Computational Modeling of Cyanine Dyes for Bioimaging

1
Computational Modeling of Cyanine Dyes for
Bioimaging
Carnegie Mellon

• Jihoon Lee
• January 31, 2008 Senior Seminar
• Department of Chemistry, Carnegie Mellon
  University

2
Carnegie Mellon
Outline

• Background
• Motivation Objectives
• Methods
• Results
• Conclusions

3
Carnegie Mellon
Introduction

• Fluoromodule-based imaging

• Thiazole Orange (TO) dye
• The change in quantum yield in viscous solution
  is due to twisting of the dye from a planar
  structure to non-planar structure

4
Carnegie Mellon
Motivation

• The goal is to design improved dyes via
  engineering their torsional potentials.
• Examine change in electronic effects due to
  acceptor / donor substituents

• Substituents used -N(CH3)2, -NH2, -CH3, -F,
  -CHF2, -CF3, -CN

5
Carnegie Mellon
Method

• Structure
• Ground state optimized using the SAM1/Restricted
  Hartree-Fock (RHF)
• Excitation energy
• Direct Intermediate Neglect of Differential
  Overlap (INDO/SCI) used to calculate excitation
  energies
• Excited State
• Energy (Ground state of SAM1) (excitation
  energies of INDO/SCI)
• Optimization done on ground-state structure
• Excited state potential surface plotted as a
  function of interplanar angle
• Principal Component Analysis (PCA)

6
Carnegie Mellon
Method

• Ground state barrier height
• Excitation energy
• Excited state barrier height

• Interplanar angle

7
Carnegie Mellon
Method

• Intuitively, there are only two resonance
  structures

• Bond length alternation (BLA) can be represented
  as the difference between 2 and 3

8
Carnegie Mellon
Method

• Feature extraction

Principal Component Analysis (PCA) is a simple
yet very powerful tool
c1
c1 c2
c1 c2 c3
9
Carnegie Mellon
Results PCA

10
Carnegie Mellon
Results Ground StateBarrier Height

Ediz, V., Lee, J.L., and Yaron,D. , Molecular
Engineering of Torsional Potentials in
Fluorogenic Dyes via Electronic Substituent
Effects, To be submitted
11
Carnegie Mellon
Results Excitation Energy
at 0o
at 90o

Ediz, V., Lee, J.L., and Yaron,D. , Molecular
Engineering of Torsional Potentials in
Fluorogenic Dyes via Electronic Substituent
Effects, To be submitted
Ediz, V., Lee, J.L., and Yaron,D. , Molecular
Engineering of Torsional Potentials in
Fluorogenic Dyes via Electronic Substituent
Effects, To be submitted
12
Carnegie Mellon
Results Excited State Barrier Height
A-B-D D-B-A A-B-A D-B-D

Ediz, V., Lee, J.L., and Yaron,D. , Molecular
Engineering of Torsional Potentials in
Fluorogenic Dyes via Electronic Substituent
Effects, To be submitted
Ediz, V., Lee, J.L., and Yaron,D. , Molecular
Engineering of Torsional Potentials in
Fluorogenic Dyes via Electronic Substituent
Effects, To be submitted
13
Carnegie Mellon
Conclusion

• Strong correlation between
• BLA and ground state barrier height
• BLA and excitation energy at planar and twisted
  structure
• Weak correlation between BLA and excited state
  barrier height
• More in-depth analysis is needed to understand
  this phenomenon

14
Carnegie Mellon
Acknowledgements

• Dr. David Yaron
• Volkan Ediz
• The National Science Foundation
• Jean Dreyfus Boissevain Undergraduate
  Scholarship for Excellence in Chemistry,
  sponsored by the Camille and Henry Dreyfus
  Foundation

15
Carnegie Mellon
Questions?