Category Archives: Organic

The “Spectrum” of Substitution vs. Elimination

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Substitution and elimination reactions (between Lewis-bases and alkyl-halides) are some of the first reactions taught in organic chemistry. The figure above, organizes the main factors that distinquish: SN1, SN2, E1 or E2 mechanisms into a single, 4-quadrant spectrum. We describe the heirarchy of these factors in more detail below.

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Understanding Reactivity with Hard-Soft Acid-Base Theory

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Hard-Soft Acid-Base(HSAB) theory one of the most useful rules of thumb for explaining and predicting chemical reactivity trends. Hard molecules tend to be small/non-polarizable and charged while soft molecules tend to be large/polarizable and uncharged. Both acids/electrophiles and bases/nucleophiles can be hard and soft and the defining reactivity rule of HSAB theory is:

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Understanding Chemical Structures/Shapes

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One of the most useful tools in organic chemists’ tool-kit is the ability to visualize molecular structures and use that information to make predictions about a molecule’s shape and reactivity. This process is called conformational analysis and in the figure above we summarize some of the most common rules for drawing out the “shape” (or most stable conformation) of linear and cyclic molecules. In the figure above, the linear “main-chain” is highlighted in red and the cyclic “main-chain” is highlighted in black.

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Engineering Molecular Electronics with Substituents

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Often, if you are trying to design a molecule which has function (e.g. catalysts, fluorophores, switches, etc.) you have to tweak the electronics of that molecule. Generally, the most important electronic energy levels are the HOMO’s and LUMO’s which can donate and accept electrons, respectively. The figure above summarizes the substituents that are most used to raise the energy (electron donating groups), lower the energy(electron withdrawing groups) or do both (extra conjugation groups).

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Understanding Aromaticity based on Molecular Orbital Theory

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Interestingly, once you understand the relative energies of linear pi-molecular orbitals the concept of “aromaticity” becomes alot simpler to understand. For example, cyclizing the frontier molecular orbitals (FMO) of butadiene gives you the anti-aromatic orbitals of cyclobutadiene. The “geometric arrangment” of these aromatic orbitals is a result of alternating stabilization (in green) or destabilization (in red) due to symmetry match or mismatch, respectively.1

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The Energies of Linear Frontier Molecular Orbitals

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The Woodward Hoffman rules are some of the most useful rules in organic chemistry. Unfortunately, because these rules are symmetry-based, they mostly ignore the relative energies of the molecular orbitals they consider. Luckily, Huckel theory (on which the Wood-ward Hoffman rules were based) gives as simple, geometric handle on the energies of these orbitals. Understanding these energies is critical for (1) rationalizing non-pericyclic reactivity trends and (2) answering the question: What exactly is aromaticity?

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How High are HOMO’s and Low are LUMO’s?

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The energies of a molecule’s Highest Occupied Molecular Orbital’s (HOMO’s) and the Lowest Unoccupied Molecular Orbitals (LUMO’s) tell us alot about that molecules reactivity. In general, molecules with high HOMO’s are good nucleophiles, bases, and reductants while molecules with low LUMO’s are good electrophiles, Lewis acids and oxidants. Unfortunately, the absolute magnitudes of “high” or “low” are very rarely treated. In the figure above, we plotted absolute values of HOMO and LUMO energies to convey more of a global understanding of reactivity trends.

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A Single pKa Chart: Visualizing Reactivity Trends

Figure 1 A. Chemical Functional Groups organized by pKa (y-axis) and acidic atom (x-axis: oxygen, nitrogen, carbon, other.)  B. Key for using A given a solution pH. First, mark the position of the solution pH on the pKa axis (dotted horizontal line). all functional groups above it are neutral or positively charged while all functional groups below it are negative or neutral. Second, the pKa axis is useful in further categorizing functional groups by their ability to participate in hydrogen bonds.

The pKa value of a chemical functional group (Figure 1A) is very useful because it can directly give you the approximate charged state of that functional group (in the context of drugs, proteins, membranes, DNA, etc.) at a specific solution pH.  As such, the pKa is critical to an intuitive understanding of electrostatics in chemical and biological contexts.

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