optional-skills/creative/concept-diagrams/examples/sn2-reaction-mechanism.md
A chemistry diagram showing the bimolecular nucleophilic substitution (SN2) mechanism between hydroxide ion and methyl bromide. Demonstrates molecular structure rendering, electron movement arrows, transition state notation, and reaction energy profiles.
This is a chemistry mechanism diagram with:
<!-- Carbon atom (dark) -->
<circle cx="0" cy="0" r="14" class="carbon"/>
<text class="chem" x="0" y="5" text-anchor="middle" fill="white" font-weight="500">C</text>
<!-- Oxygen atom (red) -->
<circle cx="0" cy="0" r="14" class="oxygen"/>
<text class="chem" x="0" y="5" text-anchor="middle" fill="white" font-weight="500">O</text>
<!-- Hydrogen atom (light with border) -->
<circle cx="38" cy="0" r="8" class="hydrogen"/>
<text class="chem-sm" x="38" y="4" text-anchor="middle">H</text>
<!-- Bromine atom (brown) -->
<circle cx="52" cy="0" r="16" class="bromine"/>
<text class="chem" x="52" y="5" text-anchor="middle" fill="white" font-weight="500">Br</text>
.carbon { fill: #2C2C2A; }
.hydrogen { fill: #F1EFE8; stroke: #888780; stroke-width: 1; }
.oxygen { fill: #E24B4A; }
.bromine { fill: #993C1D; }
.nitrogen { fill: #378ADD; } /* for other reactions */
<!-- Single bond (solid) -->
<line x1="14" y1="0" x2="38" y2="0" class="bond"/>
<!-- Wedge bond (coming toward viewer) -->
<polygon class="bond-wedge" points="0,-14 -6,-35 6,-35"/>
<!-- Dash bond (going away from viewer) -->
<line x1="-10" y1="10" x2="-28" y2="28" class="bond-dash"/>
<!-- Partial bond (forming/breaking) -->
<line x1="-40" y1="0" x2="-14" y2="0" class="bond-partial"/>
.bond { stroke: var(--text-primary); stroke-width: 2.5; fill: none; stroke-linecap: round; }
.bond-thin { stroke: var(--text-primary); stroke-width: 1.5; fill: none; }
.bond-partial { stroke: var(--text-primary); stroke-width: 2; fill: none; stroke-dasharray: 4 3; }
.bond-wedge { fill: var(--text-primary); stroke: none; }
.bond-dash { stroke: var(--text-primary); stroke-width: 2; fill: none; stroke-dasharray: 2 2; }
<!-- Lone pair electrons (dots) -->
<circle cx="-8" cy="-18" r="2" fill="var(--text-primary)"/>
<circle cx="0" cy="-18" r="2" fill="var(--text-primary)"/>
<!-- Formal negative charge -->
<text class="charge" x="12" y="-12" fill="#A32D2D" font-weight="bold">⊖</text>
<!-- Partial charges (delta notation) -->
<text class="partial" x="0" y="-18" text-anchor="middle" fill="#A32D2D">δ⁻</text>
<text class="partial" x="0" y="-22" text-anchor="middle" fill="#3B6D11">δ⁺</text>
.charge { font-family: "Times New Roman", Georgia, serif; font-size: 12px; }
.partial { font-family: "Times New Roman", Georgia, serif; font-size: 11px; font-style: italic; }
<defs>
<marker id="curved-arrow" viewBox="0 0 10 10" refX="8" refY="5" markerWidth="6" markerHeight="6" orient="auto">
<path d="M0,0 L10,5 L0,10 L3,5 Z" class="arrow-fill"/>
</marker>
</defs>
<!-- Nucleophilic attack arrow -->
<path d="M -5,15 Q 30,60 70,25" class="arrow-curved" marker-end="url(#curved-arrow)"/>
.arrow-curved { stroke: #534AB7; stroke-width: 2; fill: none; }
.arrow-fill { fill: #534AB7; }
<!-- Left bracket -->
<path d="M -75,-70 L -85,-70 L -85,75 L -75,75" class="ts-bracket"/>
<!-- Right bracket -->
<path d="M 95,-70 L 105,-70 L 105,75 L 95,75" class="ts-bracket"/>
<!-- Double dagger symbol -->
<text class="chem" x="115" y="-60" fill="var(--text-primary)">‡</text>
.ts-bracket { stroke: var(--text-primary); stroke-width: 1.5; fill: none; }
<!-- Y-axis (Energy) -->
<line x1="0" y1="280" x2="0" y2="0" class="axis" marker-end="url(#straight-arrow)"/>
<text class="t" x="-15" y="-10" text-anchor="middle" transform="rotate(-90 -15 140)">Potential Energy</text>
<!-- X-axis (Reaction Coordinate) -->
<line x1="0" y1="280" x2="600" y2="280" class="axis" marker-end="url(#straight-arrow)"/>
<text class="t" x="580" y="305" text-anchor="middle">Reaction Coordinate</text>
<!-- Filled area under curve -->
<path class="energy-fill" d="
M 40,200
Q 150,200 250,50
Q 350,200 500,220
L 500,280 L 40,280 Z
"/>
<!-- Curve line -->
<path class="energy-curve" d="
M 40,200
Q 100,200 150,150
Q 200,80 250,50
Q 300,80 350,150
Q 400,210 500,220
"/>
.energy-curve { stroke: #534AB7; stroke-width: 2.5; fill: none; }
.energy-fill { fill: rgba(83, 74, 183, 0.1); }
<!-- Reactants level -->
<line x1="20" y1="200" x2="80" y2="200" stroke="#3B6D11" stroke-width="2"/>
<text class="ts" x="50" y="218" text-anchor="middle">Reactants</text>
<!-- Transition state peak -->
<circle cx="250" cy="50" r="5" fill="#534AB7"/>
<line x1="250" y1="50" x2="250" y2="280" class="energy-level"/>
<text class="ts" x="250" y="30" text-anchor="middle" fill="#534AB7" font-weight="500">Transition State [‡]</text>
<!-- Products level (lower = exergonic) -->
<line x1="470" y1="220" x2="530" y2="220" stroke="#3B6D11" stroke-width="2"/>
<!-- Activation energy arrow -->
<line x1="100" y1="200" x2="100" y2="55" class="delta-arrow" marker-end="url(#delta-arrow)"/>
<text class="ts" x="85" y="125" text-anchor="end" fill="#3B6D11">E<tspan baseline-shift="sub" font-size="8">a</tspan></text>
.energy-level { stroke: var(--text-secondary); stroke-width: 1; stroke-dasharray: 4 2; fill: none; }
.delta-arrow { stroke: #3B6D11; stroke-width: 1.5; fill: none; }
.delta-fill { fill: #3B6D11; }
/* Chemistry notation (serif font for formulas) */
.chem { font-family: "Times New Roman", Georgia, serif; font-size: 16px; fill: var(--text-primary); }
.chem-sm { font-family: "Times New Roman", Georgia, serif; font-size: 12px; fill: var(--text-primary); }
.chem-lg { font-family: "Times New Roman", Georgia, serif; font-size: 18px; fill: var(--text-primary); }
<!-- Subscript using tspan -->
<text class="ts">E<tspan baseline-shift="sub" font-size="8">a</tspan></text>
<!-- Superscript for charges -->
<text class="chem-sm">OH⁻</text> <!-- Using Unicode superscript minus -->
<text class="chem-sm">CH₃Br</text> <!-- Using Unicode subscript 3 -->
| Element | Color | Hex |
|---|---|---|
| Carbon | Dark gray | #2C2C2A |
| Hydrogen | Light cream | #F1EFE8 |
| Oxygen | Red | #E24B4A |
| Bromine | Brown | #993C1D |
| Nitrogen | Blue | #378ADD |
| Electron arrows | Purple | #534AB7 |
| Positive charge | Green | #3B6D11 |
| Negative charge | Red | #A32D2D |
Use this diagram style for: