CHEM 106 Lecture 2—Nutrient Cycling, Spectroscopy, Teamwork & Science Writing

Water: Molecular Properties and Global Cycling

• Water is bent and tetrahedral

• Water is a polar molecule; the bent structure and electronegativity difference between O and H create a permanent dipole.

• Dipole–ion interactions allow water to solvate virtually any ionic or charged species (e.g., NaCl crystal dissolves) and interact with most biomolecules via hydrogen bonding.

• Hydrogen bonding gives water its high boiling point, surface tension, and the ability to act as a universal biological solvent.

• The Hydrologic (Water) Cycle processes:
  • Evaporation → Condensation → Precipitation (rain/snow) → Snowmelt runoff → Surface runoff → Infiltration → Ground-water flow → Plant uptake → Transpiration → Repeat.
  • Human‐relevant fluxes: potable water extraction, irrigation return flows, industrial cooling water, wastewater discharge.

Watersheds, Drainage & Local Context

• Watershed = drainage basin: all land draining to one common point (river, lake, estuary).

• Drainage divide: imaginary topographic line separating adjacent drainage basins.

• Drainage controlled by elevation gradients, geology, vegetation, and land use.

• New York contains multiple basins: St Lawrence, Lake Ontario, Finger Lakes, Upper & Lower Hudson, Delaware, Allegheny, etc.

• Campus is in the Susquehanna River Basin → Upper Susquehanna Sub-basin. Data: Susquehanna River Basin Council.

• Susquehanna River goes through Pennsylvania

Water Quality: Concepts & Parameters

• Water quality = (composition of the water) + (fitness for a given purpose: drinking, recreation, irrigation, industrial use, sustaining aquatic life).

• Suitability judged by physical, chemical, biological parameters.
  • Physical: light penetration, odor, taste, temperature, turbidity, electrical conductivity.
  • Chemical: alkalinity, hardness, major cations/anions Ca2+,K+,Mg2+,Na+,HCO3−,CO32−,Cl−,SO42−,NO3−,PO43−​; trace metals (As, Cd, Cu, Fe, Pb, Zn…); pH; TDS; nutrients (N, P); organic contaminants incl. micro-plastics.
  • Biological: organism diversity, habitat quality, bacterial indicators, toxicity tests.

Nitrogen Cycle & Limitation

• Nitrogen (N) builds amino acids, proteins, nucleic acids and used by oragnisms

• Atmosphere ≈ $80\%$ $\text{N}_2$ → unusable by most plants.

• $\text{N}_2$ uses triple bond so hard to break apart

• Plant-available forms in soil water (limiting nutrients):
  • Ammonium (NH4+)

• • Nitrate (NO3−)

• Key processes: N₂-fixation, nitrification, assimilation, ammonification, denitrification.

• N₂-fixation: is a key process that converts atmospheric nitrogen ($ext{N}\_2$), which is unusable by most plants due to its strong triple bond, into plant-available forms like ammonium ($ext{NH}4+$) and nitrate ($ext{NO}3−$).

• Assimilation: is how plants and microorganisms convert absorbed inorganic nitrogen into organic compounds.

• Ammonification: is the process where decomposers convert organic nitrogen into ammonium.

• Denitrification: is not explicitly defined in the provided note, but it is a crucial process in the nitrogen cycle. It is the microbial process where nitrate (NO3−NO3−) is converted back into gaseous nitrogen (N2N2) or nitrous oxide (N2extON2extO), which then escapes into the atmosphere. This process typically occurs under anaerobic (low oxygen) conditions and is primarily carried out by certain bacteria.

• $N20$ is a green house gas

Phosphorus Forms & Cycle

• Predominant aqueous species = phosphate (PO₄³⁻).

• Classes:
  • Orthophosphates: PO43−,HPO42−,H2PO4−(inorganic, bioavailable).
  • Organically bound phosphates (in biomolecules).
  • Condensed/polyphosphates (e.g., P3O105−P3O105−).

• Total phosphate = sum of all forms.

Too Much of a Good Thing: Eutrophication

• Excess NO3− and PO43− → algal blooms (Lake Erie 2015 record bloom).

• After bloom dies, bacterial decomposition consumes dissolved O₂ → hypoxia/anoxia (“dead zones,” e.g., 6 000–7 000 mi² in Gulf of Mexico) → fish kills, habitat loss.

• Creates ecological dead zones

• Some Algae can be toxic especially to infants, can be a neurotoxin

Spectroscopy Fundamentals

• Spectroscopy = study/measurement of light–matter interactions across the EM spectrum. (Interaction between electromagnetic radiation and matter

• Energy of light: $E = h\nu = \frac{h c}{\lambda}$ (h = Planck’s constant, c = speed of light).

Quantum view: electrons occupy discrete energy levels; light can be absorbed if $E_{photon}$ matches an energy gap.
• Absorption: photon promotes electron to higher level, photon is destroyed.
• Emission: excited electron drops, photon emitted;

• fluorescence = one spontaneous emission pathway.

• Types of instruments share basic blocks: source (lamp/laser/synchrotron), sample region (defined path length), detector.

Spectrophotometry & Beer’s Law

• Spectrophotometry is a quantitative analytical technique that utilizes absorption spectroscopy to determine the concentration of a substance in a solution. It operates by measuring the amount of light absorbed by a sample at specific wavelengths. The fundamental principle is that the absorbance ($A$) of a solution is directly proportional to the concentration ($c$) of the absorbing species, the path length ($l$) of the light through the sample, and the molar absorptivity ($\varepsilon$) of the substance, as described by the Beer-Lambert law: $A = \varepsilon\,l\,c$. This relationship allows for accurate quantification of substances based on their light absorption properties.

• Absorbance, denoted as $A$, quantifies the amount of light absorbed by a sample and is mathematically defined as the negative common logarithm (base 10) of the ratio of the transmitted light intensity ($I$) to the incident light intensity (I0I0). The relationship is expressed by the equation: A=−log⁡10(II0)A=−log10(I0​I​). This formula is crucial for spectrophotometry, as it directly links the measured light intensities to the sample's light-absorbing properties.

• Beer–Lambert law: $A = \varepsilon\,l\,c$
  • $\varepsilon$ = molar absorptivity (L mol⁻¹ cm⁻¹)
  • $l$ = path length (cm)
  • $c$ = concentration (mol L⁻¹)

• Therefore, absorption ∝ concentration → basis for quantitative analysis (Lab Exercise #3).

Lab Logistics & Reactions

• Lab Ex #3 (Intro to Spectrophotometry): begins tomorrow 12:30 PM. Pre-lab on LON-CAPA due 30 min early. Bring lab coat, goggles, pre-written intro.

• Lab Ex #4 (Phosphate in Water): Thursday 12:30 PM. Technical Lab Report required. Key colorimetric reaction:
  72H++7PO43−+12Mo7O246−→7PMo12O403−+36H2O

PFAS (“Forever Chemicals”)

• PFAS = poly- / per-fluoroalkyl substances: carbon chains fully or partially fluorinated (e.g., PFOA – polyfluorooctanoic acid).

• C–F bonds exceptionally strong → chemicals flexible, heat-resistant, non-biodegradable → bioaccumulation + carcinogenicity.

• EPA drinking-water limits: ~4–10 ppt (ng L⁻¹).

• Detection challenges: weak UV/IR absorbance; current standard = LC/MS/MS (15 min–3 h; USD 85–495 per sample).

Raman Spectroscopy & SERS Alternative

• Raman spectroscopy: laser illuminates sample; inelastic scattering (Raman shift) encodes molecular vibrational “fingerprint.”

• Pros: can detect PFAS quicker & cheaper (laser + camera).

• Sensitivity boosted by Surface-Enhanced Raman Spectroscopy (SERS):
  • Metal (Ag/Au) nanoparticles support localized surface plasmons.
  • Incident light polarizes free-electron cloud → enormous local electric fields → Raman signal ↑ up to $10^{6}$-fold.

Collaboration & Teamwork in Science

• Modern science is inherently collaborative; even single-author works build on predecessors.

• Key teamwork principles:
  • Leverage diverse strengths.
  • Leadership can be shared.
  • Delegation (“divide & conquer”) boosts productivity.
  • Clear communication prevents redundancy/conflict.

• Coursework: complete a team contract (team name, expectations, strengths, skills to improve, availability, signatures).

Scientific Literacy & Communication Channels

• Scientific literacy = understanding scientific content + process; empowers evidence-based decisions (e.g., spotting “chemical-free” misinformation).

• Media for science communication: peer-reviewed articles, reports, presentations, posters, books, blogs, news, social networks.

• >1 000 journals; peer review = primary literature. High-impact (Science, Nature) vs specialized; Open-Access (e.g., PLOS One) free to read but costly to publish.

Reading a Research Article Systematically

• Core questions: terminology, motivation, method, findings, validity, implications.

• Standard structure:
  • Title, Abstract, Introduction, Methods, Results, Discussion, Conclusions, References.

• Title → who/where/when.

• Abstract → condensed purpose, methods, key results, conclusions (often plus graphical abstract).

• Introduction → broad → narrow; literature review; hypotheses/questions.

• Methods → sufficient detail for replication (techniques, reagents, instrumentation, site/time).

• Results → data + explanatory text; each figure/table properly captioned.

• Discussion → interpret results, answer questions, compare literature, propose future work.

• Conclusion → main takeaways, broader context (not repetition of abstract).

• References → full bibliographic info; CHEM 106 uses ACS format.

Science Writing Assignments

• Assignment #1: Write Methods for “Water Hardness” lab; first-person, active, past tense; cite the Course Guidebook.

• Assignment #2: Write Results for “Chloride Concentration” lab; include all trial data, mean, standard error; table/plot with caption; justify calculation; first-person active; ACS citations.

Finding & Managing Sources

• Binghamton University library chemistry guide: databases (SciFinder-n, ACS Publications, ChemSpider, etc.).

• Reference managers (Zotero, Mendeley, EndNote): cloud storage, metadata capture, topic folders, auto-formatted bibliographies (ACS compatible).

Effective Scientific Writing: Principles

• Shift from old-school 3rd-person passive to new-school 1st-person active, accessible prose.

• Audience heuristic: “3 2’s” – reading at 2 AM, 2 screaming kids, 2 tequila shots → keep writing clear & reader-friendly.

• Stickiness (SUCCES framework): Simple, Unexpected, Concrete, Credible, Emotional, Story driven.

• Hourglass structure:
  • Opening (context/problem)
  • Challenge (questions/hypotheses)
  • Action (methods)
  • Resolution (results → discussion → specific conclusions).

Language & Style Guidelines

• English offers many near-synonyms; choose words with precise scientific meaning.

• Avoid bad habits: hiding actors, nominalizing verbs, excessive Latin-derived vocabulary, undefined jargon/acronyms.

• First-person active test: cannot append “by zombies.”
  • Passive: “A Raman spectrum was measured … by zombies” (bad).
  • Active: “We measured a Raman spectrum.” (good).

• Prefer concrete verbs (increase, identify, use) over vague (modulate, elucidate, utilize).

Drafting, Revising & Celebrating

• “Sh****y First Draft” is inevitable; perfection later.

• Revision keys:

  1. Obtain external feedback.

  2. “Murder your darlings” – remove beloved but unnecessary parts.

  3. Multiple revision rounds; accept “good enough.”

  4. Ensure every paragraph serves the story/thesis.

  5. Set frequent, hard deadlines; avoid paralysis.

  6. Save grammar/spelling for final pass.

• Celebrate submission: writing is heavy lifting; publication marks tangible scientific progress.