Chem 151 Final

Coordination #

# of ligand sites around the central metal- NOT THE # OF LIGANDS Fe(3+) almost always has CN of 6 Co(2+) can have CN of 4 or 6 CN determines geometry: 2: linear 4: tetrahedral or square planar 6: octahedral

Transmittance

%T=I/Io Transmittance=Intensity of light after going through test substance/Intensity of light after going through blank Absorbance= log(1/T)=log(Io/I)=log(Io)-log(I)

Naming Coordination complexes

1. Always name the cation before the anion (no matter if the complex is cation/anion) 2. Naming ligands first, ABC order [CHECK FOR THIS] anionic ligands: ending in -o Chloride-> chloro Chlorate-> chlorato Chlorite-> Chlorito neutral ligands: common name of the molecule is used EXCEPT FOR: H2O = aqua NH3=ammine CO = carbonyl N2/O2=dinitrogen/dioxygen C5H5N=pyridine H2NCH2CH2NH2=ethylenediamine 3. prefixes!! 4. name central metal after naming ligands: if(complex ion=cation or neutral) return elementname; else if(complex ion = anion) return elementname+-ate; omg whoever is reading please do not judge me this helps me remember stuff :( Special names of metals in Anionic complexes: Cu: Cuprate Pb: Plumbate Ag: Argenate Au: Aurate Sn: Stannate Zn: Zincate After naming the metal, put the oxidation state of the central metal in (roman numerals)

Isomerization of Retinal

11 cis retinal [hydrogen on same side of bond] absorbs photon, excites an electron from pi to pi*, breaking double bond. This allows the bond to rotate freely & forms all trans retinal. [hydrogens on opposite sides of the bond].

Disinfection

Adding Cl2 kills the majority of bacteria, but can make unwanted byproducts such as THMs (trialomethanes) which is a suspected carcinogen.

Doping

Adding small, controlled amounts of impurities in order to enhance conductivity. p type doping: adding an element with fewer elections creates a "hole" that needs to be filled in the valence band. n type doping: adding an element with more electrons forces those electrons to partially fill the conduction band. Having partially filled bands allows the electrons to move freely through the solid.

INSOLUBLE COMPOUNDS

CO3(2-), PO4(3-) SO2(3-), AsO4(3-), O(2-), OH(-): Alkali metals&NH4+, Ca(OH)2 and Ba(OH)2 are moderately soluble. Hydroxides and oxides are insoluble in water but soluble in acid. S2-: NOT ALL ALKALI METALS- only Na+,K+, NH4(+), Ba(2+), Ca(2+), Mg(2+) CrO4(2-): Na+, K+, NH4(+), Li+, Co(3+), Cu(2+)

Hemoglobin

Carries O2 from lungs->body. Individual amino acids in a protein=residue Hemoglobin is a globular protein (folded into a compact, nearly spherical shape)w/ 4 subunits known as heme groups.

Naming Ionic Compouds

Cation, then the anion

Election configuration exceptions

Chromium and Molybdenum have one e- excited from s orbital to d orbital b/c half filled d shells are more stable. Cr: [Ar](4s^1)(3d^5) TUNGSTEN DOES NOT EXHIBIT THIS! Copper, Silver, Gold have the same thing; completely filled d shells are more stable.

Flow of blood

Deoxygenated blood from heart-(pulmonary arteries)->lungs-(pulmonary veins)->back to heart->throughout body-> capillaries->systemic veins that carry blood back to heart

Changes upon the bonding of oxygen

Deoxygenated: Heme group is nonplanar: "Domed" shape because the electrons from histidine amino acid repels the electrons from polyphorin. Oxygenated: Heme group is planar b/c oxygen repels back. When oxygenation occurs, the heme group is closer to histidine amino acid. This shift in position alters the shape and makes it easier for the other heme groups to bond with O2: cooperative binding!

Conductivity of Graphite

Despite Graphite being composed of carbon, a nonmetal (that shouldn't conduct electricity well), the structure of graphite=layers upon layers of carbon rings w/ a conjugate pi bond network (electrons can move freely through this- essentially an artificial electron sea)

Determining Iron concentration in an unknown

Determine absorbance of Fe(2+) after reduction by DHF and coloring by ferrozine+waiting 30 mins. Determine concentration from the .5 mL of the Fe(II)

Hydrogen atom spectrum

Discrete absorption or emission spectrums: in a one electron atom or ion, energy levels are determined by orbital: 1s, 2s, 3s/p/d.

Heme group

Each group has an iron molecule that is able to bond w/ O2 molecule. In other words, b/c hemoglobin has 4 heme groups, hemeglobin can bond with 4 O2 molecules. Iron in heme is coordinated to the 4 N atoms in polyphorin (tetradentate), a N atom of a histidine amino acid, and O2 (when oxygenated)

Metallic Bonding

Each metal atom is weakly covalently bonded with its neighbors; e- in e- sea, overall strong bonding since e-'s are shared with each of its 12 "neighbors". Each of the valence electron orbitals mix to form a continuous band (v close in energy), called valence band.

Electrical conductivity

Elements: Metals have loosely held valence e-'s which are free to move around the electron "sea". Nonmetals (high EN) hold their electrons tightly, so are poor conductors of electricity. Solutions: Ionic compounds dissociate in water to form cations and anions (mobile charges)- soluble ionic cmpds are strong electrolyes. Covalent compounds do not dissociate/little to no ionization, weak/non-electrolytes. Ions in solids DO NOT CONDUCT ELECTRICITY.

Flame tests

Energy from the fire excites the electrons to a higher energy level; they are now more unstable. Then the electrons will then fall back down to lower energy levels; the composite of the different energy differences forms the flame colors. c=(lambda)(nu) Li: Red Na: bright orange Ba: green Mn: Yellow green K: purple

Aqueous solutions of Coordination Compounds

Generally, complex ions remain intact. *sometimes water can substitute in as the complex ion- though water is actually a v weak ligand*

Filtration

Gravity filtration: use force of gravity to push water through porous medium (gravel or sand) To clean the filter, the pipe that clean water comes out instead pumps water upwards.

Polydentate ligands

H2NCH2CH2NH2 (ethylenediamine- bidentate), ethylenediaminetetraacetate (EDTA(4-), hexadentate), C2O4(2-) (oxalate, bidentate)

Monodentate ligands

H2O, CN-, CO, NH3, Cl-, O2

Point of Use water softeners

Has a Na+ head and a COO- tail, when Ca(2+) and Mg(2+) are passed through, they replace the Na+ atoms. However, not recommended for people with high blood pressure b/c increased Na concentration in water.

Halogen Extractions

Heptane (C7H16, nonpolar) and water (polar) don't mix, like dissolves like. Because the halogens Cl2/Br2/I2 are nonpolar, they will dissolve more readily in heptane. However, their components (Cl-, ClO-, etc) will more readily dissolve in the water. Lab objective: extract the halogens Cl2/Br2/I2 into the heptane layer.

Nonmetal: Strong Covalent Bonding

Highly electronegative ions will distort the closest packed structure (crystalline metals) so nonmetal crystalline solid structures only form strong covalent bonds w/ a few (<4) neighbors.

LEDs

Light Emitting Diodes, only release one type of light and w/ very little heat. Much more efficient than traditional light bulbs. Semiconductor devices that convert electrical energy directly to light (bonding in semimetal conductor)

Light source to brain

Light enters pupil, focused by lens, hits light sensitive retina. Light hits photocells in retina, activated ones send signal to brain which reconstructs the image.

Experiment 1

Measuring the conductivity of elements+determining their bonding. More concentrated= more conductive. In semimetals, the doped ones (less pure) substances conducted electricity better.

Metal complexes in the body

Metal-ion complexes in body=bonded w/ coordinate covalent compounds. Polydentate ions are aka chelating agents (claw). Important example = polyphorins, which coordinates to a metal using its 4 nitrogen atoms as electron pair donors. (tetradentates)

Metallic behavior

Metallic and shiny Good conductor (electricity and heat) High melting points Low EN

Band Gaps

Metals: All the orbitals mix to be about the same energy, no band gap. Freely conducts electricity. Nonmetals: Strong covalent bonds, a large energy gap between the mixed orbitals (conduction/valence) forms, As EN increases, the band gap increases. Can only conduct electricity with high input of energy. Semimetals: energy gap is present but smaller than nonmetals, so they can conduct electricity with a moderate input of energy. Higher energy, unfilled orbitals = conduction band Lower energy, filled orbitals = valence band

Determining % iron released

Mols of Fe released in 20 mins/mols of Fe in ferritin (from part A)

Different Coordination Complexes in Cu(II)

Most are 6 (octahedral) but will form 4(tetrahedral) in the high conc. of halides- makes distorted octahedral with elongated axis; the ligands on the elongated axis are usually the solvent, so it's difficult to add 5th/6th ligand unless it's an especially abundant solvent molecule. Ex: Cu(NH3)4(H2O)(2+) is generally the formula; Cu(NH3)6 is only possible when the liquid ammonia is the solvent

Disproportionation

Most commonly: Hydrogen peroxide (O's ON is -1) disproportionates into water (ON=-2) and O2 (ON = 0) Halogens (XO3(-): 7+, XO2(-): 5+, XO(-): 3+, X2: 0) can disproportionate. Ex: Br2+OH(-)=> 5Br(-)+BrO3(-)+H2O

SOLUBLE COMPOUNDS

NH4+, K+, Na+, and the other alkali metals: unconditionally soluble. NO3(-), ClO3(-),C2H3O2(-): Ag(C2H3O2) is slightly soluble Cl-,Br-,I- (Halides): Ag+, Hg2 (2+), Pb(2+) Pb(halides) are insoluble in cold water but moderately soluble in hot water. SO4(2-): Pb (2+), Hg2(2+), Ag+, [Ca(2+), Ba(2+), Sr(2+)]- slightly soluble

Polyatomic Cations

Nitrosyl: NO(1+) Vanadyl: VO(2+)

Preparation of Halogens

Note: none of these are balanced Cl2: solution of HCl (ON of Cl=1-) and bleach (NaClO) (ON of Cl=1+) HCl provides acidic medium: HCl+ClO(-)=> Cl2 Light green in heptane layer. Br2: NaBr ON=1-) +NaBrO3 (ON=+5) -> Br2 Dark orange in heptane layer. I2: I3(-)<=>I2+I(-) (NOT A REDOX REACTION because in I3(1-) the central atom is has a ON of 1-, the other two have ON of 0; no electrons are being moved around Violet in heptane layer.

oxide

O(2-)

superoxide

O2 (1-)

peroxide

O2 (2-)

Redox reactions

One element is oxidized, other is reduced. Oxidizing agent is reduced, reducing agent is oxidized. Disproportionation is when the same element acts as both an oxidizing and reducing agent. Lowest ON possible for an atom = strong reducing agent Highest ON possible for an atom = strong oxiding agent

Spectroscopy of blood

Oxygenated blood absorbs blue green light, appears red Deoxygenated blood absorbs orange light, appears blue

Semimetal Conductivity

P-n junction is where a p type semiconductor and n type semiconductor are in contact with each other, the extra elections in the conduction band of the n type transfer to the conduction band of the p type, then fall to the valence band to fill the p type's valence band. This difference in energy releases energy in the form of light. Larger gaps will emit higher energies of light.

Point of use Adsorption Filters

PAC in the filter absorbs contaminants, filter must be replaced periodically to avoid clogging.

Pd

Palladium

Common reducing agents

Remember: good reducing agents have LOW oxidation #'s Sulfite: SO3(2-) (ON = 4+) as opposed to sulfate's 6+; Bisulfite: HSO3(1-) (ON=4+) ; Oxalate: C2O4 (2-) (ON =3+) as opposed to CO2's 4+

Percent Yield

Theoretical/actual

INDICATORS

Thymol Blue: 1.2->9.6: red->yellow-> blue Bromocresol Green: 3.8->5.4 Yellow->blue Neutral Red: 6.8->8.0 red->yellow Thymolphtalein: 9.3->10.5 colorless->blue Clayton Yellow: 11->13 yellow->red Phenolphtalein: colorless-> pink (up to 10) Bromothymol blue: 6.0->7.6 yellow->blue Alazarin: orange->red->purple: 4ish->9.75->13.0

Difference between Rods and Cones

Rods: as many as 10,000 share a single nerve, so the brain cannot tell which rod the signal came from. B/c the the signal is pooled, the rods are v sensitive to small amounts of light. Cones: each cone is connected to a nerve fiber, v easy for brain to tell where the signal came from+produces sharper image.

Order of treatments at a water treatment facility

Screening->flocculation and coaguation-> disinfection-> sentimentation clarifiers-> precipitation->adsorption->filters->disinfection-> fluorination

Screening

Screening: treat the water w/ large screens to eliminate trash/fish/sticks. Zebra mussels sometimes cover these screens and don't let the water flow through, KMnO4 can be used to kill them.

Sedimentation

Sedimentation: the water is allowed to sit so sand/dirt sinks to the bottom. Flocculation uses particles w/ non rigid surfaces and swirls the water so the insoluble particles in the water stick to the non rigid surfaces; once the particle gets large enough, it sinks to the bottom. Coagulation uses coagulants( Alum, Al2O3 or Al2(SO4)3) which will react with ions in the water and make them ppt out. Al(3+)+SO4(2-)+Ca(2+)+3HCO3(-) -> Al(OH)3+Ca(SO4) +3CO2

Silver Mirror (Tollen's Test for Aldehydes)

Silver nitrate reacts w/ base to form AgOH, which is used to make the Tollen's Reagent. AgOH+2NH3-> [Ag(NH3)2]OH(aq) (Tollen's Reagent) Glucose has an aldehyde group- when it is added to Tollens reagent, silver is reduced and the carbon in the aldehyde group is oxidized (2Ag from +1 to 0 and C from +1 to +3) One of the 4 NH3 groups takes an H from the aldehyde group and one of the OH's donates an O to the aldehyde group, making COO- , carboxylic acid functional group on the Glucose. Remaining atoms from OH (make H2O) and the remaining 3 NH3 are a product. Overall equation: Aldehyde (COH)+2[Ag(NH3)2]OH-=>Carboxylic acid (COO-)+NH4(+)+2Ag+3NH3+H2O

Ligand Substitution Reactions

Substitution occurs in stages, one ligand replacement at a time; each stage is reversible to some extent. Labile = rapid ligand substitution. Non-labile/intert= slow or nonexistent substitution. Controlling the concentration of the substitute ligand can determine how much substitution happens. Note: Water is a common but v weak ligand of many metal ions.

Centrifuge Safety notes

do not slow down manually, do not unbalance

Naming Covalent compounds

electropositive, then electronegative element like anion: use prefixes!

Sigma orbitals

formed from head to head overlap. cylindrical symmetry about the bond axis.

Pi orbitals

formed from sideways overlapping p orbitals, has a nodal plane containing the bond axis

Coordinate Covalent bonds

Aka Dative bonds, not as strong as Lewis Acid/Base bonding. M(n+)= metal ion that has empty orbitals to accept electron pairs. L= Ligand, anion/neutral molecules w/ an atom capable of donating pair of e-'s

References for Oxidation Number assignment

Alkali metals are always +1 Alkaline earth metals are always +2 Hydrogen is usually +1 but is -1 in metal anhydrides Oxygen is usually -2 but is -1 in peroxides and -1/2 in superoxides: only group 1 elements form these The more electronegative element takes all the bonding electrons.

Ferritin

Apoferritin with an iron core. Apoferritin is an empty protein shell [in humans, 24 polypeptides w/ 184 animo acids each], 474,000 g/mol. Can hold 4500 iron atoms in the core. Walls are approximately 10 Angstroms thick, diameter is 80 angstroms. Iron core is Ferrihydrite FeO(OH) or [FeO(OH)]8[FeO(H2PO4)] (Oxidation # of Fe is 3+) Forms a lattice inside the Ferritin

Different definitions of Acids and Bases

Arrhennius Acids/Bases- react to form a salt Bronsted Lowry: Acids donate protons and bases accept protons Lewis: Acids are electron pair acceptors, bases are electron pair donors. Acids can be: HA, A=anion or polyatomic anion -COOH, an organic acid. Bases can be: R3N: Ammonia or an organic amine with R = H, CH3, CH2CH3 or an alkyl group

Synthesizing Co(III) Compounds

As stated previously, CO(III) is inert in ligand substitutions; therefore Co(II) is used as a starting material (then oxidized to Co(III)) Ex: Synthesizing Hexaammine cobalt (III) Chloride [Co(NH3)6]Cl3 Starting out with CoCl2*6H2O, after dissolving in water becomes Co(H2O)6(2+) [the two chloride ions become counter ions]. After adding NH3, ligand substitution occurs: Co(NH3)5(H2O)(2+). Upon the addition of activated charcoal, the last H2O is substituted: Co(NH3)6(2+) HCl is added to react w/ excess NH3. H2O2 is added to oxidize Co(NH3)6(2+) to Co(NH3)6(3+). The solution is placed in a hot water bath to speed the redox rxn

Naming Inorganic compounds

Based on the naming of the anions in the acids: -ide-> hydro...ic acid (HCl => chloride => hydrochloric acid) -ate-> ...ic acid (HNO3=>nitrate=>nitric acid) -ite-> ...ous acid (HNO2=>nitrite=> nitrous acid) per...ate-> per...-ic acid (HClO4=> perchlorate => perchloric acid) hypo...ite->hypo..-ous acid (HClO=> hypochlorite=>hypochlorous acid)

Nonmetallic behavior

Brittle and dull Poor conductor (electricity/heat) Low melting points High EN

Different Coordination Complexes in Co(II)

Co(2+) can have CN of 4 (tetrahedral) or 6(octahedral). The differences in orbital energy = different colors depending on the geometry. Octahedral complexes absorb green light/look pink, tetrahedral complexes absorb orange and look blue. Co(II) complexes are v labile, Co(III) are inert. Tetrahedral complexes usually form w/ monodentate anionic ligands (Cl(-), Br(-), I(-), SCN(-), OH(-)); stable at high temperatures. Octahedral complexes are stabilized at low temperatures. Experiment: add SCN(-) to Co(H2O)6, determine substitution w/ absorption spectrum.

Elements with more than one cation

Cobalt: Co(2+) and Co (3+) Iron: Fe (2+) and Fe (3+) Copper: Cu (1+) and Cu (2+) Mercury: Hg2 (2+) and Hg (2+) Lead: Pb(2+) and Pb(4+) Tin: Sn (2+) and Sn(4+)

Alpha Helix

Coiled shape, b/c each amino acid is H-bonded w/ the amino acid 4 residues ahead. (About 75% of hemoglobin is alpha helix) In hemoglobin, NH+CO group hydrogen bond (H-O)

Colors we see

Colors we see are the COMPLEMENTARY COLOR of the color we see. Ex: Substance that absorbs orange looks blue. E(photon) = hc/(wavelength) Spectrophotometer can measure how much light is being absorbed: Beer Lambert's Law: A=epsilon(molar absorptivity)*b(path length in cm)*c(concentration in M) Absorbance is directly proportional to the concentration of the light absorbing substance, and varies with wavelength of the incident light. To get an absorption spectrum: plot absorbance as a function of wavelength

Relative Oxidizing/reducing strengths

Comparing the reducing/oxidizing strengths of the halogens: the strongest oxidizing agent is more easily reduced, and therefore will likely be found in the water layer. Best reducing agent would be found in heptane layer. In the experiment: reacted the halides to permanganate [oxidizing agent]/dioxovanadium yellow (VO2(+))/metabisulfite (S2O5(2-): ON of S=4+) [reducing agent: becomes HSO3(-) in solution ON: 5+] in solution to determine if the halides had reacted or not. Results: Cl2 was the strongest oxidizing agent (most easily reduced- makes sense bc EN) while I2 was the weakest oxidizing agent. Cl- was the weakest reducing agent while I- was the strongest reducing agent

Iron in the Body

Complexed w/ hemoglobin protein: necessary for oxygen transport Myglobin: delivers oxygen from hemoglobin to muscle cells Cytochromes: generate energy

Photoreceptor cells

Cones provide color info, Rods provide black and white (detection of white light) The tops of the cones and rods have chromophores (molecule that can absorb light @ a specific wavelength). absence of light= 11 cis retinal [bentish shape]. After light hits it, isomerization (change in molecular arrangement) -> all trans retinal.[linear shape] This causes the Na channels to close, and a large potential difference to build up inside the cell, passed along as an electrical signal to brain @ synaptic terminal (where the two cells meet)

Molecular Orbitals

Constructed by Linear Combination of Atomic Orbitals (LCAO). n Atomic orbitals mix to form n molecular orbitals. Bonding orbitals= constructive interference; antibonding= destructive interference. As you go up in energy, you also go up in # of nodes. Lowest energy level has 0 nodes, 2nd lowest has 1, etc. # of e- filling up orbitals is determined by # of atoms participating in resonance.

Proteins

Contain an Amino group (NH2), Carboxylic acid group (COOH), an H bonded to C bonded to a side chain. Amino acids link together to to make polypetides, peptide bonds can be destroyed b/ strong acids or bases (Btwn C of Carboxylic acid group and N of amino group) These peptide bonds form the "backbone" of the peptide chain. animo acids (individual ones - residues) form protein subunites called peptides. peptides bond together (C-N peptide bond) to form polypeptides and proteins.

Synthesizing [Cu(NH3)4]SO4

CuSO4 dissolves in water to form Cu(H2O)6(2+) and SO4(2-). Upon the addition of ammonia, the first substitution => Cu(NH3)4(H2O)2(2+). Wash w/ isopropyl alcohol- this lowers the solubility of the polar Cu complex and forces the copper complex to crystallize out of solution- [Cu(NH3)4]SO4*H2O (one water ligand is lost in crystallization- the other major component in solution is SO4(2-)) After drying out the solid, adding it to water makes the water cloudy- ammonia is not as labile so its replaced by hydroxides in the water.

Particle in a 1-D box

Equations: psi=sqrt(2/L) *sin(n*pi*x/L) Energy=(n^2*h^2)/(8mL^2) lambda=8(mass of electron)(speed of light)(Length of box)^2/h(N+1) x=# of double bonds-1 Relate N and L to x: N=# pi electrons=2x+6 n(energy level)=.5N L= (2x+6.6)(length of single bond) subbing in: lambda(nm)=63.7[(2x+6.6)^2)/(2x+7)] OR: 4x^2+[26.4-lambda max/31.9]x+[43.6-lambda max/9.1] solve for x ground state n = # of carbon double bonds

Extra additions to water supply

F- to help make teeth stronger.

Ligand Substitution in Fe (III) complexes

Fe(3+) has great affinity for ligands that coordinate by O (EDTA(4-)): Strong->Weak affinity EDTA>SCN(-)>Cl(-)>H2O When Fe(3+) is left to sit w/ SCN(-), SCN(-) gets oxidized over time. Fe(3+)=> Fe(2+) + 1e- (REDUCTION) SCN(-)(ON of S=)-> SO4(2-) (ON=6+) (OXIDATION)

Some coordination compounds are named classically

Fe(CN)6(3-) = ferricyanide Fe(CN)6(4-)= ferrocyanide Fe(CO)5= iron carbonyl

Synthesis of an Aqueous Ferrofluid

FeCl3+FeCl2+8NH3+4H2O=> Fe3O4+NH4Cl Fe(2+) and Fe(3+) combine with the Oxygens in the H2O to form magnetite(actually FeO and Fe2O3). Remaining H from water bond w/ NH3 to make NH4+ In order to keep the magnetite particles from sticking to each other we add a surfactant to keep them suspended. NH3(aq) is the same as NH4OH, and those OH- surround each Fe3O4 particle, which attracts the positively charged tetramethylammonium cation.

When comparing energy differences of different ligands/geometries

Figure out which wavelength or color of light is being absorbed. Absorption of orange is less energetic than absorption of green light. Therefore, the blue complex is less energetic than the red complex.

Balancing a Redox Reaction

Identify the species being oxidized and reduce, & split into reduction and oxidation half reactions. Balance all elements instead of O and H, then balance the electrons. THEN: balance net charges by adding H+ (acidic solution), OH- (basic solution), and H2O

Complex Formation Reactions

If adding a metal to a solution w/ a ppt makes some ppt dissolve, the ppt is the ligand of the metal.

Reduction of Permanganate (deep violet color)

In acidic medium: Mn(2+)(ON =2+) (colorless) In neutral/basic medium: MnO2(ON=4+) (brown ppt) In very basic medium: MnO4(2-) (ON=6+) (green soln) Reactions w/ MnO4(-) can be catalyzed by Mn(2+) and MnO2

Problems with Iron in blood

In the presence of O2, Fe(2+) is oxidized to Fe(3+), which is insoluble @ ph7. The body maintains constant iron content by storing iron in ferritin.

Bohr Effect

Increased concentration of CO2 and H(+) promote release of O2 from hemoglobin. This is advantageous b/c the muscles produce CO2 and H+ as waste products of metabolism; higher concentrations of these products where the muscles are more active and need oxygen. These species help form salt bridges (btwn positively and negatively charged amino acids) on different subunits; tugs on the histidine attached to the heme iron, so it favors the domed (deoxygenated)state. @ pH 7, concentration of H+ atoms is sufficiently high so that it can be accepted by histidine residues @ subunit interfaces (NOT THE ONES THAT BIND HEME GROUPS). Salt bridges form btwn this (+) charge and negatively charged amino acid residues. CO2 binds to NH2 (amine) group of amino acid residues & makes (-) charged group. bonds w/ (+) charge of histidine residues after addition of H+ atom & forms salt bridge

Substances dissolved in Water

Ionic substances are broken apart into their component ions [polyatomic ions remain intact] and surrounded by water molecules. (dissolving) Covalent substances remain bonded but are still surrounded by water molecules (solvation)

Different types of bonds

Ionic: EN difference is >/=3, electrons are "transferred"- highly attracted to the more electronegative atom Covalent: EN difference is </=2, electrons are shared between the two atoms. EN difference btwn 2&3: gray area, both are possible.

Determining total Iron in a Ferritin molecule

Iron content per ferritin molecule=Fe atoms/# ferritin molecules <figure these out w/ beer lambert

Iron disorders

Iron deficiency: can't make enough hemoglobin and end up with iron-deficiency anemia. Iron overload: >15g of iron in the body, hemochromatosis. Leads to cirrhosis of the liver, heart failure, diabeetus, arthritis. Ferritin acts as a "buffer", releasing iron when the body needs it and storing iron so it's not present in the blood (less effective for preventing overload)

Adsorption

Powder activated carbon has an irregularly shaped surface which organic compounds attach to- complex is removed by filtration.

Precipitation

Precipitation: adding ions to make other ions ppt out. Difference btwn this and coagulation is that the ions are actually reacting in precipitation, coagulation = particles getting trapped. Removing Ca(2+) and Mg(2+) to treat water hardness, adding lime (Ca(OH)2) and soda ash (Na2CO3) Mg(OH)2 and CaCO3 form to remove the Mg/Ca atoms from the water. If an excess of lime was added (Ca(OH)2) then bubbling CO2 through the water will form H2CO3 which will react w/ the OH- to form bicarbonate which is nontoxic. Removing Fe and Mn: add an oxidizing agent (KMnO4: Mn has 7+ oxidation #, oxidizing agents are reduced) in order to oxidize the Fe(II) to Fe(III), which will form Fe(OH)3 in an alkaline solution. After a while, the lattice will look like rust, Fe2O3, and the iron will ppt out. Fe(2+) + MnO4(-)+2H2O=> Fe(3+) + MnO2 + 4OH(-)

Ra

Radium

Extracting the Iron

Reduce Fe(III) to Fe(II) to dissolve iron: Fe(H2O)6(2+) exits sphere through channels: a 4 fold channel in center of the sphere, four 3 fold channels near the edge The channels are formed @ the intersection of 3 or 4 peptide units. 3 fold channels are polar, enabling the passage of Fe(2+) ions. Lined with Aspartate and Glutamate, polar amino acids. (On a similar note, animo acids are polar ONLY because of their side chain properties. The backbone does not contribute to polarity. 4 fold channels are nonpolar, lined w leucine. Does not interact favorably with Fe(2+), it is thought that this is where electron transfer happens. Reducing agent is DHF. Determine concentration of Fe with spectroscopy, so we have to convert to colored compound w/ ferrozine(2-) (Bidentate) Fe(H2O)6(2+)+3Ferrozine(2-) -> [Fe(ferrozine)3](4-) + 6H2O

Possible reducing/oxidizing agents

Reducing agents: highest-> second lowest stable ON Oxidizing agents: lowest-> second highest ON Middling ON are ALL capable of disproportionation

Prefixes

Regular: mono, di, tri, tetra, penta, hexa, hepta, octa, nona, deca, undeca, dodeca IF the ligand already contains a prefix (ethylenediamine) or if it is a polydentate ligand (attaches at more than one coordination site on the central atom) then use: mono, bis, tris, tetrakis, pentakis, hexakis, hepta, etc, 9 is ennea

Progressive reduction of vanadium

VO3(-) = Metavanadate. 5+ ON. Metavanadate is put in 2M H2SO4. VO3(-)+2H(+) => VO2(+)+H2O Therefore dioxovanadium yellow is formed: VO2(+). The oxidation # is still 5+. After adding Zn, VO2(+) Dioxovanadium yellow is reduced to VO(2+), Oxovanadium (IV)- a blue substance. As the Zn continues to react, Oxovanadium (IV), VO(2+) is reduced to V(3+), an aqua green solution. Finally, V(3+) is reduced to V(2+), a violet compound and V's lowest oxidation #.

Distinctions between naming gas forms/aqueous forms of acids

When HCl, HBr, and H2S are in their gaseous forms, we name them covalently. This isn't an issue for the other oxoacids because their anhydrides dissociate in the gaseous forms (H2SO4=> SO3)

Predicting products of a Redox Reaction

When V(2+) and H2O2 are added together, VO (2+) blue oxovanadium (ON =4+) is formed. [you know this from spectro) MnO4(-)+V(2+) => VO2(+) MnO2 (color change!) FeCl2+H2O2=> FeCl3+H2O (Color change from greenish to brown) KMnO4+H(+)+H2O2=>Mn(2+)+O2+H2O Na2S2O3(S ON=2+)+HCl=> H2SO3(ON=4+)+S (ON=0) +NaCl

Periodic Trends

Z*: Increases across a period, decreases down a group. Atomic Radii: Decreases across a period, increases down a group. Electronegativity: Increases across a period, decreases down a group. (Fr is the least EN, F is the most EN)

Safety issues in Experiment 5

Zinc must not be put in the acid waste container because: Zn+H(+) = Zn(2+) + H2(g) Explosions will happen

Why are coordination complexes colorful?

ligands interact w/ d orbitals, causes them to split in energy -> color change. Free ion- all d orbitals are the same energy OVERALL: orbitals bonded w/ ligands are still higher in energy than the free ion's energy. Octahedral field: 2 orbitals are significantly higher energy than the rest Tetrahedral: 3 orbitals are slightly higher than the rest Square Planar: 2 orbitals are higher energy than the original, one barely higher than the other. Geometry affects color changes in the ligands.

Wastewater

must be inspected and treated before released into environment. Household wastewater contains poop and household chemicals, but industrial wastewater which is generally used for cooling and processing can contain toxic chemicals, radioactive materials- all treated w/ same treatment up above. Agricultural wastewater contains lots of fertilizers and animal poop (lots of bac) and pesticides- nitrogen can cause red blooms bad things but this wastewater is usually released w/out treatment.

Protein Conformational Changes after Retinal Isomerization

opsin is the protein that binds the chromophore retinal; bound complex for 11 cis retinal is rhodopsin/visual purple. [11 cis retinal normally absorbs UV light but rhodopsin absorbs green light] When the chromophore undergoes isomerization, the rhodopsin-all trans retinal complex is known as bathlorhodopsin. All trans retinal = energetically unfavorable so the opsin wants to expel the chromophore. Metarhodopsin II->transducin->phosphodiesterate-> hydrolysis of cyclic GMP-> Na channels close. In color vision: red, green, yellow absorbing cones.

Beta pleated

other common structural motif for amino acids, which line up in parallel rows

Metabolism

reactions needed to perform daily activities- requires oxygen (Adults need 250 mL a minute)and nutrients

Conjugate systems

the electron density is delocalized over all the atoms in the molecule. Meaning the bonds between the electrons are not true single nor true double bonds- an in between. In a non-conjugate system, electron density is not delocalized over the entire molecule. There is a node somewhere.

Hygroscopic substances

substances that absorb water from the air- usually look sticky or wet. Anhydrides are substances without water.