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Development of a Ligand Knowledge Base. Natalie Fey Crystal Grid Workshop Southampton, 17 th September 2004. Overview. Ligand Knowledge Base Synergy of Database Mining and Computational Chemistry: Part 1: How computational chemistry can add value to database mining results.

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Development of a Ligand Knowledge Base


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development of a ligand knowledge base

Development of a Ligand Knowledge Base

Natalie Fey

Crystal Grid Workshop

Southampton, 17th September 2004

overview
Overview
  • Ligand Knowledge Base
  • Synergy of Database Mining and Computational Chemistry:
    • Part 1: How computational chemistry can add value to database mining results.
    • Part 2: How database mining can inform a ligand knowledge base of calculated descriptors.
ligand knowledge base
Ligand Knowledge Base
  • Aims:
    • Collect information about ligands and their (TM) complexes:
      • Database mining.
      • Computational chemistry
    • Exploit networked computing and data storage resources – e-Science.
    • Use data:
      • Interpretation of observations.
      • Predictions for new ligands.
ligand knowledge base1

Computational Chemistry

(e.g. DFT)

Calculate structural

and electronic parameters

for known and unknown

TM complexes

Mine Structural Databases

(e.g. CSD)

Compile systematic structural information about TM complexes

Ligand Knowledge Base

Ligand

Knowledge

Base

part 1 unusual geometries

Query CSD for

structural pattern

Main Geometry / Trends

Outliers

Optimised Geometries

Crystal Structure

and DFT agree

Crystal Structure

and DFT disagree

Part 1: “Unusual” Geometries

Automatic

statistical analysis

of results

apply outlier

criteria

DFT geometry

optimisation

compare with

crystal structures

part 1 unusual geometries1
Part 1: “Unusual” Geometries

Crystal Structure

and DFT agree

Value Added

Why outlier?

Structure Report

Comment about

structure?

Yes

No

Flag for detailed investigation

Note in database,

may confirm by DFT

Further

calculations

Additional results,

add to database

part 1 unusual geometries2
Part 1: “Unusual” Geometries

Crystal Structure

and DFT disagree

Value Added

Why?

Structure Report

Comment about

structure?

Problem with

Calculation

Yes

No

Revised Calculations

Problem with

Structure

Crystal Structure

and DFT agree

Further calculations

Crystal Structure

and DFT disagree

Flag for detailed investigation

Additional results,

add to database

Note in database

example 4 coordinate ruthenium
Example – 4-coordinate Ruthenium
  • Main geometry: tetrahedral (14 structures)
  • 2 square-planar cases: YIMLEL, QOZMEX
  • YIMLEL: cis-[RuCl2(2,6-(CH3)2C6H3NC)2]
4 coordinate ruthenium
DFT result:

Use as CSD query, any TM…

SIVGAV – Pd

Supported by structural arguments:

short Ru(II)-Cl, Ru-CNR.

correct range and geometry for Pd.

Run DFT with Pd:

4-coordinate Ruthenium
part 2 p donor lkb
Part 2: P-donor LKB
  • Range of DFT-calculated descriptors for monodentate P(III) ligands and TM complexes.
    • Capture steric and /-electronic properties.
  • Identification of suitable statistical analysis approaches:
    • Interpretation.
    • Prediction.
part 2 p donor lkb1
Part 2: P-donor LKB
  • Role of database mining:
    • Stage 1: Database generation.
      • Inform input geometries (conformational freedom).
      • Verification of chosen theoretical approach.
    • Stage 2: Database utilisation.
      • Supply experimental data for regression models.
      • Confirmation of calculated trends.
examples
Stage 1

Conformers:

e.g. P(o-tolyl)3

Method verification:

Examples
examples1
Examples
  • Stage 2:

Solid State Rh-P Distance (Rh(I), CN=4)

conclusions
Conclusions
  • Synergy of approaches allows to add value to structural databases.
  • Computational chemistry can be used to verify solid state geometries.
  • Can exploit e-Science resources to add value on a large scale.
  • Utility of large databases for structural chemistry of transition metal complexes.
    • Computational requirements.
    • Statistical analysis.
acknowledgements
Acknowledgements
  • Guy Orpen, Jeremy Harvey
  • Athanassios Tsipis, Stephanie Harris
  • Ralph Mansson (Southampton)
  • Funding: