H carboxy carboxylic acid ester carboxylic acid ester thioester X Rl 0 P O R3 R2 O E R2 R1 C N I R CEN Phosphate ester if X O Thiophosphate ifX S amide nitrile nitro nitroso L e ch CH2 CH3 Saturation H3C CH2 CH3 Unsatu ration Phylii 53 71lrw mil f7 lll quot71 Water Solubility The amount of a substance that dissolves in a given quantity of water at a given temperature to form a saturated solution Think of it as the escaping tendency of molecules from one another when placed in water Limitations to Water Solubility Regular highly ordered structure of water Results from high degree of hydrogen bonding Cause of very high surface tension for such a small molecule Surface tension is the intermolecular cohesive attraction between like molecules of a liquid that cause it to minimize its surface area Cause the high boiling point of water A solute dissolving in water has to disrupt the orderly structure of water with consequent energy costs Think of it as punching a hole in the water Orderly structure of water due to Hbonding O O O Intramolecular attractions among water molecules give water its high surface tension ie the amount of energy needed to overcome the molecular attractions Hydrophobic Molecule in Water Phase Transfer Processes Reversible partitionings of dilute concentrations of a compound between two phases Can be thought of as the escaping tendency of molecules from one phase into another aka fugacity Expressed by the partition coefficient Ratio of the concentration of the chemical in one phase air soil biological tissue organic solvent relative to the concentration in water Organic SolventWater Partitioning OctanolWater Partition Coefficient Partitioning behavior is between two immiscible liquids Octanol used as the partitioning solvent against water Surrogate for an organism s membranes KOW CSCW where CS is the abundance in the organic solvent phase amp CW in the water Kow If place an organic compound in water and then add octanol the compound will move from water into octanol until until the system is at equilibrium The concentration at equilibrium would represent the lowest energy state The lower the water solubility the greater the tendency to move into the octanol phase OilWater a a a Octanol 0 30 000 a Water Octanol Water Partition Coeff Kow Biological Significance of Kow Kow is often expressed in log form For example a Kow of 1000 would be express as log Kow 3 The higher the log Kow the comparatively greater the hydrophobicity Compounds with higher Kow s tend to diffuse across membranes faster compared to those with lower Kow s However there are some limitations to this generality at very high Kow s