Computer aided color chemistry l.jpg
This presentation is the property of its rightful owner.
Sponsored Links
1 / 46

Computer-aided Color Chemistry PowerPoint PPT Presentation


  • 266 Views
  • Updated On :
  • Presentation posted in: General

Computer-aided Color Chemistry. Methodology & Theory Practical issues. David A. Gallagher Portland, Oregon, USA [email protected] *. 2. 0. -2. -4. -6. MO Energy eV*. -8. . . -10. . Empty. Occupied. -12. 40000. 30000.

Download Presentation

Computer-aided Color Chemistry

An Image/Link below is provided (as is) to download presentation

Download Policy: Content on the Website is provided to you AS IS for your information and personal use and may not be sold / licensed / shared on other websites without getting consent from its author.While downloading, if for some reason you are not able to download a presentation, the publisher may have deleted the file from their server.


- - - - - - - - - - - - - - - - - - - - - - - - - - E N D - - - - - - - - - - - - - - - - - - - - - - - - - -

Presentation Transcript


Computer aided color chemistry l.jpg

Computer-aided Color Chemistry

  • Methodology & Theory

  • Practical issues

David A. Gallagher

Portland, Oregon, USA

[email protected]

*


Mechanism of uv absorption l.jpg

2

0

-2

-4

-6

MO

Energy

eV*

-8





-10



Empty

Occupied

-12

40000

30000

Molar

Absorptivity

PABA

20000

l/mol-cm

10000

0

200

220

240

260

280

300

320

340

360

380

400

Wavelength (nm)

Mechanism of UV Absorption

LUMO

p-aminobenzoic acid (PABA)

HOMO

*quantum mechanics calculation (EHT, MOPAC,ZINDO, etc.)


Configuration interaction c i l.jpg

-6

Transition instantly perturbs all orbitals

-7

-8

-9

-10

ZINDO

MO

Energy

eV

-11

-12

-13

40000

Configuration Interaction (C.I.)

-6

-7

-8

-9

Simple HOMO-LUMO gap over-estimates transition energy

C.I. allows for energy contribution from relaxation of orbitals

-10

Extended

Huckel

MO

Energy

eV

-11

-12

-13

40000

*Configuration Interaction (C. I.) improves accuracy


Zindo parameters l.jpg

ZINDO Parameters

Spectroscopic

Geometry

INDO/1 parameters

INDO/S parameters

Zerner’s Intermediate Neglect of Differential Overlap (ZINDO)

Semiempirical quantum chemistry method

Ridley, Zerner , Theoret. Chim. Acta. 32, 111 (1973)


Visualization of chromophore l.jpg

2

0

-2

-4

-6

MO

Energy

eV

-8

-10

-12

40000

30000

Molar

Absorptivity

PABA

20000

l/mol-cm

10000

0

200

220

240

260

280

300

320

340

360

380

400

Wavelength (nm)

Visualization of Chromophore

*Location & structure aids design of dye


Absorption intensity overlap l.jpg

Absorption Intensity ~ Overlap

Final orbital

Initial orbital

Absorption intensity depends upon the overlap of the initial and final orbitals (transition dipole).


Vibrational fine structure l.jpg

Reality

ZINDO approximation

Vibrational Fine Structure


Gradient affects band width l.jpg

high gradient* ~ broad band

15

15

10

10

5

5

0

0

-5

-5

-10

-10

1.1

1.6

2.1

2.6

3.1

3.6

1.1

1.6

2.1

2.6

3.1

3.6

Higher gradient allows access to more vibration levels from ground state

and hence, higher band width

Gradient Affects Band Width

low gradient* ~ narrow band


Band width estimation l.jpg

Band Width Estimation

Higher gradient allows access to more vibration levels from ground state and hence, higher band width

Gradient calculated from the “excited state energy”

of the ground state geometry


Fluorescence spectra l.jpg

Fluorescence Spectrum

k < 109 sec-1

vibrational relaxation

k > 1012 sec-1

S1

S0

S0

S1

excited singlet geometry

Fluorescence Spectra

UV-visible Absorpton Spectrum

k = 1015 sec-1

ground state geometry


Fluorescein dibasic spectra l.jpg

Calculated Absorption &

Fluorescence Spectra

Fluorescein (dibasic) Spectra

UV-visible* λmax ~ 500nm

Fluorescence* λ~ 535nm

fluorescein2-

*H. Du, R. A. Fuh, J. Li, A. Corkan, J. S. Lindsey, "PhotochemCAD: A computer-aided design and research tool in photochemistry," Photochemistry and Photobiology, 68, 141-142, 1998


Calculating spectra with cache l.jpg

Calculating Spectra with CAChe

UV-visible Absorption

Property of: “chemical sample”

Property: “UV-visible transitions”

Using: “ZINDO CI at PM3 geo...”

Fluorescence Emission

Property of: “excited states”

Property: “optimized geometry”

Using: “PM3/CI........geometry”

Property of: “chemical sample”

Property: “UV-visible transitions”

Using: “current geometry”


Safe laboratory procedure l.jpg

Calibrate before use

Safe Laboratory Procedure

  • Is the instrument working?

  • Do I know how to use it?

  • Is this instrument appropriate for the current research?

Questions answered:


Experimental vs calculated l.jpg

500

observed = - 41.157 + 1.0996 calculated

R^2 = 0.998

400

.

Observed absorption maximum (nm)

300

at INDO/1 geometry

at MOPAC AM1 geometry

R^2 = 0.998

Observed = - 45.277 + 1.1500 Calculated

200

200

300

400

500

Calculated absorption maximum (nm)

Experimental vs Calculated

UV/Vis Absorption Maxima for CH3-(CH=CH)n-CHO


N p transition of c o l.jpg

400

n -> p*

380

360

340

320

200

220

240

260

280

300

n ->p* Transition of C=O

CH3CHO

acetaldehyde

in hexane

CH3COCH3

acetone

in hexane

CH3COCl

acetyl chloride

in hexane

CH3COOCH2CH3

ethyl acetate

in water

CH3CONH2

R^2 = 0.988

acetamide

in water

ZINDO = 188.00 + 0.69698 obs

CH3COOH

acetic acid

Standard Deviation = 2.8 nm

in ethanol

Observed

*error bars represent bandwidth


Anthraquinones for thermal transfer wax printing l.jpg

Anthraquinones for Thermal Transfer Wax Printing

Dyes used in thermal wax printing often behave differently than they do on fabrics. Can computer-aided chemistry provide useful information about dyes that might be used in wax inks?

Intratherm Blue P1404

Dr. Wayne Jeager, Tektronix, Inc., Wilsonville, Oregon, USA.


Calculated vs experimental l.jpg

Molar Absorptivity

25000

20000

Molar Absorptivity (l/mol-cm)

1,4-amino anthraquinone

15000

25000

10000

20000

5000

1,4-amino anthraquinone

15000

1,4-diNHMe aq Exp

0

10000

350

400

450

500

550

600

650

700

750

5000

Wavelength (nm)

0

350

400

450

500

550

600

650

700

750

Wavelength (nm)

• First attempt

• Experimental

Why doesn’t the calculated spectrum agree with the measured spectrum?

Calculated vs. Experimental

*


Anthraquinone calibration l.jpg

exp  max

700

10

4

600

11

7

8

500

9

2

6

1

400

5

3

300

430

440

450

460

470

480

490

calculated  max

exp -max =3.834 *calculated -max -1251.676

r ^ 2 = 0.430

Anthraquinone Calibration

1 anthraquinone

2 1-NH2 anthraquinone

3 1-OH anthraquinone

4 1,4-diNH2 anthraquinone

5 2-NH2 anthraquinone

6 2-NMe2 anthraquinone

7 1-NHEtNMe2 anthraquinone

8 1,9-HNEtNMe2 anthraquinone

9 1,6-HNEtMe2 anthraquinone

10 1,4-diNHMe anthraquinone

11 1,4-diNH2, 2-OMe aq

Experimental data from Masafumi Adachi and Shinichiro Nakamura,

Dyes and Pigments, 1991, 17, 287-296, and Wayne Jaeger, Tektronix.


What s wrong l.jpg

What’s Wrong?

  • Is ZINDO right?

  • What is ZINDO calculating?

  • Are we comparing the right absorptions?

  • Is solvation a factor?

  • Is aggregation a problem?

  • Are the structures right?

  • Which is best geometry/conformation to use?

  • Experimental data correct?


Is zindo right l.jpg

Is ZINDO right?

  • literature

  • absolute accuracy

  • relative accuracy

  • zero-point energy corrections


Literature background l.jpg

Literature Background

  • “The literature suggests that at visible wavelengths the standard deviation of the [INDO/S] calculation is between 15 and 35 nm.

  • “-maxima calculations using INDO seem useful when the geometries including dihedral angles are correct.”

Louis E. Friedrich and James E. Eilers, “Progress Toward Calculation of the Hues of Azomethine Dyes”, J. of Imaging Science and Technology, 38, 24-27, 1994. [Eastman Kodak Company, Rochester, NY]


Dye calibrations l.jpg

600

4-NEt

, 2',4',6'-triCN

2

4-NEt

, 4'-NO

500

2

2

N

N

2-NH

2

400

Exp_max = - 534.52 + 2.7595 Calc_max

R^2 = 0.912

300

300

320

340

360

380

400

ZINDO

max

R

600

R'

Exp_max = 79.664 + 0.84424 Calc_max

R^2 = 0.947

C

p-NO

C

H

; -CH

;Anion

2

6

4

3

N

H

-H;-H;Anion

500

N

p-NH

C

H

; -CH

;Anion

2

6

4

3

NO

-H;-H;Anion

2

p-NH

C

H

; -CH

;Neutral

2

6

4

3

400

.

p-NO

C

H

; -CH

;Neutral

2

6

4

3

-H;-H;Neutral

300

NO

300

400

500

600

2

ZINDO

max

Dye Calibrations

Azobenzene Dyes

Hydrazone Dyes

Data from Masafumi Adachi and Shinichiro Nakamura,

Dyes and Pigments, 1991, 17, 287-296.

Experiment based geometries were used.


More dye calibrations l.jpg

NMe

2

NMe

2

O

+

6

2

O

4

600

700

2,3-diCN,4-NH

Obs_max = - 569.41 + 2.5311Calc_max

2

R^2 = 0.928

2,3-diCl;5-NH

;-8-OMe

2

4-CN

.

.

3-CN

None

500

5-NH

,8-OMe

600

max

2

max

5-NH

l

2

l

Exp

Exp

400

500

.

.

5-OMe

None

3,5-diNO

Obs_max = - 329.17 + 1.9616 Calc_max

2

R^2 = 0.881

4-CN

300

400

360

380

400

420

440

460

380

400

420

440

460

480

500

520

l

ZINDO

l

ZINDO

max

max

More Dye Calibrations

Napthoquinone Dyes

Cationic Dyes

Data from Masafumi Adachi and Shinichiro Nakamura,

Dyes and Pigments, 1991, 17, 287-296,


Linear fused aromatic rings l.jpg

1 benzene

2 naphthalene

3 anthracene

4 naphthacene

5 pentacene

Linear Fused Aromatic Rings

700

600

5

500

exp lambda max

4

400

3

300

2

200

1

100

0

1

2

3

4

5

6

# aromatic rings

experimental lambda max value =99.200 *# aromatic rings+ 74.600

r ^ 2 = 0.997


What geometry did we calculate l.jpg

What Geometry Did We Calculate?

Lowest energy structure from MOPAC/PM3

Heat of formation = -15.35 kcal/mol

Dihedral O-C-C-C = 158°

Expected structure

Heat of formation = -11.27 kcal/mol

Dihedral O-C-C-C = 180°


Does the geometry matter l.jpg

Does the Geometry Matter?

• First attempt

• Flattened rings


Which structure is right l.jpg

Which structure is right?

Crystal structure of

N,N’-diphenylaminoanthraquinone

(solid)

6-31G* LDF structure of

1,4-diaminoanthraquinone

(gas-phase)


Sensitivity to model l.jpg

Indigo model

lambda max

visible (nm)

PM3

413.2

AM1

400.4

6-31G*LDF

453.3

observed

546.0

6-31G* LDF using BLYP and Mulliken.

Observed value from P. W. Sadler, March, 1956.

50000

40000

30000

[email protected]*LDF ZCI

20000

10000

0

250

300

350

400

450

500

550

600

650

Wavelength (nm)

Sensitivity to Model

Indigo

6-31G* LDF (darker) vs AM1 (faded)


Processing times l.jpg

CPU time

Indigo model

PM3

00:52

00:35

AM1

1d 11:05:00

6-31G*LDF

PM3 and AM1 using MOPAC

6-31G* LDF using BLYP and Mulliken.

Processing Times

Indigo


Force a flat structure l.jpg

Force a flat structure

Lock dihedral angles to force a flat structure


Effect of ring geometry l.jpg

Molar Absorptivity (l/mol-cm)

25000

20000

15000

1;4-diNHMe anthraquinone

1;4 amino anthraquinone

10000

1;4-diNHMe aqF Exp

5000

0

350

400

450

500

550

600

650

700

750

Wavelength (nm)

Effect of Ring Geometry

• First attempt

• Flattened rings

• Experimental


Effect of ring amine geometry l.jpg

Molar Absorptivity (l/mol-cm)

25000

20000

1;4 amino anthraquinone

1;4-diNHMe anthraquinone

15000

1;4-diNHMe aqF

10000

1;4-diNHMe aqF Exp

5000

0

350

400

450

500

550

600

650

700

750

Wavelength (nm)

Effect of Ring & Amine Geometry

• First attempt

• Flattened rings,

• Flattened rings & amines

• Experimental


Methanol solvation l.jpg

Molar Absorptivity (l/mol-cm)

25000

20000

1;4-diNHMe aqF Exp

15000

1;4-diNHMe aqF

10000

1;4-diNHMe aqF/(MeOH)2

5000

0

350

400

450

500

550

600

650

700

750

Wavelength (nm)

Methanol Solvation?

• Gas-phase

• Solvated

• Experimental


Anthraquinone calibration34 l.jpg

exp  max

700

1 anthraquinone

2 1-NH2 anthraquinone

6

600

3 1;4-diOH aq

7

4

4 1;4-diNH2 anthraquinone

5

500

3

5 1-NH2;2-OPh;4-OH aq

2

6 1;4-diNHMe aq

400

7 1;4-diNH2;2-OMe aq

1

300

200

300

400

500

calculated  max

Anthraquinone Calibration

exp  max =1.606 *calculated  max -144.684

r ^ 2 = 0.958

cross validated against 5 samples with unsigned average error 20 nm

Experimental data from Masafumi Adachi and Shinichiro Nakamura,

Dyes and Pigments, 1991, 17, 287-296, and Wayne Jaeger, Tektronix.


Effect of calibration l.jpg

Effect of Calibration

Calibrated INDO/S at the PM3 geometry with a flat anthraquinone ring and flat amino groups.

• First attempt

• Flattened rings,

• Flattened rings & amines

• Flattened rings & amines, calibrated

• Experimental


Conclusions l.jpg

Conclusions

  • INDO/S can be calibrated so that it is useful for predicting UV/visible spectra of dyes. (ZINDO predictions are systematically too short.)

  • Calculated spectra are sensitive to molecular geometry. Best results are obtained with experimental geometries.

  • Vibrational structure can confuse spectral assignments.

  • Excited state gradients correlate with band widths.


Chemistry today l.jpg

Chemistry Today

Properties

Measure

Design

Structure

Compounds

Synthesize


Chemistry by simulation l.jpg

Chemistry by Simulation

Properties

Simulate

Design

Structure

Compounds

Build


Chemistry by design l.jpg

Chemistry by Design

Properties

Interpret

Simulate

Design

Structure

Compounds

Build


Summary points l.jpg

Summary Points

  • You learn something almost every time you view a molecule a new way

  • Safe laboratory procedure: calibrate before use

  • Bootstrap from small problems to large problems

  • Stretch beyond simulation of experiment to interpretation. Valuable insight will come from understanding why experiments and calculations do not agree


Zindo capabilities l.jpg

ZINDO Capabilities

  • Contains d-orbitals.

  • Geometry parameters for first two transition metal series.

  • Spectroscopic parameters for UV/visible calculations through first transition metal series.

  • Can predict singlet-triplet splittings.

  • Contains self-consistent reaction field (SCRF) for inclusion of solvent effects on geometries.


Zindo limitations l.jpg

ZINDO Limitations

  • Geometry parameters based on ab initio HF.

  • Zero differential overlap seriously over estimates the stability of small rings.

  • Optimization is too aggressive for transition metals, leading to the formation of small ring structures.

  • Transition metal INDO/1 parameters used for geometry optimizations are not sufficiently tested.

  • Absorption maxima for many dyes are systematically underestimated and calibration for each class of dyes is recommended.

  • Mono CI does not predict double excitation states.

  • SCRF is not used for spectral calculations.


Background references for zindo l.jpg

Background References for ZINDO

  • ZINDO is a semi-empirical SCF/CI package including analytical gradient optimization developed by Prof. M. C. Zerner from the University of Florida. ZINDO is based upon the INDO approximations of Pople, Santry and Segal:

    • Pople, Santry, Segal J. Chem. Phys. 43, S129 (1965)

    • Pople, Segal J. Chem. Phys. 43, S136 (1965)

    • Pople, Segal J. Chem. Phys. 44, 3289 (1966)

    • Santry, Segal J. Chem. Phys. 47, 158 (1967)

    • Santry J. Amer. Chem. Soc. 90, 13 (1968)

  • The original INDO method has been enhanced by Prof. Zerner to include spectroscopic parameterization, configuration interaction, higher angular momentum orbitals (d-orbitals), and analytical gradients:

    • Ridley, Zerner , Theoret. Chim. Acta. 32, 111 (1973)

    • Ridley, Zerner, Theoret. Chim. Acta. 42, 223 (1976)

    • Ridley, Zerner, Theoret. Chim. Acta. 53, 21 (1979)

    • Zerner, Loew, Kirchner, Mueller-Westerhoff, J. Amer. Chem. Soc. 102, 589 (1980)

    • Head, Zerner, Chem. Phys. Lett. 32, 246 (1985)

    • Head, Zerner, Chem. Phys. Lett. 131, 359 (1986)

    • Anderson, Edwards, Zerner, Inorg. Chem. 25, 2728 (1986)

    • Edwards, Zerner, Theoret. Chim. Acta. 72, 347 (1987)


Applications of zindo l.jpg

Applications of ZINDO

  • 1.J. Ridley and M. C. Zerner, Theoret. Chim. Acta (Berl.) 72, 111-134 (1973)"An Intermediate Neglect of Differential Overlap Technique for Spectroscopy: Pyrrole and the Azines".

  • 2.W. P. Anderson, W. Daniel Edwards, and Michael C. Zerner, Inorg. Chem. 1986, 25 2728-2732, "Calculated Spectra of Hydrated Ions of the First Transition-Metal Series."

  • 3.W. Daniel Edwards, Brian Weiner and Michael C. Zerner, J. Am. Chem. Soc, 1986, 108, 2196-2204, "On the Low-Lying States and Electronic Spectroscopy of Iron(II) Porphine."

  • 4.Ralph S. Becker, L. V. Natarajan, Christian Lenoble, and Ronald G. Harvey, J. Am. Chem. Soc. 1988, 110, 7163-7167, "Photophysics, Photochemistry and Theoretical Calculations of Some Benz[a]anthracene-3,4,-diones and Their Significance."

  • 5.Jikang Feng, Jerzy Leszczynski, Brian Weiner, and Michael C. Zerner, J. Am. Chem. Soc, 1989, 111, 4648-4655, "The Reaction C3H3+ + C2H2 and the Structural Isomers of C5H5+."

  • 6.Frank U. Axe, Charles Flowers, Gilda H. Loew, and Ahmad Walch, J. Am. Chem. Soc., 1989, 111, 7333-7339, "Theoretical Studies of High-, Intermediate-, and Low-Spin Model Heme Complexes."


Applications of zindo cont l.jpg

Applications of ZINDO (cont)

  • 7.Manfred Kotzian, Notker Rosch, Hartmut Schroder, and Michael C. Zerner, J. Am. Chem. Soc., 1989, 111, 7687-7696, "Optical Spectra of Transition-Metal Carbonyls" Cr(CO)6, Fe(CO)5, and Ni(CO)4."

  • 8.Wayne P. Anderson, Thomas R. Cundari, Russell S. Drago, Michael C. Zerner, Inorg. Chem. 29, 1, 1990, "Utility of the Semiempirical INDO/1 Method for the Calculation of the Geometries of Second-Row Transition Metal Species."

  • 9.David R. Kanis, Mark A. Ratner, and Tobin J. Marks, J. Am. Chem. Soc., 1990, 112, 8203-8204, "Description of Quadratic Optical Nonlinearities for Transition-Metal Organometallic Chromophores Using an SCF-LCAO MECI Formalism."

  • 10.Mati Karelson and M. C. Zerner, J. Am. Chem. Soc., 1990, 112, 9405-9408, "On the n-š* Blue Shift Accompanying Solvation."

  • 11.Yuji Kubo, Katsuhira Yoshida, Masafumi Adachi, Shimichiro Nakamura, and Shuichi Maeda, J. Am. Chem. Soc. 1991, 113, 2868-2873, "Experimental and Theoretical Study of Near-Infrared Absorbing Naphthoquinone Methide Dyes with Nonplanar Geometry."

  • 12.Masafumi Adachi and Shinichiro Nakamura, Dyes and Pigments, 1991, 17, 287-296, “Comparison of the INDO/S and the CNDO/S Method for the Absorption Wavelength Calculation of Organic Dyes.”


Acknowledgements l.jpg

Acknowledgements

Thank you to George D. Purvis for providing some of the content for these slides .


  • Login