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Folding of peptide α-helix secondary structure

  • Experimentation on 7/31/2020 with molecular model kit showed specific atoms involved in hydrogen bonds that help keep the α-helix chain in shape.
    • Per diagram on Alberts p. 134, consider N1-C1a-C1b-N2-C2a-C2b-N3-C3a-C3b-N4-C4a-C4b-N5-C5a-C5b-…
    • There is a hydrogen attached to N1, N2, N3, etc.; the “left-side” amide terminus of each amino acid.
    • Let x = 1,2,3,… There is an oxygen double-bonded to each carbon Cxb. Aka there is a carbonyl group on the “right-side” acid terminus of each amino acid.
    • The hydrogen at N1 hydrogen bonds to the oxygen at C3b.
    • The hydrogen at N2 hydrogen bonds to the oxygen at C4b.
    • The hydrogen at N3 hydrogen bonds to the oxygen at C5b.
    • and so on…

      Functional groups

Group name Class name & example Properties

Hydroxyl
-OH
Alcohols like ethanol
Polar. Hydrogen bonds with water to help dissolve molecules. Enables linkage to other molecules by deydration/condensation synthesis reaction

Aldehyde (carbonyl) group
H-C=O		 Aldehydes like Acetalaldehyde Very reactive and important in building molecules and energy-releasing reactions

Acetyl group
(carbonyl group) R-C=O-NH2
 n/a n/a

Ketone (carbonyl) group
R2-C=O
 Ketones like acetone C=O group is very important in carbohydrates and energy reactions

Ester (carbonyl) group
R-O-C(R)=O		 Carboxylate esters like vinyl acetate Derived from an acid where at least one hydroxl group (-OH) is replaced by an -O-alkyl (alkoxy) group. Glycerides are fatty acid esters of glycerol. Usually derived from combining a carboxylic acid and an alcohol.

Carboxyl group
-COOH		 Carboxylic acids like acetic acid Acidic. Ionizes in living tissues to form -COO- and H+. Enters dehydration/condensation reactions by giving up -OH.

Amino group
-NH2		 Amines like methylamine Basic. Accepts H+ in living tissues to form -NH3+. Enters dehydration synthesis reactions by giving up H+

Phosophate group
R-PO4		 Organic phosophates Acidic. Enters dehydration synthesis reactions by giving up -OH. Hydrolysis releases a lot of energy when bonded to another phosphate.

Sulfhydryl group
R-SH		 Thiols like mercaptoethanol Two -SH groups can each give up H and form a disulfide bridge that stabilizes protein structure.
  • See Sadava Biology (2014), p. 40 or table at Biology LIbreText
  • See also panels about Functional Groups on p. 107 of Alberts 5th Ed.
  • See JH handwritten notes from August 10, 2020

Names of first several saturated and unsaturated hydrocarbons

No. of carbons Alkanes Alkenes Alkynes
1 methane – –
2 ethane ethene aka ethylene ethyne aka acetylene
3 propane propene aka propylene propyne
4 butane 1-butene 1-butyne
5 pentane 1-pentene 1-pentyne
6 hexane 1-hexene 1-hexyne
7 heptane 1-heptene 1-heptyne
8 octane 1-octene 1-octyne
9 nonane 1-nonene 1-nonyne
10 decane 1-decene 1-decyne
11 undecane 1-undecene 1-undecyne
  • Note that hydrocarbons are divided into aliphatic versus aromatic subcategories.
    • Aromatic hydrocarbons include benzene and other resonant ring-structures.
    • Aliphatic aka non-aromatic hydrocarbons include straight chain alkanes like hexane as well as cyclic (non-resonant) molecules like cyclohexane. Aliphatic hydrocarbons can be saturated or unsaturated.

Resonance-stabilization and resonance hybrids

  • Wade p. 13-16
  • See also this page and Wayne Breslyn’s short and very clear YouTube video about the hybrid structure phosophate ion PO43-
  • See p. 13 for a very important table to see common charges on atoms in organic compounds and ions. See also handwritten JH notes 10/23/2020
  • See Wade p. 15 for example of H2C=NH2 which is a Primary Aldimine, a type of imine b/c there is a C=N double bond.
  • Problem 1-8f on p. 17 refers to formamide aka methanamide which has the chemical structure HC(=O)NH2.

Bond-Dipole moments (p. 59-60)

  • LG Wade, Chapter 2, Section 2-9A (10/11/2020)
  • Range of bond polarities from least to most polar: covalent (non-polar with similar electronegativities), covalent (polar which occurs when the 2 atoms have very different electronegativity), to totally ionic.
  • List from least polar (aka most non-polar) to most polar:
    • ethane – CH3CH3
    • methylamine – CH3NH2
    • methanol – CH3OH
    • chloromethane – CH3Cl
    • methylammonium chloride (ionic bond): CH3NH4+ and Cl-
  • Bond polarity is measured by the bond dipole moment μ (“mu”), which is measured by μ = δ * d where δ = amount of charge either end fo the dipole and d = distance between the charges.
  • The usual unit for bond polarity is the debye, abbreviated “D” where 1 D = ~3.336 * 10-30 Coulomb*meters.
  • In organic compounds, bond dipole moments range from zero (for symmetrically equal electronegativities) to about 3.6D for the very polarized C≡N triple bond.
  • See p. 60, Table 2-1 for a list of common 2-atom bond dipole moments

Chapter 3: Structure and Stereochemistry of Alkanes p. 83–126

  • Methylene groups are simply interior –CH2– groups. p. 84
  • Methane, ethane, propane, butane, pentane, hexane, heptane, etc. are all homologs.
  • Four Rules of Naming Alkanes per IUPAC:
    1. The Main Chain
    2. Numbering the Main Chain
    3. Naming the Alkyl Group
    4. Organizing Multiple Groups
  • Geometric isomers of cycloalkanes. A cycloalkane has two distinct faces. If substituent groups point towards the same face, they are cis. If the groups are oriented towards opposite faces, they are trans. p. 105

Chapter 4: Chemical Reactions p. 127-168

  • Start with halogenation of alkanes
  • Mechanism, thermodynamics, and kinetics p. 128
    1. Mechanism – step by step series of intermediates from reactants to final product(s)
    2. Thermodynamics – study of free energy changes, entropy, enthalpy
    3. Kinetics – study of speed of reaction (aka reaction rates) based on conditions
  • Thermodynamics is relatively static, based on overall change in Gibbs Free energy, change in BDE (bond dissassociation enthalpies) aka heat aka enthalpy changes, and change in entropy at a given temperature. No calculus needed. Concentration equation can be based on stoichiometry (I think).
  • In contrast, Kinetics and the rate equation is related to concentrations which various continuously over time. In other words, for a forward reaction with suffcient product available, the rate of reaction is varying continuously because the concentration of reactants is presumably decreasing while the concnetration of products is presumably increasing. See this PDF for example.
More detail on rate laws
  • From Laney.edu PDF
  • Differential rate laws:
    • Express the rate of reaction as a function of a change in the concentration of one or more reactants over a particular period of time
    • Describe what is happening at the molecular level during a reaction
    • Rate = -d[A] / dt = k[A]n
  • Integrated rate laws:
    • Express the rate of reacgion as a function of the initial conentration of A and the measured (actual) one or more reactants after a specific amount of time has passed
    • Used to determine the rate constant and reaction order from experimental data
    • ln[A] = -kt + ln[A]0 where [A]0 is concentration of reactant A at the very beginning and [A] is the concentration of A after time t has passed.
  • Zeroth order reactions (n = 0)
  • First order reactions (n=1)
  • Second order reactions (n=2)

Section 4.3: The Free-Radical Chain Reaction

  • Chain reaction mechanism has 3 types of steps:
    1. Initiation step
    2. Propagation steps
    3. Termination steps

Chapter 5: Stereochemistry p. 169-214

Section 5-2A: Chirality and Enantiomerism in Organic Molecules

  • Every object has a mirror image. If that mirror image can be super-imposed on the original, then that object is achiral and therefore has no enantiomers.
  • If the mirror-image demonstrates handedness, aka, cannot be super-imposed on the original, then that object is chiral and has enantiomers.
  • There are two broad classes of isomers:
    1. Constitutional isomers aka structural isomers which have the same atoms but a different bonding sequence.
    2. Stereoisomers which have the same atoms and the same bonding sequence. However, such stereoisomers may exhibit chirality aka handedness.
  • Chapter 5 is about the second broad class: stereoisomers. Stereoisomers consist of: (1) geometric isomers and (2) enantiomers but we will focus primarily on enantiomers.
  • Per this article, enantiomers are different than other isomers. Most isomers display distinct physical and chemical properties from each other. However, a pair of enantiomers have identical physical and chemical proprties except when it comes to interacting with other chiral objects.

Section 5-3: (R) and (S) Nomenclature of Asymmetric Carbon Atoms

  • The Cahn-Ingold-Prelog convention aka CIP priority rules aka CIP system is a standard process to completely and unequivocally name a stereoisomer of a molecule. The purpose of the CIP system is to assign an R or S descriptior to each stereocenter and an E or Z descriptor to each double bond.
  • Rules according to Wikipedia:
    1. Identify stereocenters and double bonds
    2. Assign priorities to the groups attached to each stereocenter or double-bonded atom
    3. Assign R/S descriptors and E/Z descriptors

Section 5-4: R/S Nomenclature Is Independent of Dextrorotatory / Levorotatory (Optical Activity and Polarimetry)

  • From Chem Libre Text, “There is no relationship between chiral compound’s R/S designation and the direction of its specific rotation. For example, the S enantiomer of ibuprofen is dextrorotatory, but the S enantiomer of glyceraldehyde is levorotatory.”
  • See also this good explanation of why biochemists prefer to use the older D/L system. It’s more relevant to the nature of what they study.
  • For a simplistic mneumonic using the CORN law which ignores R/S and focuses only on D/L, see this page. Virtually all biologically occurring amino acids are levorotatory with the exception of glycine which is achiral (b/c the side-chain is a simple hydrogen atom).

Chapter 6: Alkyl Halides: Nucleophilic Substitution and Elimination p. 215-280

Section 6-10: Factors Affecting SN2 Reactions: Strength of the Nucleophile p. 233-235

  • A base is always stronger than it’s corresponding conjugate acid
  • We might be tempted to say that methoxide CH3OH is more nucleophilic because it is a strong base. But this is a spurious correlation! p. 234
    • In fact, basicity and nucleophilicity are distinct properties. In the cases of: (1) a base stealing a proton H+ and (2) a nucleophile attaching to a central carbon, we see a two different types of new bond formation. If the new bond is to a hydrogen/proton, then the reagant is acting as a base. if the new bond is to a central carbon in the substrate, the reagant is acting as a nucleophile.
    • Basicity is the equilibrium constant Keq for abstacting a proton H+.
    • Nucleophilicity is defined as the rate (kr) by which a nucleophile attacks a substrate electrophilic carbon atom.
  • Three trends affecting the how strong the nucleophile is (p. 234-235).
    1. The negative charged species (anion form) is a stronger nucleophile than the non-charged (neutral atomic/molecular form)
    2. Within the neutral/anionic right half of the periodic table, elements to the left (e.g., Group 15) are more nucleophilic because they are less electronegative than elements to the right (e.g., Group 16-17). So NH2- is more nucleophilic than OH- which is more nucleophilic than F-. Because F is more electronegative than O and N. (see bullet below for explanation).
    3. Within a Group/column, the further down in the periodic table one goes, the less electronegative and therefore the more nucleophilic the element. At the same time, atomic radii is also increasing the further down a column one goes which also helps with nucleophilicity because of a bigger electron cloud that can reach out an attach for SN2 reactions.
  • Note, the more electronegative an element is, the less nucleophilic it is (assuming it still has a net negative rather than positive charge). At first, this may seem contradictory because negatively charged anions (e.g., halide ions like F-, Cl-, Br-, I-) act as nucleophiles much more than positively charged cations (e.g., alkali metals like Li+, Na+, K+). However, given a neutral or negative species, within that grouping, oddly enough the less electrophilc an element, the stronger a nucleophile it is! So moving left to right in Period 2, N is more nucleophilic than O which is more nucleophilic than F which is the opposite of electronegativity. N is less electronegative than O is less electronegative than F. This is because the more electronegative an element is, the more tightly its nucleus grips its electron cloud. So the electron cloud is smaller and tighter and less likely to be able to do backside attachment to the target substrate carbon atom.

Miscellaneous notes

L.G. Wade progress

  • 9/22/2020: completed p. 32 exercises on arrow-pushing, esp. for Lewis Acid-Bases, nucleophiles (electron-pair donor aka Lewis base) vs. electrophiles (electron-pair acceptor aka Lewis acid).
  • 9/24/2020: completed building periodic table of most commonly used elements for organic chemistry
  • 9/30/2020: Wade Solutions Manual arrived, solved multiple 2 reactant acid-base synthesis arrow-pushing problems.
  • October 3-7, 2020: completed all of Problems 1-45 and 1-46 in deciding which reactants are the Nucleophile (blue Lewis Base which donates electrons), which is the Electrophile (green Lewis Acid which accepts electron pair).
  • See terminology on Wade, p. 30 for conventional terminology: * When referring generically to acids and bases, chemists usually mean the in the Brønsted-Lowry sense: whether donate or* accept* protons, respectively. * However, when an acid-base reaction involves formation of a new bond to some other element (esp. carbon), chemists typically say nucleophile (for Lewis Base donating an electron pair) or electrophile (for Lewis Acid accepting an electron pair).
  • October 8: Started chapter 2, skimmed through sections on σ-bonds (single) and π - bonds (part of double or triple bonds). Also VESPR theory and Stereoismers.
  • October 12-13: Completed problems 2-24 and 2-25
  • October 15-19: Completed problems 2-26, 2-27, 2-28
  • October 20-21: Read about resonance-stabilization (p. 13-16) and problems 2-29, 2-30
  • October 22-23: Continued resonance stabilization reading, including example of formaldehyde and drawing tables from p. 9 and p. 13. (See handwritten JH notes 10/23, 10/27, 10/28/2020)
  • October 24: More work on resonance. Chatted with Mary C. about repetitive day to day nature of benchwork.
  • October 25: Completed Solved Problem 1-2 on resonance forms (p. 16)
  • October 26: Completed Problem 1-7 on resonance (p.17)
  • October 27: Redrew table of common bonds and charges for atoms in organic molecules, inspired by Table on p. 13.
  • October 28: More resonance exercises, including Problem 1-8f re: formamide.
  • October 29 - November 5: More resonance exercises. End of Chapter 1: Problems 1-37 through 1-30 on p. 36-37
  • November 6-7: Completed Problems 1-40, 1-41 on on p. 36-37
  • November 7-8: Problems 2-30, 2-31 on p. 80
  • November 9-10: Problems 2-32, 2-33
  • November 13-18: Problems 2-34, 2-35, 2-36, 2-37, 2-38, and 2-39
  • November 17: Sapp’s The New Foundations of Evolution: On the Tree of Life arrived from library
  • December 1, 2020: Valentine’s On the Origin of Phyla arrived from the library
  • December 3, 2020: Completed Problem 2-40. Completed Chapter 2!
  • December 4, 2020: Started Chapter 3 – Alkanes p. 83–126
  • 12/04 - 12/10: Completed Alkane Naming Rules, Problems 3-1, 3-2, 3-3, 3-4, 3-5 p. 86-90
  • 12/12 - 12/14: Cycloalkanes naming rules and examples p. 104
  • 12/14 - 12/16: Problems 3-14, 3-15, 3-16, 3-17
  • 12/18 - 12/19: Played with 3-d model and 2-d drawings of cyclohexane, including Problems 3-20 and 3-21. See diagram of comparative energies of chair, half-chair, twist-boat, and boat conformations of cyclohexane in JH notebook Dec 18. See also nicely labeled 3-d animation here.
  • 12/20: Problem 3-24
  • 12/21: For review, drew molecular structures of purines and pyrimidines of DNA from memory. Copied early illustrations from Valentine re: types of organizational structures.
  • 12/24 - 12/27: Completed Solved Problems 3-3, 3-4 and Problem 3-25 on p. 117
  • 12/28 - 12/30: Completed Problems 3-27, 3-28, 3-29. Bicyclic carbon rings, bridghead naming rules based on # of intermediate carbons in the rings. Also used models to examine cis vs. trans isomers of decalin and trans is more stable b/c cis forces what looks like a 90-degree angle between the 2 rings.
  • 12/31: Began problems at the end of Chapter 3. Completed Problem 3-33.
  • 1/01/2021: Problems 3-34, 3-35, 3-36
  • 1/02 - 1/04: Problems 3-37, 3-38, 3-39
  • 1/05: Problems 3-40, 3-41, 3-42
  • 1/06: Problems 3-43, 3-44, 3-46, 3-47
  • 1/07: Started Chapter 4 - The Study of Chemical Reactions
  • 1/23: Restarted Snyder Molecular Genetics of Bacteria again, after insights into archea and bacteria from reading Sapp, Quammen, N.R. Pace, and others.
  • 2/13: discussion with JRH re: future projects, 7 month budget timeline.
  • 2/14: break from ochem
  • March 2021: Compiler studies
  • May – July 2021: Axler, Linear Algebra Done Right, 3rd Edition; partway through Chapter 5, Section 5B on chained transformations on T-invariant subspaces.
  • August, 2021: Back to organic chemistry
  • 8/01: Restarted Wade Ch 4, Section 4.3: The Free Radical Chain Reaction, p. 128. Rebuilt ochem page. For older version with Khan Academy checklist, refer to ochem v01.
  • 8/02: Generation of free radicals, p. 129.
  • 8/03: Drew Lewis structures of radical species, Problem 4-1 p. 130.
  • 8/04: Definition and examples for matrix of operator T ∈ ℒ(V) and distinction from matrix of linear map T ∈ ℒ(V,W).
  • 8/05: Problem 4-2
  • 8/06: Termination steps of chlorination of methane p. 131
  • 8/07: Problems 4-3, 4-4, started Section 4-4, review of equilibrium constant and free energy, p. 133.
  • 8/08: Phone chat with MC Boston Commons re: medical affairs etc
  • 8/09: More Axler, eigenspaces, diagonalization, etc.
  • 8/10: Started Axler Section 5C, p. 155 as well as Dr. Trefor Bazett’s video series on Linear Algebra.
  • 8/11: Completed Axler Chapter 5, first pass. Need to review other resources on eigenspaces etc. again.
  • 8/12: Completed review of standard Gibbs free energy change. Began Wade Section 4-5 on changes in enthalpy and entropy.
  • 8/13: Info chats with NO and SC “M”
  • 8/14: More on Wade Chapter 4
  • 8/15: Reintegration and reinterpretation of relationship between thermodynamics and kinetics
  • 8/16: Section 4-10: Transition States p. 142. Section 4-11: Multistep Reaction Rates and Reaction Diagrams p. 144.
  • 8/17: Section 4-12: Temperature and many different halogenation (not just Cl chlorine). Section 4-13: halogenation of other alkanes (more carbons than methane)
  • 8/24: First post to IG: science.sketch
  • 8/25: lac operon posted to IG
  • 8/26: For most up to date accounting of ATP generation in electron transport chain oxidative phosphorylation, scroll to bottom of this Wiki article
  • 8/27: Day 2 of glycolysis
  • 8/28: Day 3 of glycolysis. Handy reference on organic chemistry nomenclature
  • 8/29: New issue of Nature about AlphaFold, deep learning, and protein folding
  • 8/30: Researched domain names
  • 9/05: Notes on Sections 4-14 (The Hammond Postulate) and 4-15 (Radical Inhibitors) p. 151-156. Began sketching out Section 4-15: Reactive Intermediates p. 156
  • 9/07: Prepped Stigmasterol for 9/08 IG post
  • 9/08: Posted Stigmasterol on IG and prepped Cholesterol, Estradiol (E2), and Testostorone for next few days.
  • 9/09: Posted Cholesterol on IG. Completed Wade Chapter 4
  • 9/10: Posted estradiol and testosterone on IG. Started Chap 5 Stereochemistry
  • 9/11: More Stereochemistry
  • 9/12: posted molecular model of 1,2-dichlorocyclopentane to IG
  • 9/13: posted DNA molecular model to IG
  • 9/14: More stereochemistry / chirality / enantiomer problems
  • 9/15: Built models of Norcamphor also known as: 2-norbornanone and bicyclo[2.2.1]heptan-2-one
  • 9/16: Posted Alanine model to IG and prepped next several days of amino acids. Proline is the only amino acid with a side chain that connects to the protein backbone twice, meaning that Proline is uniquely unable to occupy many of the other main chain conformations adopted by all other amino acids.
  • 9/17: More models in sunlight
  • 9/18: Posted L-phenylalanine to IG. More problems on chiral centers, Internal Mirror Plane of Symmetry (IMPoS)
  • 9/19: Posted L-tyrosine to IG
  • 9/20: Posted L-valine (first BCAA) to IG and more R/S problems
  • 9/21: Posted L-leucine. Worked through Solved Problem 5-3 p. 179-181 on R/S configurations of carvone
  • 9/22 - 9/23: Solved more R/S config problems within Problem 5-6 on p. 181.
  • 9/23: While researching methionine for today’s IG post, began reading up on DNA methylation which methionine can be a precursor for. MBOC 5th edition, p. 468 - 471. See also Figure 7-86(c) on p. 472.
    • Also researched relationship between methionine and S-adenosylmethionine aka SAM-e aka Ado-Met aka SAM. Seems like SAM-e is a co-substrate in methyl group transfers, transsulfuration, and aminopropylation.
    • According to the SAM-e wiki article,
      • “SAM-e is bound by the SAM riboswitch which regulates genes involved in methionine and cysteine biosynthesis.”
      • “In eukaryotic cells, SAM-e serves as a regulator of…DNA methylation, tRNA methylation, and rRNA methylation; immune response, amino acid metabolism.”
      • “In plants
      • See also DNA methyltransferase aka DNA MTase aka DNMT which transfers methyl groups to DNA.
  • 9/24: paper notes about polycyclic aromatic hydrocarbons (PAH)
  • 9/25: paper notes review of 5 aliphatic hydrophobic (mostly nonpolar) amino acids, including alanine (just CH3 methyl group), the three BCAAs (valine, leucine, isoleucine), and methionine (straight chain with sulfur atom).
  • 9/26: paper notes review of 3 aromatic hydrophobic amino acids: phenylalanine (just a phenyl group attached to the 1-carbon-root of alanine), tyrosine (phenyl group gets -OH attached to it), tryptophan (benzene is combined with 5-membered pyrrole ring to become an indole)
  • 9/27: posted benzene photos to IG
  • 9/28: posted naphthalene to IG right after midnight (late the night of Monday 9/27; early the morning of Tuesday 9/28)
  • 9/29: Research on Tetracene (four benzene rings arranged linearly).
    • From this 2019 article:
      • “It is the second member of the “acene” family of linearly arranged PAHs that begins with anthracene and continues to pentacene, hexacene, and beyond. The bright orange molecule is also known as naphthacene, 2,3-benzanthracene, and benz[b]anthracene.
      • “Unlike many PAHs, tetracene is not carcinogenic. But it was studied for carcinogenicity as long ago as the 1930s. Early researchers were James W. Cook and co-workers at the Cancer Hospital of London and Alfred Winterstein and Karl Schön at the Kaiser Wilhelm Institute for Medical Research1 (Heidelberg, Germany).
      • “Not much was done with tetracene until 2007, when researchers discovered that it is a semiconductor that was useful in organic field-effect transistors (OFETs) and organic light-emitting diodes (OLEDs). This year, electrical engineer Marc A. Baldo at MIT (Cambridge, MA) and colleagues there and at Princeton University (NJ) incorporated it into silicon solar cells (SSCs).
    • 2021 - https://www.pv-magazine.com/2021/05/14/new-discovery-promises-to-bring-singlet-fission-enhanced-c-si-solar-cells-nearer-to-commercial-production/
    • 2019 - https://www.wired.com/story/new-designs-could-boost-solar-cells-beyond-their-limits/
    • 2014 - https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5090406/#C22
    • 2018 - https://pubs.rsc.org/en/content/articlelanding/2018/mh/c8mh00853a
    • 2014 - https://www.rle.mit.edu/visualization-of-exciton-transport-in-ordered-and-disordered-molecular-solids/
    • Marc Baldo’s webpage at MIT
      • 2014 - https://news.mit.edu/2014/getting-more-electricity-out-solar-cells-0507
    • Reseearch on Rubrene
  • 9/30 - posted Rubrene to IG
    • Shot and posted first tiktok video for Rubrene and shared on IG.
    • researched PAHs to post on Friday, October 1.
  • 10/3 - OK, here’s the list of past and future PAH’s. Friday 10/1 - smiley face 5 ring happy friday PAH.
  • 10/4 - Posted HBC yesterday (Sunday). Posted 10/4 - Hexa-cata-hexabenzocoronene today (Monday).
  • 10/5 - Posted 1,3,5-tris(biphenyl)benzene to IG. Nice reactions to it, especially the second Story version of it with rainbow light
  • 10/6 - Now that I have a solid set of 9 photos, I’m going to go back to paper notes for 3 days of posting.
  • 10/7 - Posted diagram comparing 10/2, 10/3, and 10/4 posts of coronene, HBC, and hexa-cata-hexabenzocoronene.
  • 10/8 - first day of final amino acid sequence. 9 polar amino acids. 3 special ones (glycine, proline, cysteine). Spent Thursday evening 10/7 drawing, building models, and thinking about 5 polar charged AAs: * 3 Polar, Postively Charged AA (PPC): Lysine, Histidine, Arginine (all have Nitrogens). * 2 Polar, Negatively Charged AA (PNegC): The two acids aspartic acid, glutamic acid.
    • On Friday:
      • 4 Polar, Uncharged AA: Serine, Threonine, Asparagine, Glutamine
    • On Saturday:
      • 3 special cases: Glycine (just hydrogen so the only achiral AA). Proline which has amine ring attached to the nitrogen; only one side chain which connects to peptide backbone; used in 2021 Nobel work on organocatalysts. Cysteine.
  • 10/9 Posted about Aspartic Acid. Started reading about Glutamic Acid / glutamate / monosodium glutamate MSG. History of food, role in nervous system with GABA inhibitory / exitatory system etc.
  • 10/10 posted about Glutamic Acid / Glutamate. This is a good 2020 article about the GABA inhibitory system. Of course, glutamate is an important neurotransmitter for excitatory networks.
  • 10/11 Posted about Lysine. Good article about epsilon-amino group NH3+ in physiological conditions.
  • 10/12 Posted about Arginine. Good article about guanidino group that at physiological pH, becomes a charged guanidinium cation.
  • 10/13 posted histidine which has a 5 member, 2-nitrogen Imidazole Ring in uncharged state which converts at physiological pH to zwitterion / positive cation as an Imidazolium Ring. As usual, Arizona has good page of the zwitterion form of histidine.
    • Hm, i think i’ll start posting at like 10 PM Pacific time and then go to sleep. Post for the next day basically.
    • Here’s the list of AA’s so far: 8 nonpolar/hydrophobic: alanine, valine, leucine, isoleucine, methionine; phenylalanine, tyrosine, tryptophan. 2 polar negatively charged: aspartic acid, glutamic acid. 3 polar negatively charged: lysine, arginine, histidine. Next 4: serine, threonine, asparagine, GLUTAMINE WHICH IS NOT YET PHOTGRAPHED!
      • And then the final three: glycine, proline, cysteine.
  • 10/14 posted Serine
  • 10/15 posted Threonine. spent some time writing handwritten notes for IG Stories.
  • 10/16 set up Excel checklist planning for next week of posts
    • Cysteine info
      • Important point in wikipedia about how cysteine provides the only R stereocenter (for the alpha-carbon i believe). Whereas all other amino acids have an S-stereocenter there. Quote: “Cysteine has l chirality in the older d/l notation based on homology to d- and l-glyceraldehyde. In the newer R/S system of designating chirality, based on the atomic numbers of atoms near the asymmetric carbon, cysteine (and selenocysteine) have R chirality, because of the presence of sulfur (or selenium) as a second neighbour to the asymmetric carbon atom. The remaining chiral amino acids, having lighter atoms in that position, have S chirality.”
      • Additional good points at Arizona about cysteine, structural similarity but chemical/functional differences compared to serine (simple OH alcohol) where O is replaced by S sulfur.
    • Proline info
      • From Arizona, Proline is technically not an amino acid but an imino acid
      • From wiki, ‘The “side chain” from the α carbon connects to the nitrogen forming a pyrrolidine loop, classifying it as a aliphatic amino acid’
  • 10/17 more research on glutamine.
    • 2001 Introductory to the Symposium Proceedings remarks for the conference: Glutamine Metabolism: Nutritional and Clinical Significance by Douglas W. Wilmore and John L. Rombeau.
    • Hans Krebs 1980 Paper “Special Lecture: Glutamine Metabolism in the Animal Body” where he says at the end of the lecture: “Finally a few comments on the multiplicity of the functions of gluatmine….Most amino acids have multiple functions (Table III) but glutamine appears to be the most versatile.”
  • 10/18 Glycine, first of the 3 specials. posted Sunday evening for Monday. then did stories for Monday.
    • Cysteine is the only R- configured amino acid. All amino acids are Levorotary under the old D/L system. And 19 of the 20 amino acids are also S-configured around the cenrtral alpha carbon except cysteine because of the presence of the sulfur atom right next to the beta-carbon. Good youtube video here titled Amino Acid Stereochemistry R and S vs. D and L Configuration. Start at about 17:20
  • 10/20 Proline
    • Posted IG story about 2021 Nobel Prize in Chemistry for small safe organocatalysts
  • 10/21 spent lot of time working on my Alanine IG stories
  • 10/22 posted Valine
  • 10/23 prepped next set of days of amino acids, model building, photography. leucine, isoleucine, methionine, phenylalanine, tyrosine, tryptophan
  • 10/24 posted leucine and isoleucine
  • 10/25 prepped for methionine
  • 10/26 prepped for phenylalanine IG post
  • 10/27 Zai gave feedback on phenylalanine post via text. I think i should do more editing, revision, rewriting captions before posting. Also check out Preview iOS app for IG scheduling…
  • 10/28 prepped for Tryptophan on friday
  • 10/29 Prepped for cystine (cysteine dimer) for Sat
  • 10/30 initial test photos of adenine with all the new backgrounds
  • 10/31 more thoughts about nucleic acid series
  • 11/1 first post in nucleic acid series. Cytosine
  • 11/2 more drawing of major groove / minor groove for CG pair bonding while listening to Dust S3 Chrysalis. Posted Guanine
  • 11/3 prepped for posting of model for C-G pairing.
  • 11/4 finally figured out orientation of 4 canonical basepairs, orientation of nucleobases to ribose attachments using drawings, videos, both ochem and MBOC textbooks, and molecular models. Ribbon along arm analogy as a continuous stream also helped. Critical key is remembering that the base can rotate freely along the 1’ to 9-nitrogen (purine) or 1’ to 1-nitrogen (pyrimidine) carbon-nitrogen axis.
  • 11/7 more practice drawing base pairs with new understanding
  • 11/8 good SlideShare link explaining and visualizing major and minor grooves.
  • 11/9 prep for posting paper notes of G-C bonding
  • 11/10 prepped for thymine post
  • 11/11 prepped adenine post
  • 11/12 prepped for A-T bonding post
  • 11/13 prepped for A-T bonding post 2
  • 11/14 more prep
  • 11/15 considered what series next.
  • 11/16 prepped final A-U photo and began prepping series on terpenes and steroids
  • 11/17 made IG stories for final DNA/RNA posts. IG story about pies
  • 11/18 more prep
  • 11/19 read more Follett in prep of afternoon reading room
  • 11/20 resting from booster
  • 11/21 planning on TIS
  • 11/23 created new terpenes isoprenes steroids/sterols page
  • 11/28 changed IG account name from @science.sketch to @dailymolecule
  • 12/5 considered a post contrasting steroids and sterols -OH at carbon 3
  • 12/21 continued with Stereochemistry chapter > Fischer Projection exercises
  • 12/22 more Fischer projection exercises
  • 12/23 diastomers
  • 12/24 fiinished skim/reading through end of Chapter 5
  • 12/25 more diastereoisomer problems esp. for molecules with 2 or more chiral centers
  • 12/26 started Meso compound section
  • 12/28 completed all meso compound problems, began absolute vs. relative configuration section
  • 12/30 more stereo problems
  • 12/31/2021 completed absolute v. relative section. In general, a lot of bio organic molecules were classified as D(+) or L(-) relative to glyceraldehyde. Amino acids were generally L and were based off of (-)-glyceraldehyde. Sugars generally degrade to (+)-glyceraldehyde and are generally D-sugars. None of these map cleanly onto R/S CIP sequence rules.
  • 1/01/2022 continued end of chapter 5 problems
  • 1/02 - 1/14 more chapter 5 stereochemistry problems
  • 1/15 some tougher stereochemistry problems at the end
  • 1/18 some tougher stereochemistry problems at the end
  • 1/19 more problems
  • 1/21 didn’t do problems, started Mawdsley Russian Civil War
  • 1/22 started Chapter 6 on Alkyl Halides
  • 1/25-31 more on chapter 6 / coach em stuff / draft revs
  • 2/01/2022 More on chapter 6
  • 2/02 More on chap 6 and return(); success!
  • 2/03-2/05 Section 6:allylic bromination
  • 2/08 Began proper section on nucleophilic substitution and elimination reactions
  • 2/09-13 More on nucleophilic substitution and elimination via base. Hamlet ppt.
  • 2/15 Prepped Campesterol
  • 2/16 More on nucleophilic substitution and elimination via base.
  • 2/18-21 Examples of SN2 reactions
  • 2/22 problem 6-13 p. 231 on predicting transition state and products of ammonia + 1-bromobutane
  • 2/23 Started Section 6-9 on how the SN2 mechanism can be used to understand a wide variety of reactions
  • 2/24-26 Problem 6-14 on more examples of SN2 reactions
  • 2/27 Problem 6-14(f) learned about 18-crown-6 and other crown ethers
  • 2/28 More parts of Problem 6-15
  • 3/01/2022 More parts of Problem 6-15
  • 3/02 fiinished Problem 6-15
  • 3/03 factors affecting SN2 reactions: how strong the nucleophile is
  • 3/04-3/05 Categorized various common nucleophilic species by strength in SN2 reactions
  • 3/06-3/12 causes and trends of strength of nucleophilicity. Worked it out in Markdown before more hand drawn notes.
  • 3/13 first section on steric hindrance.
  • 3/14-3/20 Problem 6-16 on how steric hindrance and other factors influence which reagents are more nucleophilic
  • 3/22-3/23 Section 6-10B: protic solvents form hydrogen bonds to stabliize nucleophiles like -OH and -NH2
  • 3/24 started Section 6-11
  • 3/25-26 Problem 6-18
  • 3/27 Problem 6-19
  • 3/28 - 3/29 stereochemistry of SN2 reactions
  • 3/30 - 4/04 Problem 6-20. Remember, swapping any two constituents automatically switches R/S.
  • 4/05 Started Section 6-13 on the SN1 reaction
  • 4/06 more on section 6-13 reaction coordinate comparing transition states of SN1 vs SN1
  • 4/07 SN1 proceed faster when carbocations ionize more easily in Step 1 of reaction. This is helped by more substituted alkyl groups which stabilize the carbocation with the dipole moment that happen for each additional alkyl group. see p. 245.
  • 4/08 More on substituent effects on SN1 reactions
  • 4/09 Completed Problem 6-23 on substrate carbon and substrate/leaving-group effects on SN1 reactions
  • 4/10 Completed Problem 6-24 with examples of how resonance structures stabilize the carbocation resulting from Step 1 of SN1 ionization
  • 4/11 - 4/13 Previewed future sections left for SN1, E1, and E2 rxns.
  • 4/14 Solvent effects and stereochemistry of SN1 reactions
  • 4/15-4/16 Section 6-15: Mechanisms 6-5 and 6-6 for rearrangements of the carbocation of SN1: hydride shift and methyl shift, respectively
  • 4/17 More on methyl shift rearrangement prior to formation of carbocation in Step 1
  • 4/18 Redrew mechanism 6-6 of methyl shift forming tertiary carbocation prior to successive nucleophilic attack by ethanol
  • 4/19 - 4/21 Problem 6-26. extensive problems on methyl shift and hydride shift rearrangements and SN1
  • 4/22-3 Problem 6-26c. Hydride shift to a carbocation that is rearranged to be more stable because it is stabilized by allylic location of nearby double bond. Drew all associated resonance structures of protanated version of product I and product II. Key is that the nucleophile is the double-bonded oxygen, not the -OH hydroxyl group.
  • 4/24-5 Problem 6-26d. Product I result of basic hydride shift. Product II breaks cyclohexane to form 7-member cycloheptane. A new carbon-carbon bond somewhat like a methyl shift.
  • 4/26 Comparison of SN1 and SN2
  • 4/27 Problem 6-27 to predict whether SN1 and SN2 mechanisms predominate in given reactions.
  • 4/28 Problem 6-29 on silver nitrate speeding up SN1 where Ag+ encourages ionizations in Step 1 to form carbocation. Leds to ring expansion in bridgehead cyclohexane
  • 4/29 Started section on E1 elimination reactions and watched this video by Master Organic Chemistry.
  • 4/30 Problem 6-30 on how/why E1 and SN1 reactions compete with the same reactants
  • 5/01/2022 Energetics and orbitals of E1 reactions
  • 5/03 Hydride shift rearrangements in E1 reactions
  • 5/04 Completed Problem 6-32
  • 5/05 Started Problem 6-33
  • 5/07 Completed Problem 6-33 with a whole bunch of E1 and SN1 products; both with and without cation rearrangements
  • 5/08 Completed Problem 6-34. Zaitseff’’s rule on most stable alkenes are the ones with most substituted groups.
  • 5/09 Scanned future chapters on alkenes etc. Began Solved Problem 6-1 p. 260
  • 5/10 Completed Problem 6-35
  • 5/11 Began section on E2 elimination reactions. Caused by strong bases and comparison with E1 and SN2 reactions. Completed Problem 6-36
  • 5/12 Completed Problem 6-37
  • 5/13 More drawing and redrawing of ring structures resulting from E2 reactions in Problem 6-37(d)
  • 5/14 Finalized inverted cyclohexane structure after and SN2 attack in Problem 6-37(d)
  • 5/15 Started Section 6-20: Stereochemistry of E2 Reactions
  • 5/16 Used 3d models to solve Problem 6-38 on E2 reactions differentially create cis and trans alkenes with phenyl substiuent groups
  • 5/17 Completed Section 6-21: Overall comparison of E1 and E2 reactions
  • 5/18 Began final problems at end of Chatper 6
  • 5/19 - 5/22 Problems 6-42, 6-43, 6-44, 6-45, 6-46, 6-47
  • 5/24 Problems 6-48, 6-49, 6-50
  • 5/25 - 5/30 Problems 6-50…6-60
  • 5/31 - 6/01 Challenge Problem 6-61 on what happens when -OH group is protonated into becoming a good leaving group, resulting in 2 SN1 and 1 E1 products.
  • 6/01 Problem 6-62
  • 6/02 Reread p. 225 on regenerating alkyl bromination using resononant alkenes with adjacent allylic carbons, carbon radicals (3 bonds plus 1 electron; neutral species but highly “motivated” to bond), bromination chain reaction. NBS mediated. All in prep for solving Problems 6-63 and 6-64.
  • 6/03 - 6/04 Solved Problems 6-63 and 6-64 on how allylic bromination, carbon radicals, allylic radicals, NBS conversion to succinimide, etc. Also found this page detailing how NBS works; skip to section “Allylic Bromination with NBS: How It Works”.
  • 6/05 Problem 6-65 on why SN1 reactions have an excess of inverted product especially if the carbocation is unstable (e.g., primary or secondary vs. tertiary or stabilized by allylic resonance)
  • 6/06 Problem 6-66 5 products. Show mechanisms for each.
  • 6/07 Solved Problem 6-67 on impact of deuterium (C-D bonds are stronger than vanilla C-H bonds). Elimination products form 7x more slowly when C-D bonds must be broken relative to C-H bonds
  • 6/08 - 6/09 Problem 6-68
  • 6/10 Challenge Problem 6-69
  • 6/14 Challenge Problem 6-70
  • 6/17 - 6/18 Completed Challenge Problem 6-72
  • 6/19 Started Chapter 7 on Alkenes / Olefins
  • 6/20 Problems 7-1 and 7-2 to predict structures and understanding the 2n+2 formula for fully saturated hydrocarbons vs elements of unsaturation. Remember, 1 element of unsaturation (EoU)= 2 hydrogens. Therefore, 1 ring structure = 1 EoU, 1 double bond = 1 EoU, 1 triple bond = 2 EoU’s
  • 6/22 Elements of unsaturation with relation to halogens (F,Cl,Br,I) and Oxygen.
  • 6/29 Started section on naming of alkenes, esp updated new IUPAC conventions.
  • 6/30 Organic Chemistry: A Short Course, 13th Edition (2012) by Hart, Hadad, et al. arrived!
  • 7/01 Organic Chemistry, 2nd Edition by David Klein (2015) from Johns Hopkins arrived.
  • 7/02 Skimmed organization of Klein and will start with Chapter 7: Substitution Reactions. Might already be my favorite textbook! Already ordered the solutions manual.
  • 7/10 Officially began notes on Klein, 2nd Edition. Completed review of Chapter 7.3 on 4 types of arrow pushing; all used in substitution reactions. Reread Klein’s treatment of rearrangements–hydride shifts, methyl shifts, general alkyl shifts in Chapter 6.
  • 7/15 - 7/17 More on Chapter 7
  • 7/18 Before diving deeper into Sn2 mechanism, decided to review Molecular Orbital theory from Section 1.8. LCAO - Linear Combination of Atomic Orbital Theory.
  • 7/20-22 More on quantum chemical foundations of molecular orbital theory.
  • 7/23 Read up on evolution of early cetaceans from P.D. Gingrich (2015).
  • 7/24 Read more about the largest group of ancient/extinct whales, a paraphyletic group called the Archaeoceti. The earliest group of archaeocetids are the pakicetids so named because the fossils were found in Pakistan. Modern whales are classified under the Neoceti. The Neoceti include the *Parvorder Mysticeti](https://en.wikipedia.org/wiki/Baleen_whale), aka the baleen whales and *Parvorder [Odontoceti aka the toothed whales.
  • 7/25-26 Took some more notes in Klein about Molecular Orbital (MO) Theory.