1. Marine Bioinorganic Chemistry (Trace Metal Biogeochemistry) 12.741 MIT-WHOI Joint Program Graduate Course - Lecture 1 Mak Saito, Marine Chemistry and Geochemistry Department Course websites: www.whoi.edu/sites/12.741 MIT Stellar account online for schedule Outline: 1.Introductions, comments on course schedule, structure, approach, assignments 2.Introduction to Trace Metal Biogeochemistry: an evolving field 3.Classifications of TM profiles 4.Metal Speciation lecture

2. Logistics Schedule will be available at MIT stellar site for 12.741 Class readings will be available at www.whoi.edu/sites/12.741 Occasional Thursday classes to be scheduled

3. A great challenge of our field today: Connecting the Global to the Molecular

5. Class Topics Introduction to trace metal biogeochemistry, broad categories Metal Speciation Free ion model Algal uptake kinetics The Droop model and colimitations Mercury Biogeochemistry (Lamborg as guest lecturer) Iron biogeochemistry (limitation, light colimitation, redox, speciation, uptake mechanism, colloids, and policy) Trace elements and the ancient ocean Metalloenzymes Analytical approaches (in silico and proteomic/mass spec) Specific elemental biogeochemistries (Mn, Al, Pb, Co, Zn, Cd, Cu) Vitamins and cofactors

6. Events Lecture/Discussion of Mercury policy (Carl Lamborg) Lecture on Particulate metals (Phoebe Lam) Bioinformatics module working with genomic resources Phone conference with Bill Sunda, expert trace metal phytoplankton interactions (if time allows) Discussion of iron fertilization Readings on ideas in science for discussion throughout semester

7. Inorganic components are (also) required by life Marine and Environmental Bioinorganic Chemistry Trace Metal Biogeochemistry Bioinorganic Chemistry

8. Metals in Biology Gordon Research Conference Metals play many important roles in biological systems, from essential functional or structural cofactors in proteins, to environmental toxins. The Metals in Biology Gordon Research Conference is one of the longest- running GRCs (starting in 1962). It brings together researchers that span expertise from physical methods and synthetic chemistry through biology and biomedicine. The strength of this multidisciplinary group is reflected in the number of other GRCs that have "spun off" from Metals in Biology. Inorganic biochemistry continues to be an active and vibrant area, resulting in a perennial oversubscription to this GRC. To provide graduate students in this area with the possibility to participate, our community started the first Gordon Research Seminar (in Bioinorganic Chemistry), which has overlapped and met after the Metals in Biology GRC for over 10 years.Gordon Research Seminar (in Bioinorganic Chemistry)

9. Cell Biology of Metals Gordon Research Conference The 2013 Cell Biology of Metals Gordon Research Conference provides a highly interactive and collegial forum for junior and senior investigators alike to learn of the latest advances in our understanding of metal homeostasis, metabolism, and utilization in cells and organisms. The cell biology of metals is an emerging field of active research and this conference is the key venue for exciting unpublished work on nutrient metals (primarily iron, copper, zinc, and manganese), with presentations of research in humans and mice as well as plants, nematodes, and single-celled organisms. The meeting will bring together an outstanding and diverse group of molecular and structural biologists, biochemists, geneticists, cell biologists, and clinicians to bridge the gap between basic and applied research. Highlights include discussions of how dysregulation of metal homeostasis and utilization underscores human disease and how bacterial pathogens work to exploit host metal supplies to enhance their virulence in humans. Other sessions will address metalloproteomics and metallogenomics, intracellular metal trafficking, metal cofactor assembly, and metallosensor proteins and the regulation of gene expression. Oral presentations will be given by both new investigators and established leaders in the field and will be complemented by several poster sessions; some speakers will be selected from submitted poster abstracts. The broad and integrated coverage of topics will allow for extensive "cross-fertilization" of ideas among researchers studying metal nutrients from a multi-disciplinary perspective.

10. Ed Stiefel and Francois Morel Bringing fields together Metals in Biology and its Progeny In the early 1970s, as an assistant professor at the State University of New York at Stony Brook, I started attending both the Inorganic Chemistry Gordon Conference and the Metals in Biology (MIB) Conference. I had only a faint awareness of the diverse and critical roles that metal ions play in biological systems. Attending the MIB Conference convinced me of the area’s enormous potential, and I committed myself to the nascent field of bioinorganic chemistry. Three specific results came from my early attendance at MIB. First I became aware of the ignorance about critically important molybdenum enzymes, such as nitrogenase, nitrate reductase, and xanthine oxidase, and decided to focus on this area of research. Second, on the request of Steve Lippard (then at Columbia University and editor of Progress in Inorganic Chemistry) with whom I drove to the conference, I wrote a review called “The Bioinorganic and Coordination Chemistry of Molybdenum” that became a citation classic with over eight hundred citations. Third, an invitation to attend a seminar from Bill Newton of the Charles F. Research Kettering Laboratory, who I met on the tennis court during the MIB Conference, led to my joining the Nitrogen Fixation Mission at Kettering. Clearly, MIB had a tremendous influence on my early career and research. In 1980, while still attending MIB, I moved to Exxon Corporate Research, and I persuaded the company to provide some support for MIB for many years. In 1993 I chaired MIB, and, as Doug Rees presented the first nitrogenase crystal structure, I realized how far the field had come but how much was still unknown. MIB continued to meet on a yearly basis in California, but there were always good-natured complaints that only one session, at most, was spent on a particular subfield. This opened the door to new Gordon Conferences, such as the Nitrogen Fixation Conference, chaired by Doug Rees and Bill Orme-Johnson, that first met in 1994 and at which I gave the opening talk, called “Chemistry of Nitrogen Fixation.” It was great to have a Gordon Conference focused on the molecular aspects of nitrogenase. At the Nitrogen Fixation Conference I first realized that a GRC on other molybdenum enzymes would attract a large audience. A few years later Russ Hille, of Ohio State University, and I proposed a new Gordon Conference called Molybdenum and Tungsten Enzymes. Together we chaired the inaugural conference held in New Hampshire in 1999, with eighty attendees. Two years later one hundred attendees met at Oxford University. This specialized subject attracted bioinorganic chemists, crystallographers, biophysical chemists, molecular biologists, microbiologists, botanists, and physicians. The resulting cross-fertilization was remarkable, and the conference continues to meet on a two-year cycle. In 1998 my group at Exxon joined researchers from Princeton University, Rutgers University, and the University of California campuses to form the Center for Environmental Bioinorganic Chemistry (CEBIC), directed by François Morel and funded by the National Science Foundation and the Department of Energy. Many interactions among CEBIC researchers were first forged at Gordon Conferences. CEBIC was such a wonderful experience that in 2001 I moved to Princeton University with appointments in the chemistry department and the Princeton Environmental Institute (which houses CEBIC). At Princeton I have been fortunate to teach a freshman seminar called Elements of Life, which has convinced me that bioinorganic chemistry is a splendid vehicle for teaching chemistry and its relation to biology, geology, astrobiology, and environmental science. Meanwhile, CEBIC continued to thrive, and each year our summer workshop at Princeton drew more people from outside CEBIC. This success led François Morel and me to propose the Environmental Bioinorganic Chemistry (EBIC) Gordon Conference, and in 2002 François and I chaired its inaugural conference, with 125 attendees from a remarkable range of disciplines. The conference now meets regularly on a two-year cycle. Meanwhile MIB is thriving, despite the heavy attendance draw (one thousand participants) of the International Conference on Biological Inorganic Chemistry. Without losing momentum, MIB continues to spawn new conferences such as the 2002 Metals in Medicine (chaired by Nick Farrell) and the 2005 Cell Biology of Metals (chaired by Nigel Robinson and Dennis Winge). MIB is far from finished as it continues to stimulate interdisciplinary cross- fertilization of ideas in an intimate setting with a wonderfully paced program that only GRC can provide.

11. Molecular: Metalloenzymes and Marine Biochemistry ~25% of all proteins now believed to require a metal for functionality (Waldron and Robinson, 2009; Andreini et al., 2004) Metals allow proteins to have: -Site(s) for catalytic activity -Redox reaction capability -Structural features (e.g. “zinc finger” loops) Most marine biogeochemical reactions involve metalloenzymes –Photosynthesis (Fe, Mn, Cu, Zn, Co, Cd) –N 2 fixation, denitrification, nitrification, NH 3 oxidation, urea use (Fe, Cu, Mo, Ni) –Carbon remineralization (Zn, Co) –Organic phosphate utilization (Zn) –Superoxide dismutation (Cu, Zn, Fe, Ni)

12. Trace metal biogeochemistry Driven originally by analytical chemistry Initial measurements of many metals far too high due to contamination Biological or “Bioinorganic” component has grown in: Bioactive metals: Fe, Co, Cd, Zn, Cu, Ni, Mn, Mo etc. Iron limitation discovered The Role Complexation on Bioavailability Metalloenzymes Other limitations and colimitations Future roles for genomics, metagenomics, proteomics

13. 10  g/L ~= 10  M for Fe, Ni, Mn, Cu, Zn “uniformly distributed” and “random nature”

15. http://www.geotraces.org/ Global: GEOTRACES Science Plan A 10-12 year international program to map the chemistry of the oceans focusing on trace metals and isotopes. Started ~2010

16. Iron as a limiting nutrient in HNLC regions (Review of Iron Fertilization Experiments Boyd et al., 2007, Science) Purposeful (white crosses) and natural (red crosses) Fe enrichment studies have shown Fe limitation of phytoplankton growth.

18. GEOTRACES Goal: making WOCE-like sections for Trace Elements and Isotopes Meridional Pacific, Hiscock, Measures and Landing, GBC 2008

19. Four Categories of Trace Metal Profiles in 2D 1.Conservative distributions -Residence time greater than 100000 years -Much greater than the residence time of the oceans -Molybdenum, tungsten, antimony, rubidium: are involved in particle cycling, but the quantities are insignificant relative to their large seawater inventory -Concentrations of some are quite high: Mo = 105nM -Don’t increase with thermohaline circulation -Searching for the kink in Molybdenum due to nitrogen fixation

21. Four Categories of Trace Metal Profiles in 2D 2.Nutrient-type distributions: –Significantly involved with internal cycles of biologically derived particulate material –Distributions are dominated by phytoplankton uptake in surface waters followed by export of some of this material below the surface layer and subsequent remineralization and release to intermediate and deep waters –Have a low level of scavenging in intermediate and deep waters –(N, P, Si) Zinc, Cadmium, Barium, Silver, Nickel –Increase in concentration with thermohaline circulation –Can be used as paleoproxies for P (Cd) or Si (Zn) in foram tests and diatom opal.

22. Four Categories of Trace Metal Profiles in 2D 3. Scavenged-type distributions -Strong interactions with particles -Short residence times (~100-1000y) -Increased concentration near sources -Decreased concentrations away from sources -Decreased concentrations along flow path due to continual scavenging -Aluminum, lead, manganese -Nonmenclature tangent: Aluminium (British and Aussies) and Aluminum (Elsewhere)

23. Four Categories of Trace Metal Profiles in 2D 4. Hybrid-Type Metals -Strongly influenced by both micronutrient use and remineralization and scavenging processes. -Does not accumulate with thermohaline circulation -Can depend on geographic location: high dust input can obscure surface drawdown signal -“Hybrid-Type” is a relatively new descriptor -Bruland and Lohan (assigned reading this week): Iron, copper -Although not included, Cobalt is undoubtedly a hybrid-type metal -Mn could be one as well, but only at high latitudes, where nutrient-like drawdown occurs

24. These four geochemical categories of metals in seawater are a direct result of their (bio)chemical properties: Solubility Inorganic speciation Organic Speciation Redox chemistry Bioactive –Distributions affected by biota, often presumed biological function –Does not necessarily require use by biota, since there appear to be non- biological elements with nutrient-like profiles

25. Definitions Ligand – an atom, ion, or molecule that donates/shares electrons with one or more central atoms or ions. Metal- ligand bonds (inner sphere) are covalent. Chelate – (from Greek chelos = crab, with two binding claws) two or more donor atoms from a single ligand to the central metal atom

26. Coordination environment or chemistry: number of ligands that a metal can have. Most metals have a # of 6, forming octahedral complexes

27. Vraspir and Butler 2009

28. Atomic Orbitals: building-up principle Ground state electron configurations: 1s 2s 2p 3s 3p 4s 3d 4p … s subshell accommodates 2 e -, p subshell 6 e -, d subshell 10 e -, f 14 e -

29. Properties of Metal Atoms and Ions Metallic Radius of an element: half the distance from nearest neighbor atoms in the solid metal Ionic Radius – the distance between centers of the cation and anion There is a general decrease in metallic and ionic radius across a period. Due to increase in nuclear charge while electrons are added to the orbitals of the same shell (excluding d-block metals). The result is a more compact atom. Lanthanide contraction: where the f-block is filled prior to the d block, those orbitals have poor shielding properties and fail to compensate for the increasing nuclear charge, resulting in a more compact atom This effect also occurs in the d-block, due to poor shielding by d electrons (e.g. between Sc and Ni)

30. Valence, Ionization Energy, and Hardness-Softness Metal chemistry strongly influenced by the removal of electrons from a neutral atom Valence electrons are the outermost electrons surrounding a closed shell Main group elements: outer electron shells are s and p orbitals (Li, Na, K) –React violently with water (e.g. pure sodium to NaOH, +1 ions) Transition group elements (metals): have incomplete d electron shell Most transition metals have variable valence, a major component of their chemistry (Fe: +2, +3, Mn: +2, +3, +4, +6, +7) Ionization energy is the minimum needed to remove an electron from a gas phase atom Hardness is the difference between the ionization energy of the neutral atom and its anion. –Related to ability to remove electrons –Soft: large and relatively polarizable –Hard: small and less easily polarized

31. Characteristics of Metal Ion Binding to Ligands Soft vs Hard –Soft: Ions are large and easily polarizable –Hard: Small and less easily polarizable Soft metals tend to “like” soft ligands Hard metals tend to “like” hard ligands Examples: Hard: Fe 3+, Co 3+ and OH - Soft: Cd 2+, Cu +, Hg 2+ and sulfide groups

32. Characteristics of Metal Ion Binding to Ligands Soft vs Hard –Soft: Ions are large and easily polarizable –Hard: Small and less easily polarizable Soft metals tend to “like” soft ligands Hard metals tend to “like” hard ligands Examples: Hard: Fe 3+, Co 3+ and OH - Soft: Cd 2+, Cu +, Hg 2+ and sulfide groups

33. The Irving-Willliams Series Observations that complex stability for each ligand have a tendancy to rank: Mn 2+ Zn 2+ Caused by decreases in ionic radius across series and resultant ligand field stabilization effects Many implications both for ligands “L’s” in seawater and for protein binding of metals inside cells, area for much future research –For example it is hard to find any cobalt(II) ligand that is stronger than a nickel(II) ligand

34. Complexation Environment “Free ions” is really a misnomer Cu 2+ is actually Cu(H 2 O) 6 2+, if not bound by other inorganic species Water is a ligand, ligand-exchange rxn constants indicative of rate of reactivity, or the kinetics Dissociation of water molecules dependent on size and inversely to the size of the metal cation

35. Water loss exchange rates

36. Aquatic Chemistry of Trace Elements: A marine water column context Solubility Products: Example for Fe(OH) 3(s) K sp = [Fe][OH] 3 = 10 42.7 Stability constants for metal complexes (where L is ligand, M is Metal): K = [ML]/[M][L] Ligands can include inorganic chemical species: In oxic systems: OH -, CO 3 2-,SO 4 2-, Cl -, PO 4 3-, In anoxic systems add: HS -,, S 2- Ligands can also include organic chemical species: EDTA, DTPA, NTA, Citrate, Tris, siderophores, cobalophores, DFB, TETA, and the famous unknown ligand(s) “L”

37. Detailed balancing: Principle of Microscopic Reversibility k f M n+ + L - ML k b d[ML]/dt = k f [M + ] [L - ] -d[M + ]/dt = -d[L - ]/dt = k b [ML] At steady state: k f [M + ] [L - ] = k b [ML] k f / k b = [ML]/([M + ][L - ]) = K Aquatic Chemistry of Trace Elements: A marine water column context

38. However, there can be Non-Ideal effects (Morel and Hering 76-82) : -The effects of other solutes on the free energy of ion(s) of interest -Solubility product and stability constants need to be corrected, or better, determined to/at the appropriate ionic strength. -The activity of the metal is: {M n+ } = [M n+ ]  M n+ -The activity coefficient,  M n+, can be estimated by the Debye-Huckel correction or the Davies expression (modified Debye-Huckel) -I (ionic strength) = ½  (m i x Z i 2 ) (m=conc, Z = charge for each ion i) -Seawater I = 0.72 mol kg -1 -Z=charge, A = 1.17 M -1/2, B=0.3M -1/2 -Thermodynamic databases (Martell and Smith) will provide the ionic strength experimental conditions for each constant (e.g. 0.1M) Aquatic Chemistry of Trace Elements: A marine water column context

39. From Morel and Hering, 1993, p77 Quasi constant value between I=0.3-0.7

40. Average Major Seawater Ions (mM) (Morel and Hering, p291) HCO 3 - 2.38 SO 4 2- 28.2 Cl - 0.545 Ca 2+ 0.0102 Mg 2+ 0.0532 Na + 0.468 K + 0.0102

41. Average Major Seawater Ions (mM) (Morel and Hering, p291) HCO 3 - 2.38 SO 4 2- 28.2 Cl - Ca 2+ Mg 2+ 0.0532 Na + K + 0.0102

43. Abundance (or lack there of) is our friend Seawater constituents: Major ions (the salt) – millimolar and higher – Na + – Cl - –Mg 2+ –Ca 2+ –HCO 3 - Organic ligands/chelators - nanomolar –“L” Trace metals/elements – picomolar to nanomolar –M n+ With major ions, everything depends on everything (and must be considered simultaneously With trace elements, we can consider one element at a time, independently of other constituents

44. Preview: Software for Metal Speciation Mineql – Westall et al. a program made for calculating aqueous speciation and solubility at low temperature geochemical conditions Critical.exe – Smith and Martell volumes built into a DOS based- database. Paper and pencil calculations to understand, verify results, and cross-check assumptions with computer-assisted calculations.

45. Morel and Hering 1993

46. Vraspir and Butler, 2009

47. Readings – available on website www.whoi.edu/sites/12.755 Bruland and Lohan -Treatise on Geochemistry Chapter Morel and Hering, Principles of Aquatic Chemistry Chapter 6 Background: Lippard and Berg Bioinorganic Chemistry chapter 2 Goldberg Biography