# Stereochemistry Analysis AI Agent Connect

> Determine R/S configurations, E/Z geometry, and stereoisomer relationships.

## Overview
- **Category:** science
- **Price:** Free
- **Endpoint:** https://edge.vinkius.com/vk_preview_1MmD3LYv2oLyHXKTOnKQnrGLBkD0A3yWW9Q6DJAl/ai-agent-connect
- **Tags:** stereochemistry, organic-chemistry, molecular-structure, cip-rules, chiral-analysis

## Description

This MCP server provides precise tools for analyzing the spatial arrangement of organic molecules. Use `analyze_stereocenters` to determine R/S configurations, `analyze_double_bond_geometry` for E/Z geometry, `identify_stereoisomers` to classify relationships like enantiomers or diastereomers, and `detect_meso_compounds` to find achiral meso structures.

## Tools

### analyze_double_bond_geometry
Determines the geometric configuration (E/Z) for all double bonds in a molecule

### analyze_stereocenters
Determines the absolute configuration (R/S) for every chiral center within a given molecular structure

### detect_meso_compounds
Identifies if a specific molecular structure is a meso compound

### identify_stereoisomers
Classifies the relationship between different stereoisomers of a molecule

## Prompt Examples

**Prompt:** 
```
What is the R/S configuration for this molecule: [structure]?
```

**Response:** 
```
The chiral center at position 2 has an R configuration.
```

**Prompt:** 
```
Is this molecule a meso compound: [structure]?
```

**Response:** 
```
Yes, this molecule is a meso compound due to its internal plane of symmetry.
```

**Prompt:** 
```
What is the E/Z geometry for the double bond at index 1 in this molecule: [structure]?
```

**Response:** 
```
The double bond at index 1 has a Z configuration.
```

## Frequently Asked Questions

**How do I determine the R/S configuration of a molecule?**
You can use the `analyze_stereocenters` tool by providing the molecular structure. It applies Cahn-Ingold-Prelog rules to identify the configuration.

**Can this tool identify meso compounds?**
Yes, the `detect_meso_compounds` tool checks for internal planes of symmetry in molecules with stereocenters.

**How do I check if two molecules are enantiomers?**
Use the `identify_stereoisomers` tool with both molecular structures to determine if they are enantiomers, diastereomers, or identical.