Chemistry of Metals and Organics Atoms & Molecules

Chemistry of Metals and OrganicsAtoms & Molecules Bruce Herbert Geology & 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?

Contaminant Chemistry 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. • 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. 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.

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

Contaminant Chemistry and Electronic Configuration • 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 forbitals • The orbital-orientation quantum number, ml, describes the shape of the s, p, d, or forbitals. 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.

Contaminant Chemistry and Electronic Configuration Table 2.2 Number of electrons needed to fill different orbitalsdescribed by different quantum numbers.

Contaminant Chemistry and Electronic Configuration 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.

Contaminant Chemistry and Electronic Configuration • 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.

Contaminant Chemistry and Electronic Configuration

Electronic Configuration and Metal Chemistry The electronic configuration, especially that of the valence electrons, determines chemical properties and reactivity. • The base cations have valence electrons in s and porbitals. 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 forbitals. These elements lose electrons. • The nonmetals have valence electrons in s and porbitals. These elements gain electrons to achieve a noble gas configuration.

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

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 dorbitals). Soft Lewis bases tend to undergo oxidization easily. • Examples:Cd2+, Cu+, Hg2+.

Hard and Soft Acids and Bases • 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.

Hard and Soft Acids and Bases 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.

Hard and Soft Acids and Bases The Misono softness parameter is an indication of covalent bonding potential, and is defined as: • 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

Significance of the HSAB Concept HSAB concept can be used to predict complexation • 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

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 b1 3d structure http://en.wikipedia.org/wiki/File:Aflatoxin_b1_3d_structure.png Aflatoxin Sorption to Clays: Why? http://en.engormix.com/MA-mycotoxins/articles/understanding-adsorption-characteristics-yeast-t218/p0.htm 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.

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

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)

Organic Contaminant Structure • Unsaturated organics backbones: • straight chain • branched chain • cyclic compounds • Saturated organics backbones: • aromatic compounds.

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.

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.

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+Xz-, is described by Coulomb's Law 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

Organic Contaminant Structure

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

Chemistry of Metals and Organics Atoms & Molecules