Implement Algorithm for sp3d (Trigonal Bipyramidal) Bond Angles

[TharunKumarrA]

Description

Develop and implement an algorithm to calculate bond angles for sp3d (trigonal bipyramidal) hybridization. This is essential for the accurate representation of molecular geometries like PCl₅.

Acceptance Criteria

• The algorithm calculates bond angles for sp3d hybridization correctly (90°, 120°).
• Results align with standard trigonal bipyramidal geometry.
• The implementation is efficient for real-time molecular visualization.

Suggested Approach

1. Use mathematical models (e.g., vectors and rotation matrices) to derive bond angles for sp3d hybridization.
2. Ensure compatibility with existing getCoordinates() logic in Molecule.js.
3. Integrate the new functionality within the molecule construction logic to maintain modularity and scalability.

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File Locations for Implementation

File: /src/components/Molecule.js

• Update Functionality:
  • Modify the getCoordinates(molecule) function to handle sp3d hybridization bond angles.
  • Add a specific case for sp3d in the existing angles mapping object.
• Additional Logic:
  • Create helper methods to calculate bond directions for sp3d hybridization based on trigonal bipyramidal geometry.

File: /src/components/GraphADT.js

• Enhancements:
  • Add properties or methods in the Molecule class (if required) to store and retrieve calculated bond angles.

File: /src/components/EditMolecule.jsx

• Frontend Integration:
  • Update UI logic if user interaction for sp3d molecules (e.g., dropdowns or selectors) is required. [Different Issue - so optional]

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Code Changes

In Molecule.js

Update the bond angle logic:

const angles = {
  sp: { angleX: Math.PI, angleY: 0, angleZ: 0 },
  sp2: { angleX: -Math.PI / 6, angleY: Math.PI / 3, angleZ: 0 },
  sp3: { angleX: 0.615 * Math.PI, angleY: 0.955 * Math.PI, angleZ: 0.615 * Math.PI },
  sp3d: // Trigonal Bipyramidal
};

In getCoordinates() (Molecule.js)

Add specific logic for sp3d hybridization:

if (currentAtom.hybridisation === "sp3d") {
  if (isAxial(currentAtom)) {
    // Calculate coordinates for axial bonds
  } else {
    // Calculate coordinates for equatorial bonds
  }
}

[Anirudh2465]

I would like to do this please @TharunKumarrA . I feel that i would be able to solve this

[TharunKumarrA]

yes. Assigned to @Anirudh2465

[TharunKumarrA]

can you propose a possible algorithm for it after referring on how we already calculate it for sp, sp2 and sp3? We can discuss on this first before going into implementation. any queries just ping me