# 2d Nmr Pulse Sequence Implementation > Use when when you need to generate 2D metabolomic NMR spectra (COSY for homonuclear or HSQC/HMQC for heteronuclear correlations) from parsed metabolite concentration and spin-system J-coupling data, and you want to simulate realistic peak patterns including indirect-dimension evolution and phase. - Skill: `holobiomicslab/2d-nmr-pulse-sequence-implementation-2` (Agent Skill) - Install (CLI): `npx skillmds@latest add holobiomicslab/2d-nmr-pulse-sequence-implementation-2` - Raw SKILL.md: https://api.skillmd.com/api/skills/holobiomicslab/2d-nmr-pulse-sequence-implementation-2/raw - Safety review: pending - Works with: Claude Code, Claude.ai, OpenAI Codex - Category: Coding & Dev Tools - License: CC-BY-4.0 - Author: HolobiomicsLab (https://skillmd.com/u/holobiomicslab) - Updated: 2026-09-17 - Page: https://skillmd.com/skills/holobiomicslab/2d-nmr-pulse-sequence-implementation-2 --- # 2D NMR Pulse Sequence Implementation > **License: restricted** — no clear open-source license detected for the underlying tool; verify licensing before commercial use or redistribution. ## Summary Design and execute 2D NMR pulse sequences (COSY, HSQC/HMQC) to compute 1H–1H or 1H–13C correlation multiplets with appropriate indirect-dimension evolution, enabling metabolomic structure elucidation. This skill bridges simulated spin systems to 2D frequency-domain spectra by applying phase-encoding and indirect-dimension time steps. ## When to use When you need to generate 2D metabolomic NMR spectra (COSY for homonuclear or HSQC/HMQC for heteronuclear correlations) from parsed metabolite concentration and spin-system J-coupling data, and you want to simulate realistic peak patterns including indirect-dimension evolution and phase encoding. ## When NOT to use - Input is already a measured 2D NMR spectrum (no simulation needed; use acquisition software instead) - Metabolite identities or J-couplings are unknown or unavailable (simulation requires explicit spin-system topology) - Goal is to process or interpret experimental 2D spectra rather than generate synthetic reference data ## Inputs - Metabolite concentration values (numeric array or list) - Spin-system coupling constants (J-values) per metabolite (Hz) - Chemical shifts for involved nuclei (ppm) - Pulse sequence parameters (indirect-dimension increments, phase encoding steps, receiver phases) - Lineshape function specification (Lorentzian or Gaussian bandwidth) ## Outputs - 2D NMR spectral array (frequency-domain, real or complex) - Indirect and direct dimension frequency axes (ppm) - 2D spectral data in HDF5 or netCDF format - Cross-peak multiplet patterns (COSY or HSQC/HMQC correlation map) ## How to apply Starting from parsed metabolite concentrations and spin-system coupling constants (J-values), select the appropriate 2D pulse sequence (COSY for 1H–1H correlation or HSQC/HMQC for 1H–13C heteronuclear correlation). Implement the sequence by evolving the spin system through indirect-dimension time increments with phase encoding, computing cross-peak multiplets that reflect scalar coupling between correlated nuclei. Apply the same lineshape convolution (Lorentzian or Gaussian) used in the 1D simulation to account for realistic peak broadening. Fourier-transform both direct and indirect dimensions to produce a 2D frequency-domain array. Save the result in standard NMR data formats (HDF5 or netCDF) compatible with downstream NMR analysis software. ## Related tools - **MetAssimulo 2** (Web application that implements 2D pulse sequences (COSY, HSQC/HMQC) for simulating 1H–1H and 1H–13C correlations from metabolite inputs) — https://github.com/yanyan5420/MetAssimulo_2 ## Examples ``` python3 apps/index.py -p Input/parameters.txt ``` ## Evaluation signals - Cross-peaks appear at expected chemical shift intersections corresponding to coupled spin pairs (COSY) or coupled nuclei (HSQC/HMQC) - Multiplet structure in cross-peaks matches theoretical J-coupling patterns (e.g., doublet, triplet) for the underlying spin system - Indirect and direct dimension Fourier transforms produce peak frequencies (ppm) that align with input chemical shifts and J-couplings - Output 2D spectral array conforms to HDF5 or netCDF schema with labeled frequency axes and metadata - Lineshape convolution produces realistic peak widths without excessive broadening or ringing artifacts ## Limitations - Simulation uses first-order or density-matrix approximations; higher-order coupling effects are not explicitly modeled - Pulse sequence parameters (flip angles, phase cycles, gradient strengths) must be manually specified; default values may not match all experimental protocols - No experimental validation of simulated spectra against real NMR data is performed within the tool; realism depends on accurate input J-values and lineshape assumptions - Complex spin systems (>4 coupled spins) may require longer computation or density-matrix methods; scalability limits are not documented ## Evidence - [other] For 2D spectra, compute 1H–1H correlation (COSY) or 1H–13C heteronuclear (HSQC/HMQC) multiplets using appropriate 2D pulse sequences and indirect-dimension evolution.: "For 2D spectra, compute 1H–1H correlation (COSY) or 1H–13C heteronuclear (HSQC/HMQC) multiplets using appropriate 2D pulse sequences and indirect-dimension evolution." - [other] Generate theoretical spin multiplets using first-order or density-matrix NMR simulation for each spin system, accounting for chemical shift and J-coupling.: "Generate theoretical spin multiplets using first-order or density-matrix NMR simulation for each spin system, accounting for chemical shift and J-coupling." - [other] Convolve simulated multiplets with a Lorentzian or Gaussian lineshape function to approximate realistic peak broadening.: "Convolve simulated multiplets with a Lorentzian or Gaussian lineshape function to approximate realistic peak broadening." - [other] Save simulated 1D and 2D spectra as HDF5 or netCDF spectral arrays compatible with standard NMR data formats.: "Save simulated 1D and 2D spectra as HDF5 or netCDF spectral arrays compatible with standard NMR data formats." - [readme] This repository contains all the necessary code for the MetAssimulo 2 project.: "This repository contains all the necessary code for the MetAssimulo 2 project."