chemistry of metals and organics atoms & molecules

ENVIRONMENTAL GEOCHEMISTRY AT TEXAS A&M UNIVERSITY

http://environmentalgeochemistry.pbworks.com//

Chemistry of Metals and Organics

Atoms & Molecules

Bruce HerbertGeology & Geophysics



Contaminant Chemistry

■ The dominant geochemical factor that determines the fate and transport of contaminants is contaminant chemistry.

■ In this section we will describe the chemistry of metal and organic contaminants in terms of their basic properties which control their reactivity, toxicity, transport, and biodegradability.



Which Chemicals are Important Contaminants?




■ The pollutants on the list were the most common toxic compounds released from point sources by industry in 21 categories.

■ The list contained 129 compounds

■ The 13 metals are defined as total metals, since metals can combine with ligands to form thousands of different compounds in a typical environmental sample.

In 1978 the Environmental Protection Agency (EPA) created a list of toxic pollutants with wastewater effluent concentration limits and guidelines in 1978 as a result of a lawsuit brought against the EPA by a number of environmental groups. This list was called the priority pollutant list.

Under the legislative authority granted to the U.S. Environmental Protection Agency (EPA) under the Comprehensive Environmental Response, Compensation, and Liability Act of 1980 (CERCLA) and the Superfund Amendments and Reauthorization Act of 1986 (SARA), EPA develops standardized analytical methods for the measurement of various pollutants in environmental samples from known or suspected hazardous waste sites.




■ The list contains:

■ Volatile organics

■ Semivolatile organics

■ Pesticides/aroclors

■ Chlorinated Dibenzo-p-dioxins / Chlorinated Dibenzofurans (CDDs / CDFs)

■ Metals and Cyanide

■ The list is based on advances in analytical methods, evaluation of method performance data, and the needs of the Superfund program.

See http://www.epa.gov/superfund/programs/clp/target.htm

The Contract Laboratory Program (CLP) Target Compound and Target Analyte Lists (TCL/TALs) were originally derived from the EPA Priority Pollutant List.



The Chemistry of Metals and other Inorganic Contaminants



Which metals are the most toxic - make a list.

Why?



Contaminant Chemistry and Electronic Configuration

■ Classification of contaminants are based on measures of their reactivity. In general, reactivity is controlled by an atom's electronic configuration

■ Electronic configuration: distribution of electrons in an atom's orbitals.

■ Electronic orbitals: probability functions of the electron density around a nucleus.

Figure 2.1 The electron density around a positive nucleus. Circle shows 90%-99% probability region for a 1s orbital. Taken from Gray. 1973. Chemical Bonds: An Introduction to Atomic and Molecular Structure. Benjamin/Cummings Publ., Menlo Park. p. 21.




■ The distribution of electrons, and the type of orbital, around a nucleus is describe with quantum numbers.

■ Electrons have energy levels or shells designated by "n", the principle quantum number. The energy levels determine the effective volume of an electron orbital, the volume increases as n increases.

■ The orbital shape quantum number, "l" describes the type of orbital. There are (n-1) orbital-shape quantum numbers.

■ The 0, 1, 2, and 3 values of l are often designated as s, p, d, and f orbitals

■ The orbital-orientation quantum number, ml, describes the shape of the s, p, d, or f orbitals. It can have values equal to -l, -l+1,..0,..l-1, l.

■ The spin quantum number, ms, describes the electron spin, which can be one of two directions.




Table 2.2 Number of electrons needed to fill different orbitals described by different quantum numbers.




Electron orbitals for different quantum numbers.

Taken from Gray. 1973. Chemical Bonds: An Introduction to Atomic and Molecular Structure. Benjamin/Cummings Publ., Menlo Park. p. 22.

l = 0

l = 1

l = 2

n = 1

n = 2

n = 3




■ Electrons are filled in sequence of increasing relative energies of the orbitals (Figure 2.3). No two electrons can have the same quantum numbers. This is the Pauli Exclusion Principle.

Increasing

Energy

n = 1 2 3 4 5 6

s

s

p

s

s

s

s

p

p

p

p

d

d

d

d

f

f



The Periodic TableSubshells being completed

PrincipalQuantumNumber

n1

2

3

4

5

6

7

ns

Transition Metals( n- 1 ) d

Nonmetalsnp

(n-2)f

Base Cations

Lanthanide Series

Actnides Series

Posttransition Metals

1 2

3 4 5 6 7 8 9 10

11 12 13 14 15 16 17 18

19 20 21 22 23 24 25 26 27 28 29 30 31 32 33 34 35

37 38 39 40 41 42 43 44 45 46 47 48 49 50 52 53 54

55 56 57

58 59 60

2

36

72 73 74

87 88 89 104 105 106

51

81 82 83 84 85 86

61 62 63 64 65 66 67 68 69 70 71

90 91 92 93 94 95 96 97 98 99 100 101 102 103

H He

L i Be

Na Mg

K Ca

Rb S r

Cs Ba

F r Ra

Sc

Y

La

Ac

T i

Z r

Hf

Rf

V

Nb

Ta

Ha

C r

Mo

W

Mn

Tc

Ce P r Nd Pm Sm Eu Gd Tb Dy Ho E r

Th Pa U Np P u Am Cm Bk Cf Es Fm

Fe Co N i Cu Zn Ga Ge

Al S i

In Sn

T l Pb

Ru Rh Pd Ag Cd

Re Os I r Pt Au Hg

Tm Yb Lu

Md No L r

He

B C N O F Ne

Ar

K r

Xe

RnAtPoB i

Sb Te I

B r

ClP S

SeAs




Electronic Configuration and Metal Chemistry

■ The base cations have valence electrons in s and p orbitals. These elements lose electrons to achieve a noble gas configuration.

■ The transition metals, either as a neutral atom or an ion, have valence electrons in the d and f orbitals. These elements lose electrons.

■ The nonmetals have valence electrons in s and p orbitals. These elements gain electrons to achieve a noble gas configuration.

The electronic configuration, especially that of the valence electrons, determines chemical properties and reactivity.



Atomic Properties

■ The effective atomic radii, R, of an atom is defined as one half of the distance between two nuclei of the element that are held together by covalent bonds.

■ The atomic radii increases as you move down the periodic table and decreases across a row of the periodic table

■ The radii is used to calculate the charge-to-radius ratio (Z/R) or ionic potential (IP), which is an important factor in determining the polarizability of an atom.



Atomic Properties

■ The first ionization energy, I1, of an atom is defined as the energy required to remove an electron from a gaseous atom.

■ The ionization potential decreases as you move down the periodic table and increases across a row.

■ The electron affinity (ea) of an atom is defined as the energy change accompanying the addition of one electron to a neutral gaseous atom.

■ The electron affinity decreases as you move down the periodic table and increases across a row.



Atomic Properties

■ The electronegativity (EN) of an atom is the relative ability of an atom to attract electrons to itself in a chemical bond

■ Electronegativity qualitatively describes the sharing (covalent character) of electrons between 2 different atoms.

■ High electronegativities indicates electrons will be transferred in a chemical bond (ionic).

■ Polarization: the ease to which an electron cloud is deformable



Atomic Properties

Lanthanide Series

Actnides Series

58 59 60 61 62 63 64 65 66 67 68 69 70 71

90 91 92 93 94 95 96 97 98 99 100 101 102 103

Ce Pr Nd Pm Sm Eu Gd Tb Dy Ho Er

Th Pa U Np Pu Am Cm Bk Cf Es Fm

Tm Yb Lu

Md No Lr

Transition Metals

Nonmetals

Base Cations

Posttransition Metals

1 2

3 4 5 6 7 8 9 10

11 12 13 14 15 16 17 18

19 20 21 22 23 24 25 26 27 28 29 30 31 32 33 34 35

37 38 39 40 41 42 43 44 45 46 47 48 49 50 52 53 54

55 56 57

2

36

72 73 74

87 88 89 104 105 106

51

81 82 83 84 85 86

H He

Li Be

Na Mg

K Ca

Rb Sr

Cs Ba

Fr Ra

Sc

Y

La

Ac

Ti

Zr

Hf

Rf

V

Nb

Ta

Ha

Cr

Mo

W

Mn

Tc

Fe Co Ni Cu Zn Ga Ge

Al Si

In Sn

Tl Pb

Ru Rh PdAg Cd

Re OsIr

Pt Au Hg

He

BC N O F Ne

Ar

Kr

Xe

RnAtPoBi

Sb Te I

Br

ClP S

SeAs

The Periodic Table

Effective Atomic Radii

and Ionization Energies

Increasing

Radii

Decreasing IP

and EA

Increasing

IP and EA

Decreasing

Atomic RAdii

Increasing

Electronegativity



Hard and Soft Acids and Bases■ Atoms can be classified as either "hard" or "soft" Lewis acids or bases (HSAB)

based on their properties. These are relative terms.

■ Lewis acids and bases

■ Lewis acids are any species that employs an empty electronic orbital to initiate a complexation reaction. Lewis acids accept electrons.

■ Lewis bases are species that employs a doubly occupied electronic orbital to initiate a complexation reaction. Lewis bases donate electrons.

■ Lewis acids and bases can be neutral molecules, ions, or neutral or charged macromolecules.

■ Complexation is the reaction between Lewis acids and bases. It is one of the basic chemical reactions in solution and during sorption.

■ Compare the definition of a Lewis acid or base to that of a Bronsted acid or base. A Bronsted acid donates protons (H+). A Bronsted base accepts protons (H+)



Hard and Soft Acids and Bases

■ Hard Lewis acids and bases are species, respectively, that are small, high oxidation state, slightly polarizable species with high electronegativities. Ions typically have electron configurations of an inert gas. Hard Lewis bases tend not to undergo oxidization.

■ Examples: cations of H, Na, K, Ca, Mg, Al3+, and Fe3+.

■ Soft Lewis acids and bases are species that are large, more polarizable species with low electronegativities. Ions typically have electron configurations with 10 or 12 valence electrons (filled d orbitals). Soft Lewis bases tend to undergo oxidization easily.

■ Examples: Cd2+, Cu+, Hg2+.




■ HSAB can be used to organize complexation reactions because hard acids typically complex with hard bases, and vice-versa under similar conditions of acidity.

■ Many of the bivalent trace metals (transition metals) are borderline.

■ Generally, those ionic species with high electronegativities are hard and those with low electronegativities are soft.




Several parameters have been used to help classify atoms as either "hard" or "soft" acids or bases (HSAB).

The ionic potential is the charge to radius ratio.

IP =valence

radius(nm )




■ R is the ionic radius (nm), Z is the valence, and Iz is the ionization potential of the ion with a valence of Z.

■ For Y < 0.25 nm, metal ions form ionic bonds and are hard acids

■ For Y > 0.32 nm, metal ions form covalent bonds and are soft acids

■ For 0.25<Y<0.32, metal ions are borderline whose tendency to form covalent bonds depends on solvent, stereochemical, and electronic configurational factors

The Misono softness parameter is an indication of covalent bonding potential, and is defined as:

Y =10IzRZ • Iz+1



Significance of the HSAB Concept

■ Complexes form when an ions acts as a central group to attract and form a close association with other atoms or molecules

■ The associated ions or molecules are ligands

HSAB concept can be used to predict complexation



Significance of the HSAB Concept

■ The principles of HSAB can be used to predict the speciation of transition metals in subsurface systems as well as their relative toxicity.

■ The speciation of transition metals is more affect by the presence of natural organic matter than the speciation of the base cations.

■ Likewise, changes in the concentrations of Cl-, and S2- in subsurface waters will also strongly affect the speciation of trace metals.

■ Finally, metal toxicity is often due to the complexation of a trace metal with a biologically important molecule in an organisms. Because these organic molecules are soft, the HSAB would predict that toxicity is directly related to the softness of a trace metal.



Representative Metal Toxicity Sequences



Organic Molecules



Aflatoxin

http://www.niehs.nih.gov/health/impacts/aflatoxin/index.cfm

http://www.icrisat.org/aflatoxin/aflatoxin.asp

http://www.ces.ncsu.edu/depts/pp/notes/Corn/corn001.htm

Aflatoxin Sorption to Clays: Why?

http://en.engormix.com/MA-mycotoxins/articles/understanding-adsorption-characteristics-yeast-t218/p0.htm

Aflatoxin b1 3d structurehttp://en.wikipedia.org/wiki/File:Aflatoxin_b1_3d_structure.png

http://wgharris.ifas.ufl.edu/SEED/COMPONENTS.HTM



Structure-Activity Relationships



Quantitative Structure-Activity Relationships (QSARs)

■ We are interested in the environmental fate, toxicity, and contaminating potential of over 70,000 natural and man-made organics chemicals.

■ Obviously, we can not memorize the chemical properties of such a large number of organics, therefore structure-activity relationships have been developed.

■ Structure-activity relationships are quantitative relationships between the chemical structure of an organic and its chemical and physical properties.

■ ECOSAR (Ecological Structure Activity Relationships) is a personal computer software program that is used to estimate the toxicity of chemicals used in industry and discharged into water. The program predicts the toxicity of industrial chemicals to aquatic organisms such as fish, invertebrates, and algae by using Structure Activity Relationships (SARs). The program estimates a chemical's acute (short-term) toxicity and, when available, chronic (long-term or delayed) toxicity.

http://www.epa.gov/opptintr/newchems/21ecosar.htm



Structure-Activity Relationships

■ We can predict the properties of organic contaminants based on their structure.

■ The two complex structures shown below are pesticides. Aldicarb is on the left and aldrin is on the right.

C

CH3

S CH NOCNHCH3

CH3

CH3

O

CCl2

CH2

Cl

Cl

Cl

Cl



Chemical Bonds and Organic Contaminant Structure



Chemical Bonds

■ There are several types of bonds which can form between atoms, or between molecules.

■ Chemical bonds are forces of attraction between two atoms or molecules.

■ Bonds hold molecules together, control the interaction of metals with ligands, or control the interaction between solutes and solvents.



Covalent Bonds

■ Reactivity of organic compounds is related to the strength of chemical bonds between the atoms in an organic molecule.

■ Almost all atoms within an organic molecule are bound together with covalent bonds.

■ Covalent bonds form when two atoms share electrons that exist in similar orbitals.

■ Pure covalent bonds: electrons are shared equally in the bond

■Molecules such as Cl2, H2, and O2

■Polar covalent bonds form when electrons are share unequally



Chemical Bonds and Organic Contaminant Structure

■ The structural backbone is generally composed of carbon atoms (though N, S, and O can also compose part of the backbone) covalently bonded together to give the overall shape to the molecule.

■ Covalent bonds are formed when electrons are shared between atoms in order to fill their valence shell. Each covalent bond shares two electrons.

The overall structure of organic contaminants, or their spatial arrangement of atoms, is determined by their structural backbone.

C

CH3

S CH NOCNHCH3

CH3

CH3

O



Organic Contaminant Structure

■ Single, double, and triple covalent carbon bonds are possible in the structural backbone.

■ Saturated hydrocarbons are compounds formed with single bonds in their structure.

■ Unsaturated hydrocarbons are compounds with double and triple bonds .

■ Single carbon bonds: Alkanes(CnH2n+2)

■ Double carbon bonds: Alkenes(CnH2n)

■ Triple carbon bonds: Alkynes(CnH2n-2)

CH3 −(CH2)6 −CH3 n −oc tane

CH2 =(CH2)6 −CH3 1−octene




■ Unsaturated organics backbones:

■ straight chain

■ branched chain

■ cyclic compounds

■ Saturated organics backbones:

■ aromatic compounds.

CH3 - (CH2)6 - CH3

CH2 = (CH2)6 -CH3 CH2 = (CH2)6 = CH2

CH3 - C - CH2 - CH

CH3

CH3

CH3

CH3

CH3

CH3

Octane Isooctance

1-Octene 1,7 Octadiene

Cyclopentane Methyl-cyclohexane



Covalent Bond Energies and Bond Lengths



Electronegativity and Bond Polarity

■ Differences in electronegativity: electron cloud around a bond is not shared equally.

■ The bond then has a partial ionic character, and is termed a polar covalent bond. Polarization is important in determining the organic compound's

■ Solubility in polar solvents

■ Directing the course of chemical reactions

■ Polarity: ■ A molecule is polar if its electron cloud is not evenly distributed around the

nuclei. ■ This imparts a net charge to different parts of the molecule.



Polarity of Water

■ Electronegativity differences between O and H create polar O-H bonds

■ Water is one of the most polar solvents known.

d−

d+d+Solvent Polarity IndexHexane 0.1Toluene 2.4

MethyleneChloride

3.1

Methanol 5.1Water 10.2



Electronegativity and Dipole Moment

■ Dipole moment: sum of all bond dipoles. ■ Dipole moments are

given in arbitrary units called Debye units.

■ The arrow points to the negative part of the molecule.

F

CH3

NO20.43D 3.93D 4.39D Debye Units

CH3

NO2

COHO

F CH3H

COHO

COHO

4.14 4.20 4.38 pKa at 25C



Electronegativity of Functional Groups and Bond Polarity



Ionic Bonds

■ Ionic bonds: electrons are transferred between two atoms and the atoms are then attracted by electrostatic forces.

■ Ionic bonds are found in the alkali metal-halides such as NaCl.

■ The electrostatic energy of an ion pair, Mz+X

z-, is described by Coulomb's Law

E =+q −q4πer

E =+Z −Z 2e4πer

E: energy (Jmol-1)

Q: charge (Coulombs (C))R: distance of separation (m)Z: ionic charge (none)E: electronic charge (1.6 x 10-19 C)E: permittivity (dielectric constant) (C2m-1J-1



Other Intermolecular Forces

■ Intramolecular forces are bonds that hold a molecule together.

■ Intramolecular forces are dominated by strong covalent and ionic interactions

■ Other, weaker bonds may be important in different situations

■ There are several types of weaker, intermolecular bonds which form between molecules.

■ These bonds are the forces which

■hold some solids together,

■allow a molecule to sorb to a mineral surface

■determine the interaction between a solute and a solvent■may be important in giving macromolecules shape.



Hydrogen Bonding and Other Dipole Interactions

■ Weak, intermolecular bonds include van der Walls forces, dipole-dipole interactions including hydrogen bonds, ion-dipole bonds, and pi () bonding.

■ H bonding is the result of the polarization of a bond formed between H and O, F, or N. ■ H bonding between solvent and solute greatly increases solubility

■ H bonding causes lack of ideality in ideal gas and solution laws

■ Intramolecular H bonding changes reactivity compared to compound without intramolecular bonding

■ H bonding plays a significant role in the 3-D conformation of large macromolecules such as proteins and other biomolecules

Bond Bond Energyvan der Waals 1-2 kcal mole-1

dipole-dipole <2 kcal mole-1

H-bonding 2-10 kcal mole-1

ion-dipole ~5 kcal mole-1

pi bonds ~5 kcal mole-1

−O −H• • • • : X −−δ ⋅⋅ +δ ⋅⋅⋅⋅⋅ −δ



Organic Contaminant Structure: Structural Backbone

■ Aliphatic compounds do not have delocalized electrons, though they can have double bonds.

■ Compounds that have delocalized electrons form aromatic molecules,

■ Delocalization occurs in ring structures where pi bonds can form between electrons in adjacent p orbitals.

■ Multiple aromatic rings for polycyclic aromatic hydrocarbons.

■ Because of delocalization, benzene and other aromatics experience increased resonance energy (stabilization) which leads to stability and long term persistence.



Aliphatic and Aromatic Organics

CH3 - (CH2)6 - CH3 CH2 = (CH2)6 -CH3

Octane 1-Octene Cyclopentane

ALIPHATICS

AROMATICS

CH3

Methylbenzene (toluene)PyreneBiphenyl



Isomers

■ If two compounds have the same molecular formula but different structures, they are called isomers.

■ Structure determines reactivity: half-life of hydrolysis at 25° C is 1 yr for isomer I and III, 1 month for compound II, and 30 s for compound IV.

CH3

(CH2

)3

Cl

Butyl chloride isomers

CH3

CH2

CH( Cl) CH3

(CH3

)2

CHCH2

Cl (CH3

)3

CCl

Cl

Cl Cl

Cl

III

IIIIV



Organic Contaminant Structure: Functional Groups

■ To the structural backbone are attached various atoms or groups of atoms, these are called functional groups .

■ Position of functional groups on structural backbone are designated by number.

■ Position for two functional groups on aromatics can also be designated using ortho, meta, or para designations.

orthoor 1,2

AB A

BB

A

metaor 1,3

paraor 1,4

34

5

6 2

45

6 2

5

6

3



Chemistry of Functional Groups: Alkyl Halides

■ Properties (R-X where X is F, Cl, or Br)

■ dipole moment, higher e- density around the halide

■ generally compounds are insoluble in water

■ Some compounds have high vapor pressure [inversely correlated with molecular weight]

C

CCl Cl

ClCl

H

Cl

p,p' DDT

CH

Cl Cl

HMethylene Chloride



Chemistry of Functional Groups: Alcohols and Ethers

■ Properties (R-OH and R-O-R’)■ dipole moment: higher e- density around the oxygen

■ generally compounds are soluble in water, solubility is inversely correlated with molecular weight

■ low vapor pressure

■ H bonding potential, electrostatic bonding at high pH when alcohol dissociates

■ Alcohols are weak acids with pKa’s above 8.

CH

HH OHC

H

HEthanol

CH3 O C CH3CH3

CH3

Methyl-tertButyl Ether

OH

Phenol



Chemistry of Functional Groups: Acids & Esters

■ Properties (R-COOH, R-(C=O)-O-R’)■ dipole moment, higher e- density around the oxygen


■ H bonding potential; can form dipole-dipole bonds; electrostatic interactions if COOH is deprotonated (anion exchange, ligand bonding with metals

■ Weak Bronstead acid (H+ donating) and weak Lewis acid (e- accepting group) in acid solution

COOCH3

COOCH3

Dimethyl phthalate

OCH2

COOH

Cl

Cl

2,4-(Dichlorophenoxy) acetic acid



Chemistry of Functional Groups: Aldehydes & Ketones

■ Properties (R-(C=O)-R’)■ dipole moment, higher e- density around the oxygen


■ H bonding potential

■ weak lewis base (e- donating group) in acid solution

H

H

H

C C

O

H

Acetylaldehyde



Chemistry of Functional Groups: Amides

■ Properties R-(C=O)-NH2

■ dipole moment, higher e- density around the oxygen and nitrogen


■ H bonding potential, may also form electrostatic bonds if amide group protonates.

H

CH2

C C

O

NH2

Acrylamide



Chemistry of Functional Groups: Nitriles

■ Properties (R-CN)■ dipole moment, higher e- density around the nitrogen



H

CH2

C C N

Acrylonitrile



Chemistry of Functional Groups: Amines

■ Properties (R-NH2; R2NH; R3N)

■ dipole moment, higher e- density around the nitrogen


■ H bonding potential, may also form electrostatic bonds if amine group protonates.

■ Amines are weak bases, the amine group will protonate at low pH

NH2

Aniline



Chemistry of Functional Groups: Nitro

■ Properties (R-NO2)

■ dipole moment, higher e- density around the oxygens



OH

NO2

NO2

2,4 Dinitrophenol



Structure-Activity Relationships of Pesticides

Notes: aqueous solubility is in umoles/L; Units for Kd are (umoles/kg adsorbed)/(umoles/L)Low pH refers to pH=4, high pH>6.

chemistry of metals and organics atoms & molecules

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