V?- .v
4.. Eir...
:. .L.

£2.71 .vl. e.
new “wanna

.122.
I .:.-IS..:
3.3.;

.. .

 

 

 

 

J

a.

“ r) \
‘4 '.i

Q

SITY UBRAR

11111111111111111111111111111111 1111111111

3 1293 014201

1112111111

 

 

 

 

 

 

This is to certify that the

dissertation entitled

C—Clamp Porphyrins: Models for

H—Bonded Heme Active Site

presented by

Ying Liang

has been accepted towards fulfillment
of the requirements for

Ph.D Chemistry

“10%

degree in

 

 

C. K. Chang

 

Major professor

DMe 09/19/95

 

MSU is an Afflrmuu’w Action/Equal Opportunity Institution 042771

 

LIBRARY
Mlchlgan State
Unlverslty

 

 

 

PLACE N RETURN BOX to roman this chockout from your rocord.
TO AVOID FINES mum on or Moro 6‘. duo.

DATE DUE DATE DUE DATE DUE
1—1 ——
|1__i 9—1
__ F —

4—1
, 1—3,

usu IoAnAIflnnotIvo Won-l Oppomnnylmwon
“W’s-“.1

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

C-CLAMP PORPHYRINS: MODELS FOR H-BONDED
HEME ACTIVE SITE

By

Ying Liang

A DISSERTATION

Submitted to
Michigan State University
in partial fulfillment of the requirements
for the degree of

DOCTOR OF PHILOSOPHY

Department of Chemistry

1995

ABSTRACT

C-Clamp Porphyrins: Models for H-Bonded Heme Active Site

By

Ying Liang

Heme proteins play many critical roles in biological systems such as
02 binding, activation and reduction. H-bonding to the heme-bound 02 is
an important factor in affecting their activities. Synthetic model
compounds previously have established the positive effect of H-bonding in
increasing 02 affinity. However, it has not been possible to examine how
much the influence on heme-substrate reactions are brought about by
structural and steric perturbations of the proton donor. In an effort of
providing better understanding on the influence of H-bonding effect on
heme proteins, C-clamp porphyrins and derivatives have been designed and
synthesized. Among these compounds, the Naphthalene Kemp’s Acid
Porphyrin (NKAP), is equipped with a carboxylic acid hovering over the
porphyrin center through a naphthalene spacer linked with a Kemp’s
tn'acid. This intramolecular acid proton is in close distance (4-5A) to the
porphyrin center to achieve effective H—bonding according to the X-ray
single crystal analysis.

This naphthalene C-clamp porphyrin and its zinc complexes are
capable of recognizing small neutral molecules such as water or methanol

through multiple H-bonding network, which is evidenced by X-ray crystal

structure and UV-vis and NMR studies. The extended Anthracene Kemp’s
Acid Porphyrin (AKAP) has a similar ability to recognize even larger
substrates such as purine, imidizole and triazoles. We have analyzed the
contribution of each individual H-bond and predicted that NKAP is the best
host for mono atomic ligands.

Oxygen binding to CoHNKAP exhibits such a high affinity constant
that breaks all record reported so far in literature. In comparison with
Naphthoic Acid Porphyrin (NAP), the AS of 02 binding in CoHNKAP is
relatively small suggesting a higher degree of freedom of motion. It is
interpreted that the NKAP system allows the H-bond occur at the proximal
oxygen (01) or the 0:0 n-bond instead of the distal oxygen (02) only.
Further evidence from 15N NMR on (CN)2FePorphyrins supports our
interpretation.

Additionally, we have investigated the H-bonding effect on oxo-metal
porphyrins. Ferryl (Fe=O) species is an important intermediate of heme
proteins and the H-bonding effect on ferry] heme in various enzymes
remains to be established. Stable V=O (vanadyl) porphyrins are used as a
model, and the H-bonding effect on the 5- and 6-coordinated vanadyl
porphyrin causes V=O vibration shift from 4 to 20 cm'l. Also, H-bonding
is found to be an important factor in directing the orientation of vanadyl
oxygen. Both “cis” and “trans” isomers have been identified for vanadyl
Naphthalene Kemp’s Amide Porphyrin (NKAmideP) and NAP(VO).

Finally, H-bonding on C0 heme complexes is shown to be not
important. However, H-bonding to the coordinated methanol or water
ligand trans to the metal-bound CO shifts the uc=o in a predictable

manner.

To my husband (Tie Lan) and my grandmother (Xiangrui)

ACKNOWLEDGMENTS

I would like to express my deepest respect and gratitude to my
research advisor and mentor, Dr. C.K. Chang, for his guidance, inspiration
and support during the course of this work. I refer myself exceptionally
lucky of being his graduate student. I thank him for accepting me to his
research group which has provided me great opportunities to learn the
most outstanding researches at MSU. His excellent research expertise and

enthusiasm have inspired and always will inspire me.

I would like to thank Dr. Jackson for serving as the second reader in
my research committee. Drs. Pinnavaia, McCracken and Babcock are
appreciated for being my research committee members and for their

helpful discussions.

I want to thank Dr. S.-M. Peng at National Taiwan University for
solving all the X-ray single crystal structures I presented in this
dissertation. Without the help of the X-ray structure, I cannot explore a lot
important aspects of the systems I studied.

Dr. Rui Huang is appreciated for teaching me of running the bench-
top GC-MS spectrometer and I thank Drs. Long Lee and Kermit for their
help in NMR techniques.

Also, I am grateful to the past and present group member in Dr.

Chang's group, especially for their helpful discussions and friendship.

V

Among them are: Dr. N. Bag, Dr. E. Schmidt, Dr. W. Wu, Dr. W. Lee,
Dr. A. M. Gladys, Mr. J. P. Kirby, Ms. D. M. Conrad-Vlasak, Ms. E.
Guerin, Ms. 1. M. Morrison, Dr. S. Lee, Dr. S.-S. Chern, Dr. M. Sato, Mr.
C. Shinner, Mr. B. Guo, Mr. Y. Deng...

Friendship from Carolyn Hsu, Zoe Pikramenou, Gregory R. Cook,
Scott J. Stoudt, K. Paulvannan and lot of graduate students and postdocs is
always appreciated. I will never forget their understanding, supports and
helpful discussions. Thank you, all my friends, for sharing my tears and

happiness at MSU.

I'd like to thank my best friends, Zhixia Wu, Xinhua Yu, Yiliang
Liu, Jiahwa Yeh, Qing Yang, Feng Tian, Xiaoming Chen, Weishih Wu,
Hongjun Yan and Weiqing, who spent a lot of wonderful moments with Tie
Lan and me. Their friendship made my life and study at MSU an enjoyable

0116.

At last, but not the least, I want to thank my husband, Tie Lan, for
his encouragement, support and understanding during my Ph.D. studies. I

am looking forward to our better lives together with the coming baby next
March.

vi

TABLE OF CONTENTS

CHAPTER Page

LIST OF FIGURES ................................................................. xii
LIST OF TABLES ................................................................ xviii
ABBREVIATION ................................................................... xxi

CHAPTER I Introduction
Introduction..................... ............................................................ 1
References .................................................................................. 29
CHAPTER 11 Synthesis and Characterization of C-

clamp Porphyrin
A. Introduction .......................................................................... 32

B. Synthesis ............................................................................... 33

Vii

1. Tetrapyrrole Pathway .......................................................... 33

2. Dipyrrole Pathway by McDonald Condensation ..................... 37
C. Variant Temperature N MR ...................................................... 49
D. Experimental .......................................................................... 52
E. References .............................................................................. 72

CHAPTER III Hydrogen Bonding in Molecular
Recognition: Inclusion Complex and
Substrate Recognition by C-Clamp

Porphyrins
A. Introduction ........................................................................... 74
B. Experimental .......................................................................... 76
1. Crystal Structure Analysis .................................................... 76
2. Determination of Binding Constants ...................................... 76
a) NMR Method .................................................................. 76
b) UV-Vis Method .............................................................. 77
c) DSC Method ................................................................... 77
C. Result and Discussion ............................................................. 77
1. Structure of Receptors and Their Znic Complexes ................ 77
2. Substrate Binding Studies ................................................... 91
a) Substrate Binding of Metal-free Systems .......................... 91

viii

b) Substrate Binding of Zinc Porphyrins ............................ 100

3. Discussion ....................................................................... 106
D. Conclusion .......................................................................... 108
E. References .......................................................................... 109

CHAPTER IV Conformational Control of
Intramolecular Hydrogen Bonding in
Heme Models: Maximal Co(II)-Oz
Binding in Naphthalene Kemp's Acid

Porphyrin
A. Introduction ........................................................................ 1 1 1
B. Experimental ...................................................................... 112
1. Cobalt Insertion ............................................................... 112
2. 02 Binding Studies ........................................................... 113
3. Iron Insertion .................................................................. 116~
4. 15N NMR Studies ............................................................. 117
C. Result and Discussion ........................................................... 117
1. Oxygen Binding ............................................................... 117
2. Further Information from 15N NMR ................................. 122
D. Conclusion .......................................................................... 125‘
E. References .......................................................................... 126

CHAPTER V Structural and Vibrational Character
of H-Bonded Vanadyl Porphyrins.
Models of H-Bonded Ferryl Heme

A. Introduction ........................................................................ 129
B. Experimental ....................................................................... 131
1. Reagent ........................................................................... 131

2. VO Insertion .................................................................... 131

a) NKAP(VO) .................................................................. 131

b) NKAmideP(VO), NAP(VO) and OEP(VO) ..................... 132

3. Instrumentation ................................................................ 132

a) Spectroscopy ................................................................ 132

b) X-Ray Determination .................................................... 134

C. Result and Discussion ........................................................... 136
1. H-Bonding for 5-Ligated VO-porphyrins ........................... 136

2. H-Bonding for 6-Ligated VO-porphyrins ........................... 140

3. X-Ray Single Crystal Structure of NKAP(VO) and

NAP(VO) ....................................................................... 146

4. Orientation of the V0 Dictated by H-Bonding .................... 156

D. Conclusion ......................................................................... 159
E. References .......................................................................... 162

X

CHAPTER VI Structural and Vibrational Properties
of RuCO and FeCO C-clamp Porphyrin
and Derivative

A. Introduction ......................................................................... 166
B. Experimental ........................................................................ 167
1. Preparation of RuCOporphyrins ......................................... 167

2. Preparation of FeCOporphyrins ......................................... 168

3. Instrumentation ................................................................ 169

a) Spectroscopy ................................................................ 169

b) X-Ray Determination .................................................... 169

C. Result and Discussion ............................................................ 171

1. X-Ray Single Crystal STructures of RuCONKAP(MeOH)

and RuCONKAmideP(MeOH) ............................................ 171
2. IR studies of RuCOporphyrins ........................................... 181
3. IR studies of FeCOporphyrins ........................................... 181

4. Trans Ligands Effect in Affecting CO Vibration in M-

COporphyrins .................................................................. 185
D. Conclusion .......................................................................... 186’
E. References .......................................................................... 187

LIST OF FIGURES

FIGURE Page

I-l.

I-2.

I-3.

I-4.

I-5.

L6.

L8.

I-9.

I-10.

Structure of the [3 subunit of hemoglobin. (M. F. Perutz,

Nature, 1970, 228, 726) .................................................... 3
(a) Structure of Fe(II) protoporphyrin IX ............................ 4
(b) Histidines near the oxygen bound heme active site ............ 4
Cytochrome c oxidase ........................................................ 8

Proposed catalytic cycle for oxygen reduction by

cytochrome c oxidase ....................................................... 10
The reduction pathway proposed by Caughey ...................... 11
Some heme enzymes capable of reducing 02 to water .......... 13

Schematic representation of the cytochrome c peroxidase

heterolytic cleavage of the ROI-02H bond .......................... 14
"Push-pull" for 0-0 bond cleavage of Fe-bound

cytochrome P450 (left) and horseradish peroxidase (right).... 16
Anthracene diporphyrins ................................................... 17

Some structures of porphyrin models for studies of

H-bonding effects ............................................................ 19
a) basket handle porphyrin-through ether linkage;
b) basket-handle porphyrin-through amide linkage;
c) picket-fence porphyrin;

d) substituted picket-fence porphyrin.

LI 1. Naphthalene porphyrin model compounds ........................... 22
I-12. Essential components of the C-clamp porphyrins .................. 23
I-13. Structure of series of anthracene Kemp’s porphyrins ............ 25

I-14. Co-02 complexes of naphthalene Kemp’s isomer and

anthracene Kemp’s acid porphyrin (AKAP) ........................ 26
II- 1. Target compound NKAP ................................................... 34
II-2. Two synthetic approaches to naphthalene linked porphyrin...35
II-3. Synthetic route to 2-carboxybenzyl porphyrin and

proposed synthetic pathway to naphthalene ester
porphyrin ........................................................................ 36

II-4. Synthesis of corrole, failed attempts to make porphyrin ....... 38
II-5. MS and UV-vis spectra of corrole ...................................... 39

II-6. (a) The equilibrium between 8-formyl-1-naphthoic acid

II-7.

II-8.

II-9.

II-lO.

II-ll.

II-12.

II-l3.

II-14.

II-15.

II-16.

II-17.

II-18.

II-l9.

II-20.

II-21.

and its lactone form ................................................... 41

(b) The equilibrium between 8-formyl-l-naphthoic ester

and its lactone form.ester .................................................. 41
Synthesis of naphthalene mesylate porphyrin ....................... 42
Synthesis of N KAP ........................................................... 44
Naphthalene Kemp’s isomer porphyrin ............................... 45
1H NMR of NKAP and NKEsterP ...................................... 46
Synthesis of NKEsterP and NKAmideP .............................. 48
Variant Temperature NMR of NKAP ................................. 50
1H NMR spectrum of 2 ..................................................... 61
1H NMR spectrum of 3 ..................................................... 62
1H NMR spectrum of 4 ..................................................... 63
1H NMR spectrum of 5 ..................................................... 64
1H NMR spectrum of 6 ....................................................... 65
1H NMR spectrum of 8 ....................................................... 66
IR spectrum of 8 ................................................................ 67
1H NMR spectrum of 9 ....................................................... 68
1H NMR spectrum of N KAP .............................................. 69

xiv

II-22. 1H NMR spectrum of 10 ..................................................... 70

II-23. 1H NMR spectrum of 11 ..................................................... 71

III-1

III-2

III-3

III-4

III-5

(a) ORTEP plot and labeling scheme for NKAP-H20 ........... 78
(b) Side view of the X-ray structure showing H-bonds.

The distance between the water oxygen and the

porphyrin center is 231(4) A ..................................... 79
(c) Another view showing distortions around the

C20-C33 connetor ..................................................... 79
(a) ORTEP plot and labeling scheme for ZnNKAP-MeOH...80
(b) Side view of the X-ray structure of ZnNKAP-MeOH ...... 81

(c) Side view from another angle showing the porphyrin

outward bending .............................................................. 81
1H NMR Titration of H20 into NKAP. [NKAP] = 3 mM,
[H20] in a: 0.000; b: 0.022 ; c: 0.037; d: 0.047 M

............................................................................... 93
DSC measurement of NKAP-H20 complex ......................... 94
1H NMR of Irnidazole titration of AKAP. [AKAP]

= 0.00276M, [1m] in a: 0.0000; b: 0.0082; c: 0.0272;

XV

(1: 0.3264 M ...................................................................... 95

III-6 Schematic structure of AKAP—imidazole and plot of
the anthryl methylene protons as a function of
concentration of imidazole in CDCl3 .................................... 97
111-7 Schematic structure of AKAP-Purine and plot of
the anthryl methylene protons as a function of
concentration of purine ...................................................... 98
111-8 1H N MR titration of methanol to ZnNKAP.
[ZnNKAP] = 0.014 M, [MeOH] in a: 0.000;
b: 0.013; c: 0.032; d: 0.064; e: 0.132; f: 0.395 M
............................................................................... 101
III-9 (a) ZnAKAP-1,2,4-triazole. (b) ZnAKAP-1,2,3-triazole ..... 105
111-10 (a) Calculated structure of syn acid monohydrates .............. 107
(b) Partial X-ray single crystal structure of NKAP-H20....107
IV-l. Typical 02 titration spectra of Co(II)porphyrins ................ 114
IV-2. Van’t Hoff plot of UT vs Ln(1/P1/2) ................................ 118
IV-3. The equation of reversible 02 binding and the
definition of P1/2 ............................................................ 121
IV-4. Side-view of NKAP-H20 complex ................................... 124
V-l. VO insertion to NKAP ....................................................... 133

xvi

V-2. IR Spectrum of NKAP(VO). The Sample was layered
on N aCl plate ................................................................. 138

V-3. IR Spectra of NKAmideP(VO): (a) Major Product;
(b) Minor Product. The Sample was layered on N aCl
plate ............................................................................. 141

V-4. The optical spectra of N KAmideP(VO) in (a)

CHzClz; (b) pyridine; (c) 1-methy1-imidazole .................. 143
V-S. (a) ORTEP structure of NKAmideP(VO) ........................ 153
(b) Sideview of NKAmideP(VO) .................................... 155
V-6. (a) X—Ray crystal structure of NAP(VO). ....................... 157
(b) Unit cell structure of NAP(VO) ................................ 158
VI-l ORTEP structure of RuCONKAP(MeOH) ....................... 179
VI-2 ORTEP structure of RuCONKAmideP(MeOH) ................ 180

xvii

LIST OF TABLES

TABLE Page
111-] Crystallographic Data of NKAP and ZnNKAP ....................... 82
III-2 Atomic Parameters x, y, z and B150 for N KAP and

111-3

III-4

III-5

IV-1.

IV-2.

ZnNKAP with E.S.Ds. Refer to the Last Digit Printed

.................................................................................. 83
Selected Bond Distances (A) and Angles (deg) and Their
Estimated Standard Deviations for N KAP and ZnNKAP ......... 89
Association Constants (M'l) of AKAP and NKAP with
Substrates ......................................................................... 99
Association Constants of Zn-porphyrins with MeOH
and Triazoles .................................................................. 104
02 Binding Parameters to Co(II)porphyrins ........................ 119
15N NMR Chemical shift of Fe(CN)2porphyrins .................. 123
Crystallographic Data for NKAmideP(VO) and NAP(VO)...135
IR Data of Vanadyl Porphyrins .......................................... 137
The Optical Absorption Spectral Data of Several
Vanadyl Porphyrins ......................................................... 145

xviii

V-5

V-6

V-7

VI-l

VI-2

VI-3

v1-4

VI-5

Atomic Parameters x, y, z and Biso for N AP(VO)

with E.S.Ds. refer to the last digit printed. ......................... 147

Atomic Parameters x, y, z and Beq for NKAmideP(VO)
with E.S.Ds. refer to the last digit printed ........................... 149

Selected Bond Distances (A) and Angles (deg) and Their
Estimated Standard Deviations for NKAmideP(VO) and
NAP(VO) ......................................................................... 152

Structural Data of several vanadyl compounds ..................... 160
Crystallographic Data of RuCONKAP(MeOH) and
RuCONK-AmideP(MeOH) ................................................. 170

Atomic Parameters x, y, z and Biso for
RuCONKAP(MeOH) with E.S.Ds refer to the last
digit printed ..................................................................... 172

Atomic Parameters x, y, z and Biso for
RuCONKAmideP(MeOH) with E.S.Ds refer to
the last digit printed .......................................................... 175

Selected Bond Distance (A) and Angles (deg) and

Their Estimated Standard Deviations for

RuCONKAP(MeOH) and RuCONK-AmideP(MeOH)
................................................................................ 178

Bond Distance (A) and Angle (deg) Comparison

xix

of Selected Carbonylated Metalloporphyrins ................... 182
VI-6 C-O Vibrations for RuCOporphyrins ............................. 183

VI-7 C-O Vibrations for FeCOporphyrins .............................. 184

OEP

TPP

DeutP

ETP

ABBREVIATIONS
Octaethylporphyrin
meso-Tetraphenylporphyrin
2,7 , l2, 1 8-tetramethyl- 1 3, 17-dipropionicacidporphyrin

Etioporphyrin

"Picket-fence" Porphyrin

PovPivP

NAP

NKAP

NKEsterP

NKAmideP

meso-tetrakis(a,0t,0t,a-o-pivalamidophenyl)porphyrin

"Small Pocket" = 5,10,15((1,3,5-benzenetriyltri-
acetyl)tris(a,a,a-o-aminophenyl))-20-(oz-o-
pivalamidophenyl)porphyrin

"Naphthoic Acid Porphyrin" = 5-(8-Hydroxycarbonyl-
l-naphthyl)-2,8,l3,17-tetraethyl-3,7,12,18-
tetramethylporphyrin

"Naphthalene Kemp's Acid Porphyrin" = 5-{8-[endo-
7-(Hydroxycarbonyl)- 1 ,5,7-trimethyl-2,4-dioxo-3-
azobicyclo[3 ,3, l]non-3—yl]-methy1-l-naphthyl )-

2,8, 13,17-tetraethyl-3 ,7, 12, 18-tetramethylporphyrin

"Naphthalene Kemp's Ester Porphyrin" = 5-{8-[endo-
7-(Methoxycarbonyl)- l ,5 ,7-trimethyl-2,4-dioxo-3-
azobicyclo[3 ,3, l]non-3-yl]-methyl- l-naphthyl }-

2,8, 13, 17-tetraethyl-3 ,7, 12, 18-tetramethylporphyrin

"Naphthalene Kemp's Amide Porphyrin" = 5-{8-
[endo-7-(Aminocarbonyl)- l ,5 ,7-trimethyl-2,4-dioxo-
3-azobicyclo[3,3 ,1]non-3-yl]-methyl-1-naphthyl }-
2,8, 13, l7-tetraethyl-3 ,7,12, 18-tetramethylporphyrin

"Anthracene Kemp's Acid Porphyrin" = 5-{8-[endo—7-
(Hydroxycarbonyl)- 1,5 ,7-trimethyl-2,4-dioxo-3-
azobicyclo[3,3, l]non-3-yl]-methyl- 1 -anthryl }-

2,8, 13,17-tetraethyl-3 ,7 , 12, 18-tetramethylporphyrin

XXI

AKEsterP

AKOHP

DBN

Py

l -MeIm

DSC

FT-IR

FAB-MS

"Anthracene Kemp's Ester Porphyrin" = 5-{8-[endo-
7-(Methoxycarbonyl)— 1 ,5 ,7-trimethyl-2,4-dioxo-3-
azobicyclo[3,3,1]non-3-yl]-methyl-l-anthryl }-
2,8,13,17-tetraethyl-3 ,7,12,18-tetramethylporphyrin

"Anthracene Kemp's Alcohol Porphyrin" = 5-{8-
[endo-7-(Hydroxymethyl)-1 ,5 ,7-trimethyl-2,4-dioxo-
3-azobicyclo[3,3,1]non-3-yl]-methyl-l-anthryl }-
2,8,13,17-tetraethyl-3,7,12,18-tetramethylporphyrin

1,5-Diazabicyclo[4.3.0]non-5-ene
Pyridine

l-Methylimidazole

Differential Scanning Calorimetry
Fourier Transformed Infra Red

Fast Atom Bombardment Mass Spectroscopy

CHAPTER I

Introduction

Hemes and heme proteins play many critical roles in biological
systems. They are vital components of essentially every cell of nearly all
living organisms. Even though their active sites all contain heme (iron
porphyrin), their functions are quite diverse. To name a few of their
functions in life processes, they include:

Hemoglobinandmyoglgbm: transport and storage of Oz in higher
animals;1

W : the last enzyme in the respiratory chain for 02
activation and reduction;2

WW: electron transport in the respiratory chains
of organisms as diverse as bacteria, yeasts, plants and animals, and in

photosynthetic cells from those of the simplest photosynthetic 1

bacteria to those of higher plants;3

2

W : synthesis, modification and/or degradation of fatty
acid, steroid and adrenal hormones, anesthetics, polycyclic aromatic
hydrocarbons and other xenobiotics. By doing so, it detoxifies
poisonous compounds in living organisms;4

Wages: activation and metabolism of hydrogen peroxide.5

The many functions of heme proteins depend on the properties and
the micro-environments of their active sites. Among the heme proteins, a
variety of axial ligations, oxidation states, and spin states of the central
metal ion are stabilized by the particular protein environments created

within the heme pockets of these proteins.

Among all the heme proteins, hemoglobin has been the most
extensively studied system. It was the first protein crystallized, the first
protein recognized for its physiological purpose of 02 and C02 transport,
the first to have its amino acid sequence determined, and one of the first
proteins whose tertiary and quartenary structure was determined by X-ray
crystallography. Hemoglobin (MW 64,500) is a tetrameric protein, having
four subunits, two a and two [3, chains with 141 and 146 amino acid
residues, respectively. Each subunit (Figure H) has one iron(II)
protoporphyrin IX complex as the active site (Figure I-2). The four-chain
structure of hemoglobin is directly related to the way it behaves in
fulfilling its biological role. The interactions between the subunits are
known as allosterism and they determine the cooperative binding of 02.
Myoglobin is a monomeric protein of 160 amino acid residues (MW
17,800) and one heme molecule. It is found in the skeletal muscles and
stores dioxygen, transported to it by hemoglobin, for use in the

mitochondria.

....... .di--.
\ z m
\/z\VIm Masada: 3%

.33 268 can: 233 cowaxo 05 So: 85ng 3v

.5 3.393805 aven— mo 2825a 3 .NA Bowman

5 3

\ mmoo m~oo

 

In the native deoxy form, the heme contains a five-coordinated
ferrous ion. It recognizes and reversibly binds to dioxygen at its sixth
coordination site. Other small substrates, such as CO, can also bind at this
site. The amino acid residues dictatethe immediate environment around
the heme and help to discriminate between CO and 02. The iron atom is
approximately 0.5 A out of the plane of the porphyrin and the Fe-
N(imidazole) bond vector is approximately 10° off the heme normal. This
iron atom incorporated in the protoporphyrin IX is high-spin (8:2) iron
(11). Upon the binding of O2 to heme, structural and conformational
changes occur around the active site. The oxygenated heme has a low-spin
six-coordinated iron(II) which is nearly centered in the porphyrin plane.
Along with a lateral shift of the protein F helix (Figure I-l), the Fe-N
(imidazole) off-axis tilt is reduced. 02 binds in an end-on fashion with a
bent geometry.6 X-Ray7 and neutron diffraction8 data have provided

strong evidence for H-bonding between the distal histidine and the bound
02 (Figure I-2B).

Model compounds have been proposed and synthesized to help the
understanding of the mechanism of O2-binding in heme proteins. If we
look back at the evolving theories of how the hemoglobin molecule
functions, we can see a classic example of the way that protein structures
suggest mechanistic theories and models, which in turn suggest new
chemical experiments, whose results provide feedback that forces the
original theories to be abandoned, modified, qualified, and improved until
the truth is finally approached. During the course of the theory
development, model compounds have played important roles in

understanding the relationships between structure and functions. 0n the

6

bases of results from the studies on proteins, models can be designed and
synthesized to mimic their active site. Due to its flexibility and simplicity,
the synthetic analog approach may lead to a better understanding of the
active site than that obtained directly from the protein itself. Without the
influence and complexity of the protein, the models provide the essential
properties of the active site of the heme protein, and by changing their
structure systematically, the functions of the heme protein environment

may be revealed.

The sequence of the model studies is as follows: 1) Isolate and purify
the proteins; 2) study the structural information and physical properties of
the active site; 3) design and synthesize analog molecules; 4) investigate the
structural, spectroscopic, and the chemical reactivity properties of the
model compounds; 5) compare between the protein and the analogs to
reveal new structure-function relationships. A major advantage in the
study of synthetic analogs, compared to the heme proteins, is the level of
control and flexibility in systematic variation of a single variable (such as
axial ligation, binding site polarity, steric restraint, solvent). There are
three synthetic challenges in designing synthetic analogs for Hb and Mb9:
1) the preservation of coordinative unsaturation at the iron, 2) the
prevention of irreversible bimolecular oxidation of the iron, and 3) the

control of substrate recognition (specifically 02 over C0).

The success in synthesis of model compounds capable of binding 02
reversibly made it possible to study in detail the distal (steric, local
polarity, and hydrogen bonding) and proximal binding site effects9 ( distal
and proximal sites are described in Figure I-2). Among them, hydrogen
bonding effect as proposed from the distal E7 histidine of hemoglobin is

7

considered as a major factor affecting O2 affinity. Therefore, it is

important to design and synthesize model compounds to probe this effect.

Besides hemoglobin, another heme protein, cytochrome c oxidase,
located at the inner mitochondrial membrane, plays a central role in the
cellular respiratory process. This enzyme catalyzes the reduction of 02
(Equation 1) and functions as a proton pump coupled to electron transfers
from cytochome c to 02. The free energy developed in this process is used
in the synthesis of ATP. It is estimated that 90% of the energy for heart
muscle contraction is provided through aerobic metabolism via cytochrome

c oxidase.

 

02 + 4 Cyt.c2+ + 4 11+ CW = 4 Cyt.c3+ + 2 H20 (1)
Oxrdase

The enzyme transfers four electrons to bound 02 one at a time from

cytochrome c2+; four O-H bonds are efficiently formed without release of

incompletely reduced 02 species such as superoxide, H202 or 0H.

It has been well established that the active unit of this enzyme
contains four metal centers: two heme groups, associated with heme a and
a3, and two copper atoms with distinct properties (Figure I-3).10 Heme a
is usually low spin and does not bind ligands while heme a3 is high spin
and capable of binding various ligands, such as 02 and CO in the ferrous
state and cyanide and azide in the ferric state. Heme (1 serves as a shuttle

that mediates the electron transfer from cytochrome c to the heme a 3,

33:8 0 2:25in .mA 053m

 

 

05582:

2%.: 023.5

---------------d

\

N
O

 

.588
3302.3

 

 

 

 

 

080: l curl
5%-32 .
,1m1.—.—

 

 

 

 

cognac

Shoo—o

 

------J

 

 

 

Heme a3 is associated with the binding and subsequent reduction of the 02
molecule. Electrons are transferred from the heme of cytochrome 6,
through Cup, and heme a, to the bimetallic 02 reduction center which

contains heme a 3 and Cu};-

Although the structural relationship between iron and copper of the
enzyme is far from established, it has been suggested that the Fe-Cu
distance in the binuclear site is less than 5 A in the oxidized enzyme, and

the Fe-Fe distance between the hemes is 15 to 20 A.

Many mechanistic studies of the reduction of O2 to water have been
carried out.2 The proposed mechanism for dioxygen activation and
reduction in cytochrome c oxidase is shown in Figure I-4. The chemistry
of equation 1 necessarily involves a number of steps: 02 binding, electron
transfers to oxygen, hydrogen transfers to oxygen, cleavage of 0-0 bond,
and release of products. Some of the intermediates shown in the Figure I—4
have been observed or identified by spectroscopic methods, but not every

intermediate is fully established and some of them remain speculative.

In order to understand the mechanism by which cytochrome c
oxidase reduces oxygen to water, it is important to clarify the function of
Gun. Although u-peroxo complexes such as Cu-O-O-Fe are expected to be
present during the enzymatic cycle, there has been no direct evidence for
its existence. Alternatively, as Caughey recently suggested,ll CuB does not
serve as a direct coordination site for 02 or for its reduction intermediate;
its role could be more as an anchor and for electron storage (Figure I-5).
The similarity between the function of Cu and H-bonding effect is that they

both may serve as polarizing factors to assist in pulling the two oxygen

\

G onN in no

lo
‘11 All I .2.
+050 +m0m AC1 57% IOIHMm :Rw Omwm :W m m6

+u He

@ m m@ .05”V m :

 

*1/10
-0 umfi MW
fix +~=QX JOIN-mom @
a
< 30/
© To 0"; 000208 0 08020030 .3 c2832 :5 -Onlhm @
a. 5998 .8 08.3 £5.38 Baonoem :1 0.5me
(E
-0 fig .0
:6 Jolt? 0
R T...
O -O
// /Olu+mm

 

11

$2300 .3 00385 no .8 @353 cocoa—000 05. .nA BswE

 

 

 

 

 

 

 

 

 

 

 

 

 

€+NGW
m NM 3.. m \J
1 a 5;. so I
Ni— .wRVX-I 4m Z/\Z
TH nm— -
CU+NGN
mm.N.E
am
AMVI m}— .>I IE +.N.—O 129
dynamo-x _
cm

 

 

 

12

atom apart. Therefore, the 02 adduct can be stabilized as well as reduced

easily.

Among the known terminal oxidases in nature (Figure I-6), many
bacterial enzymes, such as cytochrome bd oxidase and cd oxidase, do not
contain either a copper ion or another heme group at the 02 coordination
site yet the reduction of O2 to H20 in these systems occurs unhindered. It
is possible that nearby proton donors may provide strong H-bonding to the
Fe-02 complex thereby facilitating the 0-0 bond cleavage.

The importance of the hydrogen bonding is also shown in the
cytochrome c peroxidase in which hydrogen bonding is thought to promote
heterolysis of peroxides by stabilizing a developing negative charge on the
leaving group of the substrate. From the crystal structure determination,
Poulos12 showed that peroxidase has a water ligand at the sixth
coordination site which in turn is hydrogen-bonded to a distal histidine side
chain. Close to the sixth position there are a tryptophan and an arginine
side chain. Based on the X-ray crystal structure, Poulos proposed a
mechanism (Figure I-7) that utilizes the distal arginine and histidine
hydrogen bonds with subsequent proton transfer to effect heterolytic
hydroperoxide cleavage-l3 This transfer has a "push-pull" effect, as
discussed by Poulos.l4 In cytochrome c peroxide the proximal histidine
hydrogen bonds more strongly to neighboring groups than in the globins.
This makes the axial histidine a better electron donor (in other words, a
better "push") to the heme than in the globins. This may help to stabilize
higher oxidation states of the iron. Meanwhile, the distal histidine serves as

a proton donor, while arginine acts to stabilize the developing negative

13

 

 

 

 

 

 

 

 

 

 

 

 

00260.0 ocoo Ono
_ -
a .-
2. ....~O.€ 050: 0...... O E 050: .030: «0.00 0:. 0 2 4.4.0: «0.00 0E0...
.: ..o no“. .I 3.30....
_ 050:... No _
.0 2:0: 0 2:0: _ . «no» 0 0E2. «no» 0 0E0:
2000 000: £000 000:

 
 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

a _ . 0052. a .
.0 050: u .b 080: .02....- 30 .o 050: 0:0 no 050:
a H » Wowg 050-.- / d 9
0 0E0: m 0 050: 05-0 050: g o 0&0: _ «:0 o 050:
0002.8 0805023 0002.8 00 0502085 0002.8 0 0522330 0002.6 0 059.5030
000.0302 0:5: €00 Sou 03203003 3:085 36:232.:

_1 _ _

.1
£0.03 3 NO act-60.. .00 03.300 008.35 050: 08.5 GA 0.503

 

 

4

1

.0000 ENOAOM 05 mo 0w0>00~0 033000008
000308000 0 08080030 05 00 020080000000 0508008 . N...“ 000me

 

15

charge on the Fe bound oxygen atom. Consequently, the system is more
polar than globins and the polar distal side can "pull' apart the 0-0 bond of
the bound peroxide by stabilizing the separating charge.

In cytochrome P450, the thiolate ligand aids the cleavage of the 0-0
bond by "pushing" the electron density from the proximal side on to the
metal (Figure I-8). The "pull" element is less evident but may come from
hydrogen binding to 02 by Thr 252, which has been investigated recently
by Harris.15 In the ferrous dioxygen form of the enzyme, a H—bond
between T252 and G248 diminishes while the T252 interaction with
terminal oxygen of the bound dioxygen simultaneously forms. This T252
not only stabilizes the ferrous dioxygen form of the enzyme, but also helps

the formation of compound I.

A variety of metalloporphyrins have been designed and examined for
their catalytic effects on 02 activation and reduction.16 Chang has shown
that dimeric porphyrins substituted with one or two cobalt centers17 can
successfully carry out a four-electron reduction of 02 electrocatalytically
with no hydrogen peroxide intermediate detected (Figure L9). The most
surprising observation is that with only one cobalt ion present in the
dimeric porphyrin ligand, it is still capable of catalyzing the four-electron
pathway for reduction of 02. The unexpected high activity might arise
from the proximity of the second porphyrin ring which would be
protonated in acid. It is conceivable that these protons, juxtaposed to the
coordinated 02, could prevent the premature dissociation of, as well as
assist in proton transfer to, the partially reduced 02 coordinated to the

cobalt center in the second porphyrin ring. The function of the second

16

.9035 000208000 8:888: 0:0 906 0000
08080030 08.00-0m .«0 0w0>00~0 0:00 0-0 00.0 2:985: .mA 0.8me

\
.m

0: 2.0...
U

\5
t g-

l7

0

(C)

 

Figure l—9. Anthracene diporphyrins.

18

metallic center close to the heme active site is similar to that of a Lewis
acid in helping the 0-0 bond cleavage. Therefore, H—bonding effect has
been one focus of various studies of heme proteins and their model

systems.

Synthetic models that address the H-bonding interactions first came
from solvent effect.20 The affinity of 02 for cobalt Schiff base complexes
increased in the presence of H-bonding solvents. Recently, synthetic
models with intramolecular H-bonding ability have also emerged. Some of
these models are shown in Figure I-lO. In 'picket-fence' porphyrin21 the
amide proton, located 431 away from bound dioxygen, does not make direct
I-I-bonding possible. This has been proven by 170 NMR studies.22 The
first successful model is the 'basket-handle' porphyrin.23 A nearly 10 fold
increase in 02 affinity was observed when an ether linkage was transferred
into amide linked basket handle porphyrin. Evidence from 1H and 170
NMR verified the interaction of the bound dioxygen with the secondary
amide N-H.22 Even greater effects came from an “tailed” porphyrin model
equipped with an alcohol or a secondary amide.24 A substituted picket
fence porphyrin synthesized by Reed25 showed ca. 10-fold increase when
one pivalamide substituent of picket—fence porphyrin is replaced by a
phenylurea substituent.

In an effort to create an ideal environment for hydrogen bonding to
occur, Chang and Kondylis26 designed a series of U-shaped porphyrin
models in which an intramolecular proton donor is juxtaposed to the
terminal oxygen atom of the coordinated dioxygen. These models should

provide a means of determining quantitatively the influence of H-bonding

l9

FigureI-lO. Some structures of porphyrin models for studies of
H-bonding effects.
a) basket handle porphyrin-through ether linkage;
b) basket handle porphyrin-through amide linkage;
c) picket—fence porphyein;
d) substituted picket-fence porphyrin.

20

 

21

on the formation of dioxygen adducts. A series of Co11 l-naphthyl
porphyrins substituted with amido, carboxyl, and hydromethoxy at the 8-
naphthyl position were prepared (Figure I—ll). In the oxygen binding
study of these compounds it was observed that the 02 affinity increased by
1500 fold on going from the CoII naphthalene porphyrin (11a) to the Co11
naphthoic acid porphyrin (11d). Kinetic measurements of oxygen binding
to metal porphyrin complexes27 have shown that functional groups capable
of hydrogen bonding make a significant contribution to the stability of the
oxygen-heme complexes by decreasing the dissociation rate of the bound

ligand.

While all these models have clearly established the positive effect of
enhancing the 02 affinity, they have not permitted a closer look at how
structural and steric perturbations made on the proton donor would
influence the heme-substrate reactions. For example, from X-ray and
neutron diffraction data it has been noted that the H-bonding between the
distal histidine and Fe-02 in Mb and Hb is an oblique one. With the H-
bond not coplanar with the Fe-Oz moiety, the oblique interaction raised the

possibility of H-bonding correlated with both 01 and 02 or only on O_1_.

In an attempt to provide better understanding on the influence of H-
bonding in 02 activation, a series of novel model compounds, C-Clamp
porphyrins have been designed and synthesized (Figure I-12). This C-
clamp porphyrin has a carboxylic acid pointing towards the porphyrin
center. This acid functional group combined with the metal ion of the
porphyrin furnishes a ditopic binding site for 02, CO, etc. As shown in
Figure I-12, the acid functionality is linked to the porphyrin ring via two

22

00850800 3008 853800 0003500002 A Z 08me

 

 

 

 

come moouum 85
E Nmzooum 62v
2 000008 35
0 .mum 3:

 

 

00:02 No

 

 

23

 

.8383 080—00 05 00 080000800 380mmm .N: Bawfi

 

 

 

1 rounds

 

: 008% f

 

 

24

perpendicular spacers. Spacer I is a rigid aromatic moiety attached to
porphyrin meso-position and flanked by two methyl groups to limit its
freedom of rotation. Spacer II is conveniently part of the Kemp's triacid
whose utility as a convergent building block for molecular receptor has
been well demonstrated by Rebek.27 This combination of the Kemp's
triacid and a naphthalene or anthracene connector thus provides a C-shaped
porphyrin model with a relatively rigid acid hovering over the porphyrin.
The structure should minimize the intramolecular attack on the porphyrin

ring to avoid self-decomposition, thus allowing further studies on the

reaction of H-bonded heme-02 species.

Avilés28 has synthesized an anthracene Kemp’s acid porphyrin
(Figure I-13) and found that the 02 affinity increase by 90 fold on going
from the Co11 Kemp’s ester porphyrin to the Kemp’s acid porphyrin. She
also observed that the 02 affinity increased as the hydrogen-bonding ability
of the model compound increased. 02 affinity for the CoII Kemp’s acid
model is 14 times better than the 02 affinity for the alcohol.

The naphthoic acid porphyrin (NAP) still has better 02 affinity (P1 /2
= 0.028) than the anthracene Kemp’s acid porphyrin (AKAP) (Pl/2 = 2.4)
at -42°C. This may be due to the larger than 4 A distance between the
Kemp’s acid and the porphyrin ring in AKAP so that the carboxylic proton
may not achieve an optimal interaction with the terminal oxygen of the Co-

02 complex in order to stabilize it. The 02 affinity for the naphthalene
Kemp’s isomer (Figure I-14) is approximately 2.5 times better than the 02
affinity for the anthracene Kemp’s acid. This is surprising since the

carboxyl group of the anthracene Kemp’s acid is expected to be

25

 

Figure I-13. Structure of series of anthracene Kemp's porphyrins.-

26

#223 80.3800 200 0083— 00000880
000 00808 0.080M 0:205:00: .8 0053800 00.00 .0: 08mm”—

m<v~< 080% 0.083— 0003:8002
-Inlloz IO'UI I s
r, _ fl . / ._,-....z I .
0&0 1. , r H w x /
m / \ a0
C :
oxWO o /0

 

27

a better proton donor (pka~4.6) than the imide of the naphthalene Kemp’s
isomer (pka~9.6). The reason for this may be that the imide proton in this
model is positioned closer to the Co-02 center, thereby stabilizing it more

effectively.

Based on this discussion, the carboxylic acid of the anthracene
Kemp’s acid porphyrin (AKAP) may be too far away from the bound 02,
and a naphthalene Kemp's acid porphyrin should be a better model. The
synthesis of the naphthalene Kemp's acid porphyrin (N KAP) and

derivatives are described in Chapter II.

The unique opportunity that the C-clamp porphyrins provided is that
these ditopic receptors can accommodate substrates between the NH or
metals of the porphyrin and the acid functional group. Guest-host
interactions in free base and metallated C-clamp porphyrins is the topic of
Chapter III. The recognition of 02 and 02 affinity studies will be
discussed in Chapter IV. Also in this chapter, comparison between C-
clamp porphyrins (N KAP and AKAP) and U-shaped porphyrin will be
addressed.

One important intermediate in cytochrome c oxidase and cytochrome
P-450 is the ferry] (iron oxo) species. It is still debatable whether H-
bonding exists in these natural heme enzymes. Therefore, it is necessary to
set up benchmark data on how much the H-bonding affects the vibrational
frequency of Fe=O. Stable model compounds, vanadyl (vanadium oxo)

porphyrins were used in this study and the result is discussed in Chapter V.

28

The carbonylated-ruthenium (RuCO) complexes of C-clamp
porphyrins are in a ‘trans” configuration, in which the CO is on the
opposite site of the intramolecular carboxylic acid. In between this acid
and the Ru-porphyrin, one solvent molecule, methanol, is trapped and
serves as the sixth ligand to the metal. H-bonding from the acid proton
affects this methanol trans ligand field and consequently shift the CO
vibration. Chapter VI describes the result and X-ray structure of this

study.

29

References

l. Perutz, M. F.; Fermi, G.; Luisi, B.; Shaanan, B.; Liddington, R. C.
Acc. Chem. Res. 1987, 20, 309-321.

2. Babcock, G. T.; Wikstrém, M. Nature (London), 1992, 356, 301-309.

3. Electron Transfer Reactions in Metalloproteins in 'Metal Ions in
Biological Systems, Vol. 27, Sigel, H. and Sigel, A; Eds. Dekker, New
York, 1991.

4. a) Ortiz de Montellano, P. R. Acc. Chem. Res. 1987,20, 289-294.
b) "Cytochrome P-450 Structure, Mechanism and Biochemistry".
Ortiz de Montellano, P. R., Ed., Plenum Press, New York, 1986.

5. a) Gunter, M. J.; Turner, P. Coord. Chem. Rev. 1991, 108, 115-161.
b) Dawson, J. H. Science, 1988, 240, 433-439.

6. Jongeward, K. A.; Madge, D.; Taube, D. J .; Marsters, J. C.; Traylor,
T. G.; Sharma, V. S. J. Am. Chem. Soc. 1988, 110, 380-387.

7. a) Shaanan, B. Nature (London) 1982, 296, 683-684.
b) Condon, P. J.; Royer, W. E. J. Biol. Chem. 1994, 269, 25259-
25267.

8. Philips, S E. V.; Schoenborn, B. P. Nature (London) 1981, 292, 81-
82.

9. Suslick, K. S.; Reinert, T. J. J. Chem. Edu. 1985, 62, 974-983.

10.

11.

12.

l3.

14.

15.

16.

17.

18.

3O

Beinert, H.; Griffiths, D. E.; Wharton, D. C.; Sands, R. H. J. Biol.
Chem. 1962, 237, 2337-2346.

a).Yoshikawa, S.; O'Keeffe, D. H.; Caughey,W. S., J. Biol. Chem,
1985, 260, 3518-3528.

b) Yoshikawa, S. ; Caughey, W. S. J. Biol. Chem. 1990, 265, 7945-
7958.

Poulos, T. L.; Freer, S. T.; Alden, R. A.; Edwards, S. L.; Skogland,
U.; Takio, K.; Eriksson, B.; Xuong, N.; Yonetani, T.; Kraut, J. J. Biol.
Chem. 1980, 255, 575-580.

Poulos, T. L.; Kraut, J. J. Biol. Chem. 1980, 255, 8199-8205.
Poulos, T. L. Adv. Inorg. Biochem. 1987, 7, 1-36.

Harris, D. L.; Loew, G. H. J. Am. Chem. Soc. 1994, 116, 11671-
11674.

a) Collman, J. P.; Deniserich, P.; Konai, Y.; Marrocco, M.; Koval, C.;
Anson, F. C. J. Am. Chem. Soc. 1980, 102, 6027-6036.

b) Durand, R. R.; Bencosme, C. S.; Collman, J. P.; Anson, F. C. J.

Am. Chem. Soc. 1983, 105, 2710-2718.

(c) Collman, J. P. J. Electroanal. Chem. 1979, 101, 117-122.

Liu, H.; Abdalmuhdi, I.; Chang, C. K.; Anson, F. C. J. Phys. Chem.
1985, 89, 665-670.

Momenteau, M.; Lavalette, D. J. Chem. Soc. Chem. Commun. 1982,
341-343.

19.

20.

21.

22.

23.

24.

25.

26.

27.

28.

31
Young, R.; Chang, C. K. J. Am. Chem. Soc., 1985,107, 898-909.

Drago, R. S.; Cannady, P. J .; Leislie, K. A. J. Am. Chem. Soc. 1980,
102, 6014-6019.

Jameson, G. B.; Molinaro, F. S.; Ibers, J. A.; Collman, J. P.; Brauman,
J. 1.; Rose, 8.; Suslick, K. S. J. Am. Chem. Soc. 1980, 102, 3224-
3237.

Gerothanassis, I. P.; Momenteau, M.; Loock, B. J. Am. Chem. Soc.
1989, 111, 7006-7012.

Mispelter, J .; Momenteau, M.; Lavalette, D.; Lhoste, J .-M. J. Am.
Chem. Soc. 1983, 105, 5165-5166.

Chang, C. K.; Ward, B.; Young, R.; Kondylis, M. P. J. Macromol.
Sci, Chem. 1988, A25, 1307-1326.

Wuenschell, G. E.; Tetreau, C.; Lavalette, D.; Reed, C. A. J. Am.
Chem. Soc. 1992, 114, 3346-3355.

Chang, C. K.; Kondylis, M. P., J. Chem. Soc. Chem. Commun., 1986,
316-318.

Rebek, J ., Jr. Science, 1987, 235, 1478-1484.

Aviles, G. M., "Interaction of Intramolecular Carboxylic Acid with
Heme-02 Complex", Ph.D. Dissertation, Michigan State University,
1991. f

32

CHAPTER II

Synthesis and Characterization of C-Clamp Porphyrin

A. Introduction

As already mentioned in chapter I, distal hydrogen bonding has
been considered as one of the important factors affecting reversible
dioxygen binding to several 02 binding heme proteins as well as to
cobalt(II) and iron(II) porphyrin models. To design and synthesize model
compound that mimic this effect has been a research goal in our group.
The naphthoic acid porphyrin (NAP) system, a model capable of
intramolecular H-bonding, has displayed high 02 affinity.l However, the
curious decomposition of its Co(II) complex3 made the NAP a better
model for the studies of heme degradation. Converting this NAP system
to the Kemp’s triacid porphyrin switches the acid group from the 8-
position of the naphthalene ring an overhanging positionand therefore
prevent the ring degradation (Figures I-11 and I-12). Additionally, with

an acid proton hanging down from a vertical position instead of the

33

horizontal hydrogen bond donor as in the NAP system, would allow the
study of orientation effects about hydrogen bonding.

Our target compound is naphthalene Kemp’s acid porphyrin
(NKAP) as shown in Figure II-l. Its derivatives, naphthalene Kemp’s
ester porphyrin (NKEsterP) and naphthalene Kemp’s amide porphyrin

(NKAmideP), were synthesized as well for comparison purposes.
B. Synthesis

The synthetic strategy is to link the naphthalene (spacer I) with
porphyrin followed by linking the Kemp’s acid (spacer II) to the
naphthalene (Figure I-12). There are two proposed synthetic routes
(Figure II-2) to the naphthalene linked porphyrin. One is through a
tetrapyrrole pathway, and another is to follow the previous procedure to
make a dipyrrole, then by MacDonald 2+2 condensation2 to generate NAP.
After functional group transformations, a coupling reaction in the last step
produces the N KAP.

1. Tetrapyrrole Pathway

This approach is illustrated by the synthesis of a related 2-benzoic
acid porphyrin. Starting with a 2-carboxybenzaldehyde and a a,c-biladiene
dibromide, the porphyrin benzoate was synthesized in one step (Figure II-
3). Since methanol wasused as the reaction solvent, the ester was produced
as a consequence. The ester was hydrolyzed into acid porphyrin by

refluxing with KOH in pyridine for three days.

This implied that if we started with a 1,8-naphthaldehydic acid, the

product from coupling with a tetrapyrrole would be a naphthalene ester

34

.m<v_z 0850800 00300. .Tm 088m

 

 

35

 

80.30000 000—0: 000005000: 00 0000000000 03058? 030. .00 0830

 

 

 

8823 a
n 200 00.8080 00023-0
I I
OED Z 2 USO
/ \ / \

 

003080—800 2000:0030 N + N a.

 

 

:00:
000040~ um: 00%

 

 

000000.: 0.0800053. 00

 

 

 

36

 

80.30000 00000 00005000: 00 003500 0005000. 00000000
000 80.30.80 300000000009N 00 0800 00050.3 .m

3002

.5 x / 00055: .000

$002

 

0 2:00...

37

porphyrin (Figure II-3). However, contrary to what we anticipated, the
product was not the desired naphthalene ester porphyrin. We obtained a
corrole instead (Figure II-4). The evidence came from the strong
fluorescence and visible absorptions of the compound at 534, 547 and 592
nm, characteristic absorption of corrole (Figure II-5). Since most of the 8-
formyl-l-naphthoic acid might exist in its lactol form as shown in Figure
II-6 instead of the free aldehyde form, the acid group was converted into
an ester, and the reaction with tetrapyrrole was tried one more time. It
still gave corrole as the product indicating that the lactone was not

destroyed by converting to ester.

For a typical synthesis of corrole, basic reaction conditions are
used.4 Our reaction condition was acidic (acetic acid) and seemed to offer
reasonably high yield. A control experiment with the a,c-biladiene in 30%

HBr/HOAc provided corrin in similar yield.

Even though we were excited about this discovery, we still need to
make the target compound NKAP. Therefore, the 2+2 pathway was

followed.
2. Dipyrrole Pathway by MacDonald Condensation

The synthesis of the naphthalene Kemp's acid porphyrin (N KAP) is
outlined in Figure II-7 and H-9. The starting acid porphyrin NAP (Figure
II-2)1 was converted into naphthalene ester porphyrin by diazomethane.
Since direct reduction sometimes gave aluminum porphyrin, the porphyrin
ring was protected by transforming to its zinc complex. The ester

porphyrin was then reduced with LiAlH4 in dry THF.

38

80.30.00 00—08 00 308000 00:00 0.0800 00 8,0050% .00-: 0.830

l
A

$002
=00< hm: 000m

:00:
- :02. :00 000

j

 

I002
$0000~ um: 003“

as O
as C

\

 

 

 

39

Figure II-S. MS and UV-vis spectra of corrole.

 

‘40

 

Emno.ou 220.com _

 

 

 

 

 

 

 

 

mpoom A.:~o\zzvo.oo. o.oom

\E‘.JAY- ‘ - - - coo.o+

fl

r

f A.:~o\cv
oom.o

a » dnwv. ~+
”mum "azam

 

 

 

 

\
0.60!

 

CNOthC d.=nf

 

 

 

~.=o«

 

condo.gunoco¢:;ao:_
co«uam sung w:-ou «lo—mu as“

hovuvm cachm .0: ~osoa wo—c—no_ 16%

mwcnIQCA OD

 

N\t

yukx

 

 

 

0'962
0’929
B'QO
B'BZS
6'269

ZIZ'I

29"8

0'19?
S'ZPS
8'999

618'0

'0

291
£9B'B

ébt'a

S49 990'0
S8I'B

9.

{98'0
868'8

SSU

SSU

-- XUBd --

-- A311un --

 

 

 

41

A58 2.82: m: 28 8.3 065:3: Rah—8-x c8253 Esta—Eco 2? 3V
A58 2583 m: can Eon assign: 358% 5253 63.5233 2F A3 6-: oSwE

: 8m:
0 O a
o O
z o:
E

 

42

53:93 8232: 0:03:53: :8 mfiofiim 8-: oSwE

 

 

c5 g m
£2: .m

k

1:295 A

 

 

43

The resulted alcohol was treated with excess (10 equiv.) methanesulfonyl
chloride without heating to minimize decomposition. The excess reagent

was removed by vacuum pump.

Direct coupling of the mesylate porphyrin with potassium imide-
carboxylate salt has been shown to give Kemp’s isomer porphyrin (Figure
II-8).5 In order to synthesize the target compound, an alternative pathway
was employed. Since Rebek’s has reported the condensation of various
amines with the acid chloride anhydride,6 the mesylate was converted into
an amine before coupling. The mesylate reacted with excess sodium azide
in DMF to give the azido-porphyrin in 99% yield. IR spectrum of this
porphyrin showed a strong azide absorption band at 2096 cm'l. After
reduction of the zinc azido-porphyrin with LiAlH4, the amino porphyrin
was coupled with the acid chloride-anhydride to generate NKAP (Figure
II-9). The overall yield was 60% for NKAP. 1H NMR of NKAP showed
that the capping cyclohexyl protons have substantial upfield shift (Figure
II-lO). The gem-methyl to the COzI—l was found at -O.26 ppm in NKAP
compared to 1.40 ppm in the starting Kemp's acid chloride-anhydride,

which is obviously caused by the diamagnetic ring current.

Figure lI-ll shows the reactions in synthesizing derivatives of
NKAP. The naphthalene Kemp’s ester porphyrin (NKEsterP) was obtained
in quantitative yield from the reaction of NKAP with diazomethane. In
making naphthalene Kemp’s amide porphyrin (N KAmideP), NKAP was
exposed to oxalyl chloride followed by ammonia. These NKEsterP and
N KAmideP were characterized by proton NMR and Mass spectra and used

for the purpose of property comparison.

duEan 880% $an! ocofifinmmz .w-= Sawfi

55388 380$
thov— egg—Ema Z n

 

 

45

 

    

8
1. Zn OAc)
2. LiAlH4 2
61%

 

 

C-Clamp Porphyrin: NKAP

Figure II-9. Synthesis of NKAP.

46

Figure II-10. 1H NMR of NKAP and NKEsterP.

 

47

5%. m-

.7

-
bPDDD-nbhwpbohonombnbl’L-rbobhpn

o
.

 

131
12

. Ema m-

.DDD

 

#71

0.20

 

NI

urn-.ppp-b-uppn-o

.23 as.

o

..b--b—

mgj

 

_ ~

urbanbbrubrcLPlPht-[rb’bbor-Pbohb.

47

 

 

p-nbhrpnb

 

o.~

 

 

 

 

. ~

.hrnlplinPPanprpb.p.

 

 

 

 

 

48

.%28§z 2a madam—v.2 no again a T: mama

 

1 £2 a
l 5208 2 .302

 

 

 

49

C. Variant Temperature-NMR

In the 1H NMR studies of NKAP, the typical NH proton signals in
the -3 to -4 ppm region were not detected at room temperature, instead a
broad peak around 0 ppm was observed (Figure II-lO). This phenomenon
suggests proton exchange among the NH protons of the porphyrin and the
proton of the carboxylate acid. When the acid group was methylated by
CH2N2, the NH protons emerged at -3.2 ppm as a doublet. Similar
behavior for AKAP was observed. In order to probe the exchange, the
variant temperature N MR technique7 was employed to monitor the
dynamics of the proton exchange at 500 MHz in these two systems. The,
~90 to 40 °C range accessible in CD2C12 was sufficient to allow the
observation of a sharp peak around -4 ppm at -90 °C, which gradually
broadened out. When temperature reached 20 °C, a new signal centered at
0. ppm appeared (Figure II-12). Over the entire temperature range (-90 to
40 °C), the signal of the carboxylic acid proton was not obvious, possibly
due to overlapping with other signals, and this acid proton was identified
later at 3.6 ppm by saturation spin transfer techniques8 under conditions of
slow exchange. The coalescence temperature detected for NKAP was -10
°C and 15 °C for AKAP. This agrees well with the expectation that in
N KAP the acid proton is closer to the porphyrin center and less energy is

needed for the coalescence to occur.

50

Figure II-12. Variant Temperature NMR of NKAP.

CW €33,045

_. L44. m ..
lULLmLLg . 0..
Ln 11.1%.,
L3. in... . ”6
JULLMLJL—UJLJLLLL :C
A . j:

JLLMJLLL . L

ppm-3.2 -3.6 «.4 r?-

 

 

 

 

 

 

L

 

 

 

 

 

 

 

VvarVfi—rv' rfi—I I v‘vvvvhvvv‘VVfi I VT

8.5 6.0 75 7.0 6.5 4.5 4.0 3.5 5.0 2.5 2.9 v.5 1.0 0.5 o.

52

D. Experimental

Materials and measurements. Reagents and solvents for synthesis
were used as received unless otherwise stated. CHzClz and DMF were
distilled from CaHz. THF and toluene were freshly distilled from LiAlH4.
UV-visible spectra were measured on a Cary 219 or a Shimadzu 160
spectrophotometer. 1H NMR spectra were recorded on Varian Gemini-300
in "100%" CDC13 (minimum 99.8 atom % D, Cambridge Isotope
Laboratories) with the residual CHCl3 as the internal standard set at 7.24
ppm. Variant temperature NMR measurements were conducted on Varian
500 MHz spectrometer. Mass spectra were measured from a benchtop VG
Trio-l mass spectrometer or FAB (fast atom bombardment) mass spectra
on a JEOL HX-l 10 HF double focusing spectrometer in the positive ion
detection mode. Infrared spectra were obtained from sample film on a

NaCl plate and recorded on a Nicolet IR/42 spectrometer.

5- (2-Methoxycarbonylphenyl)-13,1 7-diethyl-2,3, 7, 8,12,18-
hexamethylporphyrin 2

l , l9-Dideoxy-8, 12-diethyl-2,3 ,7, 13, 17, 18-hexamethyl-biladiene-a,c-
dihydrobromide (100 mg, 0.166 mmol) and 2-carboxybenzaldehyde (97%,
257 mg, 1.66 mmol) were suspended in 15 ml methanol. To this solution,
4 drops of 30% HBr in acetic acid was added. After being refluxed in the
dark for 24 hours under argon, the reaction mixture was cooled and
treated with saturated sodium bicarbonate solution. The product was
washed with water and extracted by methylene chloride. Chromatography

over silica gel using methylene chloride as the eluant gave 34.5 mg of 2
(35.6%). 1H NMR (300 MHz, CDC13) 5 ppm -3.19 (d, 2H, NH), 1.84 (6H;

53

t, Et), 2.38 (6H, 8, Me), 2.72 (3H, s, OMe), 3.50 (6H, 5, Me), 3.62 (6H, 5,
Me), 4.05 (4H, q, Et), 9.92 (1H, s, meso), 10.12 (2H, s, meso), phenyl:
7.83 (2H, m), 7.96 (1H, d), 8.37 (1H, d); MS, m/z, 584 (M, 53%); UV-vis
Amax nm (rel intens) 404 nm (1.00), 502 (0.08), 536 (0.04), 572 (0.04),
624 (0.01).

5-(2-Carboxyphenyl)-13,1 7-diethyl-2,3, 7, 8,12,18-
hexamethylporphyrin 3

A KOH solution (4 g in 2 ml H20) was added to a pyridine solution
of 2 (20 mg, 0.034 mmol). The mixture was heated to reflux under argon
for 3 days. The reaction was monitored by TLC which showed a lower Rf
upon the product formation. The hot solution was then poured into ice
water and washed with brine. The product was extracted with CHzClz and
purified by TLC plate to provide 19 mg (97%) of 3. 1H NMR (300 MHz,
CDCl3) 5 ppm 0.65 (br, 3H, NH and COOH), 1.69 (6H, t, Et), 2.24 (6H, s.
Me), 3.29 (6H, 8, Me), 3.45 (6H, 3, Me), 3.88 (4H, q, Et), 9.82 (1H, s,
meso), 10.02 (2H, s, meso), phenyl: 7.67 (1H, d), 7.75 (2H, m), 8.21 (1H,
(1); MS, m/z, 570 (M, 81%); UV-vis Kmax nm (rel intens) 404 nm (1.00),
503 (0.07), 537 (0.04), 571 (0.04), 622 (0.01).

2,3, 7,13,] 7,1 8-hexamethyl- 8, 12-diethylcorrole 4

1 , 19-Dideoxy-8, 12-diethyl-2,3,7, 13, 17, 18-hexamethyl-biladiene-a,c~
dihydrobromide (100 mg, 0.166 mmol) and 1,8-naphthaldehydic acid (365
mg, 1.66 mmol) were suspended in 15 ml methanol. To this solution, 4
drops of 30% HBr in acetic acid was added. After being refluxed in the
dark for 24 hours under argon, the reaction mixture was cooled and

treated with saturated sodium bicarbonate solution. The product was

54

washed with water and extracted by methylene chloride. Chromatography
on a silica gel column using methylene chloride as the eluant gave 30 mg of
corrole 4 (41%). Under the same reaction condition, using methyl 8-

formyl-l-naphthoate as starting material gave the same product.

1,19-Dideoxy-8,12-diethyl-2,3 ,7, 13,17,18-hexamethyl-biladiene-a,c-
dihydrobromide (100 mg, 0.166 mmol) was dissolved in 15 ml methanol.
To this solution, 4 drops of 30% HBr in acetic acid was added. After being
refluxed in the dark for 24 hours under argon, the reaction mixture was
cooled and treated with saturated sodium bicarbonate solution. The
product was washed with water and extracted by methylene chloride.
Chromatography over silica gel using methylene chloride as the eluant gave
30 mg corrole 4 (41%). 1H NMR (300 MHz, CDCl3) 8 ppm 1.74 (t, 6H,
Et), 3.31 (s, 6H, Me), 3.40 (s, 6H, Me), 3.48 (s, 6H, Me), 3.87 (q, 4H, Et),
9.18 (s, 1H, meso), 9.27 (s, 2H, meso); MS, m/z, 438 (M, 100%); UV—vis
lmax nm (rel intens) 395 nm (1.00), 534 (0.13), 547 (0.12), 592 (0.15).

5-(8-Methoxycarbonyl-1-naphthyl)-2,8,13,1 7-tetraethyl-
3, 7, 12, 18-tetramethylporphyrin 5

5-(8-Hydroxycarbonyl-l-naphthyl)-2,8,13, l7-tetraethyl-3,7,12,18-
tetramethyl porphyrin (NAP) (1.09 g, 1.65 mmol) was dissolved in 200 ml
THF. To this solution, 10 equivalents of freshly prepared diazomethane
ether solution was added and stirred at room temperature for 30 minutes.
5% HOAc (40 ml) was added slowly to quench the excess diazomethane.
The THF was removed and the residue was redissolved in methylene
chloride, washed with saturated NaHCO3 solution and water, dried over
anhydrous N a2804. Purification by column chromatography over silica

55

gel with methylene chloride as eluant gave purple crystals in quantitative
yield of 5: 1H NMR (300 MHz, CDCl3) 8 ppm -3.10 (2H, d, NH), 0.07
(3H, OMe), 1.71 (6H; t, Et), 1.88 (6H, t Et), 2.13 (6H, s, Me), 3.65 (6H, 3,
Me), 3.94 ( 4H, q, Et), 4.08 (4H, q, Et), 9.97 (1H, s, meso), 10.17 (2H, s,
meso), naphthyl: 7.61 (1H, s), 7.63 (1H, t), 7.78 (1H, t), 8.00 (1H, d), 8.16
(1H, t); 8.34 (1H, d); MS, m/z 662 (M, 100%); UV—vis kmax nm (rel
intens) 407nm (1.00), 505 (0.08), 538 (0.05), 573 (0.04), 627 (0.02).

5-[8- (Hydroxymethyl)-I-naphthylj-Z, 8, 13,1 7-tetraethyl-
3, 7, 12, 1 8-tetramethylporphyrin 6.

To 5-(8-methoxycarbonyl-1-naphthyl)-2,8,13,17-tetraethyl-
3,7,12,18-tetramethylporphyrin 5 (2.1 g, 3.17 mmol) dissolved in
methylene chloride (400 ml) was added a saturated methanol solution of
zinc acetate containing sodium acetate. The mixture was heated to reflux
for 10 minutes before being washed with water (50 ml), dried over
NazSO4 and evaporated to dryness to give the zinc porphyrin. To this
material dissolved in freshly distilled THF (300 ml), a suspension of
LiAlH4 (0.5 g) in THF was added slowly. The reaction solution was
stirred at room temperature for another hour. Completion of the reaction
was monitored on TLC by the disappearance of the fast moving starting
material. After the reduction was complete, the mixture was quenched by
addition of ice water and the product was isolated by extraction with
CH2C12 from water. The crude product was purified by column
chromatography over silica gel using 2% MeOH/CHzClz. The purified
zinc porphyrin was redissolved in methylene chloride (200 ml), and
demetalated by washing with 10% HCl (200 ml). The organic solution was
then washed with saturated NaHCO3, water and dried over anhydrous

56

NazSO4. Evaporation afforded 1.63 g (81%) purple crystal of 6. 1H
NMR (300 MHz, CDCl3) 6 ppm -3.09 (2H, d, NH), 0.20 (1H, t, OH), 1.71
(6H; t, Et), 1.88 (6H, t Et), 2.13 (6H, s, Me), 3.08 (2H, d, CH20-), 3.65
(6H, 8, Me), 3.96 ( 4H, m, Et), 4.08 (4H, q, Et), 9.97 (1H, s, meso), 10.17
(2H, s, meso), naphthyl: 7.61 (1H, s), 7.63 (1H, d), 7.78 (1H, t), 8.01 (1H,
d); 8.17 (1H, t), 8.35 (1H, d); MS, m/e (relative intensity) 634 (M+, 86.89);
UV-vis kmax nm (EM) 625 (2100), 572 (6400), 538 (6500), 503 (15000),
405 (190000).

5-[8-(Methanesulfonylmethyl)-1-naphthyl]-2,8,13,1 7-
tetraethyl-3, 7, 12, 1 8-tetramethylporphyrin 7.

The above alcohol 6 (100 mg, 0.16 mmol) was dissolved in 5 ml dry
methylene chloride with 3 drops of trimethylamine. To this mixture
stirred under argon in an ice bath, methanesulfonyl chloride (2 ml) was
slowly added. The system was continuously stirred for 14 hours at room
temperature. The solvent and excess methanesulfonyl chloride was pumped
away with a vacuum pump (room temperature until almost dry, then at
60°C for 2 hours). This product was used for the next step without further

purification.

5-[8-(Azid0methyl)-1-naphthyl]-2,8,13,1 7-tetraethyl-
3, 7, 12, 18-tetramethylporphyrin 8.

The porphyrin mesylate 7 was dissolved in dry DMF (10 ml) and
sodium azide (300 mg) was added. The mixture was heated to 90°C for 5
hours under argon. After the reaction was done, water was added to the
solution and the porphyrin was extracted to the organic layer by methylene

chloride. The crude product was purified by column chromatography over

57

silica gel using methylene chloride as solvent and crystallized from
CH2C12/CH3OH (3:2) to give 103 mg (99%) of 8. 1H NMR (300 M Hz,
CDCl3) 6 ppm -3.08 (2H, (1, NH), 1.73 (6H; t, Et), 1.89 (6H, t Et), 2.12
(6H, s, Me), 2.95 (2H, d, CH2N3), 3.66 (6H, 5, Me), 3.98 ( 4H, q, Et), 4.10
(4H, q, Et), 9.99 (1H, s, meso), 10.19 (2H, s, meso), naphthyl: 7.49 (1H,
d), 7.64 (1H, t), 7.80 (1H, t), 8.03 (1H, dd); 8.22 (1H, d), 8.36 (1H, dd);
FAB-MS, m/e (relative intensity) 660 (M+1, 3.17); UV-vis kmax nm (EM)
625 (2100), 572 (6400), 538 (6500), 503 (15000), 405 (190000); IR: 2096
cm-1 (strong).

5-[8-(Aminomethyl)-1-naphthyl]-2,8,13,1 7-tetraethyl-
3, 7, 12,18-tetramethylporphyrin 9.

Zinc was inserted into 50 mg of porphyrin 8 using the procedure
described previously for porphyrin 5. To the dried zinc porphyrin
dissolved in freshly distilled THF (15 m1), cooled in ice bath and stirred
under argon, a suspension of LiAlH4 (20 mg) in THF was added slowly.
The mixture was stirred for another 10 minutes. The reduction was
monitored by TLC as the product has a relative smaller Rf value compared
to that of the starting material. After the reaction was done, ice water was
added cautiously to the reaction flask. The THF was evaporated, and the
porphyrin was extracted into methylene chloride and evaporated to
dryness. Column chromatography (silica, CH2C12) provided the pure zinc
amino-porphyrin. The zinc complex was then partitioned between CH2C12
and 10% HCl, and the CH2C12 layer of porphyrin was washed with
saturated NaHCO3, water, and evaporated to give 29 mg (61%) of 9. 1H
NMR (300 MHz, CDCl3) 8 ppm -3.09(2H, br, NH), 0.89 (2H, t, NHz), 1.70
(6H; t, Et), 1.88 (6H, t Et), 2.12 (6H, s, Me), 2.39 (2H, s, CH2N), 3.65

58

(6H, 8, Me), 3.88 ( 2H, q, Et), 3.97 (2H, q Et), 4.08 (4H, q, Et), 9.97 (1H,
s, meso), 10.16 (2H, s, meso), naphthyl: 7.52 (1H, d), 7.61 (1H, t), 7.77
(1H, t), 8.00 (1H, dd); 8.13 (1H, dd), 8.32 (1H, dd); MS, m/e (relative
intensity) 633 (M+, 2.56); UV—vis Kmax nm (EM) 625 (2100), 572 (6400),

538 (6500), 503 (15000), 405 (190000).

5-{8-[endo-7-(Hydroxycarbonyl)-I,5, 7-trimethyl-2,4-
dioxo-3-azabicyclol3,3,1]non-3-yl]-methyl-1-naphthyl}-
2, 8,1 3,1 7-tetraethyl-3, 7,12,18-tetramethylp0rphyrin (NKAP).

The Kemp’s imide-acid chloride was prepared as reported
previously5. 9 (57 mg, 0.09 mmol) was dissolved in freshly distilled
toluene (5 m1) and stirred under argon. To this solution, a catalytic
amount of dimethylaminopyridine (DMAP) and 2,6-di-t-butylpyridine (46
mg) and Kemp's imide-acid chloride (28 mg, 1.0 mmol) were added. The
mixture was refluxed under argon for 19 hours. The solvent was
evaporated and methylene chloride was added. Purification from
preparative TLC plate (silica gel, 1% CH3OH/CH2C12) and recrystallization
from CH2C12/CH3OH (3:2) gave 77 mg (75%) of NKAP. mp: 298°C dec;
1H NMR (300 MHz, CDCl3) 8 ppm 1.73 (6H; t, Et), 1.88 (6H, t, Et), 2.21
(6H, s, Me), 3.28 (2H, s, CH2N), 3.62 (6H, 5, Me), 3.82-4.08 (8H, m, Et),
9.93 (1H, s, meso), 10.19 (2H, s, meso), naphthyl: 6.67 (1H, d), 7.45 (1H,
t), 7.69 (1H, t), 7.78 (1H, dd); 8.04 (1H, d), 8.27 (1H, dd), Kemp's: -0.26
(3H, 8, Me), 0.23 (2H, d, CH2), 0.80 (6H, 8, Me), 0.88 (1H, d, CH2), 1.30
(2H, t, CH2), 1.63 (1H, (1, CH2); MS, m/e (relative intensity) 855 (M+,
7.86); UV—vis lmax nm (EM) 622 (2000), 570 (6300), 540 (6000), 507
(12000), 406 (140000).

59

5-{8-[endo- 7- (Methoxycarbonyl)-1,5, 7-trimethyl-2,4-
dioxo-3-azabicyclo[3,3,1]nan-3-yl]-methyl-1-naphthyl}-
2, 8,1 3,1 7-tetraethyl-3, 7,12,18-tetramethylporphyrin 10

N KAP (10 mg, 0.012 mmol) was dissolved in 10 ml freshly distilled
THF. 10 equivalents of fresh prepared diazomethane ether solution was
added and the mixture was stirred at room temperature for 30 minutes.
5% Acetic acid (1 ml) was then added to quench the excess diazomethane.
After THF was evaporated, the product was extracted with methylene
chloride and washed with saturated solution of NaHCO3 and water. The
removal of the solvent and recrystallized from CH3OH/CH2C12 (2:3)
afforded quantitative yield of 10: 1H NMR (300 MHz, CDCl3) 8 ppm -3.22
(2H, d, NH), 1.74 (6H; t, Et), 1.86 (6H, t, Et), 2.20 (6H, 5, Me), 3.56 (2H,
s, CH2N<), 3.63 (6H, 5, Me), 3.92-4.11 ( 8H, m, Et), 9.89 (1H, s, meso),
10.16 (2H, s, meso), naphthyl: 6.58 (1H, d), 7.46 (1H, t), 7.70 (1H, t), 7.82
(1H, dd); 8.08 (1H, d), 8.28 (1H, dd), Kemp's: -2.61 (3H, s, -OCH3), 0.13
(3H, s, Me), 0.44 (2H, (1, CH2), 0.92 (6H, 3, Me), 1.02 (1H, d, CH2), 1.66
(2H, t, CH2), 1.76 (1H, d, CH2); MS, m/z 869 (M, 58%); UV—vis lmax nm
(rel intens) 406 nm (1.00), 504 (0.09), 538 (0.04), 573 (0.04), 627 (0.01).

5-{8-[endo- 7- (Aminoearbonyl)-1,5, 7-trimethyl-2,4-dioxo-
3-azabicyclol3,3,1]non-3-yl]-methyl-1-naphthyl}-2, 8, 13,1 7-
tetraethyl-3, 7, 12, 18-tetramethylporphyrin 1 1

To a solution of NKAP (15 mg, 0.018 mmol) in 2 m1 dry methylene
chloride, oxalyl chloride (3 ml) was added. The mixture was stirred under
argon for 6 hours at room temperature. The excess oxalyl chloride was

pumped away by vacuum pump. Dry methylene chloride (20 ml) was

60

introduced to dissolve the compound and ammonia gas was bubbled in for
20 minutes. The solvent was evaporated and the residue was purified on a
preparative TLC plate (silica gel, 1% CH3OH/CH2C12) to give 14 mg (95
%) of 11: 1H NMR (300 MHz, CDCl3) 5 ppm -3.16 (2H, br, NH), -1.19
(2H, br, -CONH2), 1.75 (6H; t, Et), 1.89 (6H, t, Et), 2.22 (6H, 3, Me), 3.60
(2H, s, CH2N<), 3.64 (6H, s, Me), 3.94-4.11 (8H, m, Et), 9.93 (1H, s,
meso), 10.17 (2H, s, meso), naphthyl: 6.73 (1H, d), 7.49 (1H, t), 7.69 (1H,
t), 7.76 (1H, dd); 8.08 (1H, d), 8.30 (1H, dd), Kemp's: -1.19 (2H, s,
CONH2), -0.19 (3H, 5, Me), 0.32 (2H, d, CH2), 0.83 (6H, s, Me), 0.90 (1H,
d, CH2), 1.24 (2H, t, CH2), 1.65 (1H, d, CH2); MS, Hill 854 (M, 100%);
UV-vis lmax nm (rel intens) 407 nm (1.00), 506 (0.08), 540 (0.04),
570(0.04), 623 (0.01).

61

Eng m: «I o

rh__—_______—_______.______________._r_____L—__b__.___P—______._

.N oo 8.58% «22 E 3-: 23E

a

 

1;! a I- lb 411.

L. -

j

 

.U
C

j

 

 

:

m

3

 

 

2

 

 

v

m

m m

a - 1 -J

m

m

_

O“

p___—.__._

 

331

 

fit

 

 

62

.m Lo 8.58% mzz E .E.: an?
Egg w; u «I

C1 o d m m w o m m

L
__»r»_.ppc___r_r%~__m

m . m 0“

~—___—_~—_~__»—_mb_rrmb_mp_____.-

5 4112;? . - 33 - -

.
.~____»__——_

>—
y—
p...
b
p—
>—
H
L.

 

 

 

 

 

 

 

 

 

 

 

 

63

H 2% m

____H_~____+_~N

 

_»F_~_u—LH

... 8 858% 822 E 5-: 8:58

v

__W—~5__u___n__

3

D

 

 

 

L

l:
1141' 1‘!

m
H»H_N_,__ML..

r

m \

._______—_[rt_

*‘FI
4 ‘41 1‘

L~H__~_..

 

m m

____5__r_____~____

.m 8 8.58% 822 E 2-: 8888

2%. m- o m w m m 2

WIL_________pP______LPL_L_.._.__._Lp._____.____._._.p___.L_L__r_.r.__..

1.1 :1 A J - 131.- 53213 5.3%,- - -

 

 

 

 

 

 

 

 

 

 

 

 

 

65

8 8 8.58% :22 E .2: 888:

2% m: o m w

_l___L..___._bL.__._.____.p__....__L___

w a E

__L.___.»_.b.._.:_L...b..._...rr.

411-..- .8317 - .5 1%.

 

 

 

 

 

 

 

 

 

 

 

66

288 mu

_b_____~__._~:_»

.m 8 8.58% :22 :5 .57: 888:

o m

»_.~_.__»_»~_..»_.p.»

v

_..____:_____..~»..__

m

m . 2

.L_._....

n

u

 

 

g

3

DJ

 

 

 

 

 

‘

 

8.. :

 

 

 

67

.w 8 8.58% E .2: 888:

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

coflumgoagoo
pcmezgumcH umfioofiz
mmmmzszwi: ~88
com 0555 can“ ooom comm 848m 5885
.— b p — n b p F b _ r b — n p p b p p n — 0.0m
w r
m 1....
n
I x
a
5 - m
a r W
S
c 19.5 M
.n m .- 1 ll...
8 .8 .5 w v
.5 m a w - mm
mm .- .. 3
.818. a m } o...
a .2 I.
% 1.
.1585
mvdm

 

 

wqazfiw

68

.8 8 858% :22 E .8: 8882

v- 2;: m- o w v w m 3

—r»»n_:pppbP._P_h_LLr_FFL__.LLL_Lp.—»pr.rpp.__.-:»b..-P75~.LT.__P-.pp.b..

 

 

1.1%,- 1924 1 5:3. : -

 

 

 

 

 

 

 

69

v: 2% m:

___»»-__________..___L_rl_[Llp___

 

J

 

.322 .6 838% ~32 E .5: 2:3

o

3:;

 

:

 

 

m

3

 

 

9

 

v

n»_._._.__~bL»—»__.P.____F_Pp_p____._.p_L.

J

 

c m

 

fl

 

o“

 

 

j

 

7O

.2 .8 580% ~52 E .8.: 2&5

v: 23 m- o m w w c 3

rrlELlF_-rFLILL-L-t—:LIELI..___.h.b—p»_FP...__L.rbr__~_—?_p__p.._~_.F»—_.rb_pr

11.151le 11. 3 4 i jwdlfilfi

 

 

 

 

 

 

 

 

 

 

 

910

 

 

71

2% m:

o
L_P_L|_h__..___.hr.~.p»._._L__.F_._b__»__.»__._.L__..._._»Ptrp.Lpp._

I.III/\\x-nl|||av-llu.lb |J< 'llJ

.: Mo 8.58% mzz E .3: 05mm

o

1:22

 

 

2

 

 

m

3

 

 

‘1‘}.-th

 

 

v m

it

1.1.?

m

:3

 

 

3

__.

fill .

 

 

72

E. References

1. Chang, C. K.; Kondylis, M. P. J. Chem. Soc. Chem. Commun. 1986,
316-318.

2. Paine, J. B., H1, in "The Porphyrins", Dolphin, D. Ed.; Academic
Press, 1978. Vol. 1, p177

3. Chang, C. K.; Avilés, G.; Bag, N. J. Am. Chem. Soc. 1994, 116,
12127-12128.

4. a) Harris, R. L. N .; Johnson, A. W.; Kay, 1. T. J. Chem. Soc. (C)
1966, 22-29.
b) Dolphin, D.; Harris, R. L. N.; Huppatz, J. L.; Johnson, A. W.;
Kay, I. T. J. Chem. Soc. (C) 1966, 30-40.
c) Engel, J .; Gossauer, A.; Johnson, A. W. J. Chem. Soc. Perkin I
1978, 871-875.
(1) Pandey, R. K.; Zhou, H.; Gerzevske, K; Smith, K. M. J. Chem.
Soc. Chem. Commun. 1992, 183-185.

5. Aviles, G. M., "Interaction of Intramolecular Carboxylic Acid with
Heme-02 Complex", Ph.D. Dissertation, Michigan State University,

1991.

6. Rebek, J ., Jr.; Marshall, L.; Wolak, R.; Parris, K.; Kolloran, M.;
Askew, B.; Nemeth, D.; Islam, N. J. Am. Chem. Soc. 1985, 107,
7476-7481. '

7. a) Sandstrom, J. “Dynamic NMR Spectroscopy”. Academic Press:
New York, 1982, p97.

73
b) Cki, M. “Applications of Dynamic NMR Spectroscopy to Organic
Chemistry”. VCH Publishers: Deerfield, 1985, p 1-12.

Dahlquist, F. W.; Longmuir, K. J .; Du Vernet, R. B. J. Magn. Reson.
1975, 17, 406-410.

74

CHAPTER III

Hydrogen Bonding in Molecular Recognition: Inclusion
Complex and Substrate Recognition by C-Clamp Porphyrins

A. Introduction

Molecular recognition plays an important role in biological systems.
Highly specific interactions between proteins and ligands provide the basis
for protein function. There have been extensive studies focusing on the
design and synthesis of biomimetic host-guest systems that may provide
insights to biological processes.1 In efforts to mimic heme proteins,
numerous model porphyrins have been synthesized for studies of mainly
metal-centered interactions such as dioxygen binding.2 The porphyrin
macrocycle, despite the crucial biological functions of its metal derivatives,
usually does not have enough functionalized binding sites to interact with
substrates. However, the porphyrin ring can be easily linked to other
functional groups at the peripheral meso and B-pyrrole positions. Recent

advances in the synthesis of functionalized porphyrins have made it possible

75

to develop porphyrin-based receptors with a variety of sizes, shapes and
functional surfaces. The relatively rigid and disk-shaped porphyrins are
suitable to serve as frameworks in building molecular clefts that function
independently of the porphyrin. The presence of N-H protons or metal ion
at the porphyrin center can provide additional binding sites to aid the
complexation of guest molecules. The flexibility in design and synthesis
makes modified porphyrins useful not only in mimicking their biochemical
functions, but also in developing new types of receptors for artificial
molecular recognition. The mechanism which allows the binding of
specific ligand can be ascribed to hydrogen bonding, n-n stacking and
metal-ligand coordination. Various porphyrin receptors have been
designed for recognizing amino acids, nucleobase pairs, barbiturates and

polyols.3

In Chapter II, we already discussed the synthesis of a novel C-clamp
shaped molecular receptor in which a porphyrin ring is supplemented by a
carboxylic acid group pointing towards the porphyrin center. This acid
functional group combined with the pyrrole NH or metal ion of the
porphyrin furnishes a ditopic binding site capable of specific substrate
recognition. The combination of the Kemp's triacid and a naphthalene or a
anthracene connector thus gives a C-shaped receptor with a relatively rigid
acid hovering over the porphyrin. The C-clamp porphyrins have been
used to enhance 02 binding to the Co(II) porphyrin,4 which will be
discussed later in Chapter IV. In this chapter, the emphasis will be on the

formation of inclusion complexes with small neutral guest molecules.5 1

76

B. Experimental
1. Crystal Structure Analysis.

Data collection was performed on a Nonius CAD4 diffractometer at
room temperature using graphite-monochromated Cu Ka or Mo K;
radiation. The crystals used for analysis were of approximate dimensions
0.30 x 0.35 x 0.40 mm for NKAP and 0.40 x 0.40 x0.70 mm for
ZnNKAP. The unit cell parameters were determined by a least square fit
of 25 machine-centered reflections having 20 values in the ranges of 39.6-
44.4° for NKAP and 20.10-27.12° for ZnNKAP. The intensity data were
reduced and corrected for Lorentz and polarization factors using the
applied programs. Semiempirical absorption corrections were applied.
The crystal structures were solved by direct methods using the NRCVAX
program package. All non-hydrogen atoms were refined anisotropically.
The hydrogen atoms of the carboxylic group and methanol were located
from the difference map and refined positionally. All other hydrogen
atoms were calculated with fixed isotropic thermal parameters. The
highest difference Fourier peak was 0.31 and 0.35 e A‘3 for NKAP and
ZnNKAP, respectively. For NKAP, the final R is 0.047 and Rw is 0.044;
and for ZnNKAP, R and Rw are 0.040 and 0.042, respectively.

2. Determination of Binding Constants.

a) NMR Method. The receptor molecules N KAP, AKAP, ZnNKAP and
ZnAKAP (2-5 x 10'3 M in 0.8 ml CDCl3) were titrated with a solution of

the substrate (2-5 M) dissolved in CDC13 or methanol-d4. The downfield
shifts of the naphthyl and anthryl methylene protons linked to the imide

were monitored as a function of substrate concentration. Addition was

77

continued until up to 10-15 equivalents of the substrate have been added.

The resultant titration curve was analyzed by nonlinear regression
methods.6

b) UV-Vis Method. A similar protocol to a) was followed. The
increase in absorbance of the Soret peak of the molecular complex and the
decrease of the receptor Soret peak were monitored upon the addition of

substrate molecules.

c) DSC Method. DSC measurements were carried out for the NKAP-
HzO crystal under N2 with heating rate at 5 °C/min.

C. Results and Discussion

1. Structure of Receptors and Their Znic Complexes

The crystal structures of NKAP and ZnNKAP are shown by the
ORTEP drawings in Figures III-1 and 111-2, respectively. Crystal data and
refinement parameters are given in Table III-1. Table 111-2 lists the atomic
coordinates of non-hydrogen atoms. The data for selected bond distances
and angles for both compounds are given in Table 111-3. For both
compounds, the porphyrin structural features essentially remain

unchanged.

X-ray structure analysis of N KAP receptor showed a C-shaped
structure with the acid pointing towards the porphyrin (Figure II-l).4 The
cavity between the porphyrin and the acid is occupied by a water molecule
of crystallization. As shown in Figure II-2, there are multiple H-bonds that

brought about the water inclusion. To accommodate this H20 molecule,

the porphyrin ring undergoes several noticeable deformations at the

78

.omzdfiz .8 0828 2:32 as ea $55 3 .2: 05mm

‘

Hmuaww
0.
.§ mm) emu/a
m8 0» 5, 3
MHUQM \
3 S? i in... .
mmo.ma .m_ a
:0... .e.
a. mz
wNU OHQK. NZ

 

    

ea .
«Nu Ho mmu x
a _ .
3 t 2.... «:8
mags;
my. ./
m0 .l. NO “WW” 6 W". mmu
., hm. man.
«3 an...

79

.8858 mmUémU 05 258a 809936 wEBofi 33> 3522. 3

:m. €30N fl 5E8 55393 2: can cowzxo $83 05 :83qu

mosaic 2E. 40655-3 wage—mm 8225a 30-x 05 mo 32> 02m A8 .75 8:me

arm. www.‘

0e 0

003.3. .omr

 

.‘...OFO .. wro
7.0-0....0 0....0.‘

.0.
O .-
.. n.
< SN... .....<mm.m

a. e
97‘»...
0.0._0
0~ 70 .0

0 0 000 0 0

BC

          

 

 
     
 

 

 

80

.EOoz-m<MZ:N H8 080:8 $532 use 53 mmhmc A3 .N

.5 05mm
.954
fink

80m. $3

30AM“... B 61.. 302.80

         
       

    

ago .5

//// a

J. K

.5. 0..., . s
omO va / ® - mmO
m2 ‘ NO DVD

Bo «xv
. 80 2‘30
MO@MVO
80.... mm. a, $0
. .._=' me a... 4va
$0 kw Afiwkvlflbe

9.0 lMmemo

81

 

.wcfiaon c.8350 532809 05 m53oam Ems“ .8505 8on 33> 85 A3

._o:m5oE-m<MZ:N we 8825a 32-x 05 Co 32> 8% EV NA: 8:me

xx
$1322"

. .H. .mm.
aw“. . . 91...... xx“.

may

 

3v

82

 

 

Table III-1. Crystallographic Data of NKAP and ZnNKAP
NKAP ZnNKAP
Formula C55N505H63 ZnC56N505H63
fw 876.14 951.51
cryst syst monoclinic Triclinic
space group C 2/c PT
a, A 19.557(4) 9.1228(2)
b, A 11.954107) 11.789(9)
c, A 42.602(8) 23.583(5)
01, deg 90 7658(4)
[3, deg 105.201(17) 8683(2)
7, deg I 90 8828(4)
V, A3 9611(3) 2462.9(20)
Z 8 2
made), gem.3 1.211 1.283
LLcm'l 0.58 0.56
transm coeff 0974-09994 09629-09965
scan speed, deg min‘l 1.37-8.24 2.35-8.24

scan width, deg

no. of measd refins
no. of obsd reflns
no. of refined params
R, Rw

Gof

2(0.85 + 0.35tan0)
6008

4758 (I>20(I))
608

0.0047, 0.044

1.39

2(0.65+ 0.35tan0)
8662
5855(I>20(I))

609

0.040, 0.042

1.80

83

Table 111-2. Atomic Parameters x, y, z and Biso for NKAP
and ZnNKAP with E.S.D.'s. refer to the last digit printed

 

 

NKAP
x y z Biso
N1 0.81974(13) 0.27970(20) 0.13701( 5) 3.40(12)
N2 0.8511303) 0.25643(20) 0.07115( 6) 3.62(12)
N3 0.76212(13) 0.44434(21) 0.04749( 5) 3.53(12)
N4 0.73450(12) 0.47166(20) 0.11398( 6) 3.3101)
N5 0.55610(12) 0.2134209) 0.15560( 5) 3.10(10)
C1 0.80080(15) 0.30197(25) 0.16530( 7) 3.19(13)
C2 0.8360606) 0.2196 ( 3) 0.18915( 7) 3.53(14)
C3 0.87552(l6) 0.1533 ( 3) 0.17488( 7) 3.58(14)
C4 0.86535(15) 0.19145(25) 0.14188( 7) 3.40(14)
C5 0.89815(16) 0.1445 ( 3) 0.11993( 7) 3.72(15)
C6 0.8926906) 0.17341(25) 0.08793( 7) 3.58(14)
C7 0.9281707) 0.1185 ( 3) 0.06643( 8) 3.9505)
C8 0.9053407) 0.1681 (3) 0.03695( 7) 3.9805)
C9 0.8568606) 0.25603(25) 0.03987( 7) 3.5104)
C10 0.8215906) 0.3284 ( 3) 0.01580( 7) 3.53(14)
C11 0.7785306) 0.4167 ( 3) 0.01917( 7) 3.3903)
C12 0.7459107) 0.4964 ( 3) -0.00529( 7) 3.6705)
C13 0.7105306) 0.5708 ( 3) 0.00866( 7) 3.8505)

 

Table III-2 (cont'd)

84

 

C14
C15
C16
C17
C18
C19
C20
C21
C22
C23
C24
C25
C26
C27
C28
C29
C30
C31
C32
C33
C34
C35
C36
C37

0.7209105)
0.6949106)
0.7003105)
0.6700906)
0.6864006)
0.7278805)
0.75743( 14)
0.83102(20)
0.9252009)
0.99932(23)
0.97957(21)
0.92755(20)
0.98527(24)
0.75334(20)
0.8213 ( 3)
0.66651(20)
0.6302209)
0.67496(23)
0.66376(23)
0.7534205)
0.8089208)
0.8181 1(20)
0.7725909)
0.7132507)

0.53772(25)
0.5901 ( 3)
0.56221(25)
0.6251 ( 3)
0.5709 ( 3)
0.47243(24)
0.39216(24)
0.2024 ( 3)
0.0616 ( 3)
0.1014 ( 4)
0.0236 ( 3)
0.1440 ( 3)
0.2210 ( 5)
0.4964 (3)
0.5462(4)
0.6672(3)
0.7335 ( 3)
0.8333 ( 3)
0.6098 ( 3)
0.41373(25)
0.4764 ( 3)
0.4982 (q)
0.4542 ( 3)
0.3926 ( 3)

0.04230( 7)
0.06537( 7)
0.09775( 7)
0.11962( 7)
0.14874( 7)
0.14537( 7)
0.16893( 7)
0.22384 ( 8 )
0.19019 ( 8 )

0.20408 ( 12 )

0.07582(9)
0.00633( 8 )

0.00283( 11 )
-0.03951 ( 8 )
-0.04242( 11 )
-0.00752 ( 8 )

0.11179( 8 )
0.1251101 )
0.17786( 9)
0.20349 (7 )
O.22124(8)
0.25425( 8 )
0.26962 ( 8)
0.25261 (7 )

3.2903)
3.7004)
3.3503)
3.7604)
3.6904)
3.1303)
2.9602)
5.4109)
4.8807)
8.4(3)

5.67(20)
5.3509)
9.5(3)

5.0909)
8.8(3)

5.4108)
4.7507)
7.14(25)
6.23(22)
3.2803)
4.9307)
6.05(20)
5.2108)
3.9206)

 

Table III-2 (cont'd)

85

 

C38
C39
C40
C41
C42
C43
C44
C45
C46
C47
C48
C49
C50
C51
C52
C53
C54
C55
01

02

03

04

05

0.6660109)
0.6074109)
0.5939407)
0.6389105)
0.7013805)
0.6209505)
0.5634906)
0.4972108)
0.4341608)
0.4254406)
0.49196(16)
0.4145807)
0.4702407)
0.48519( 18 )
0.44276(22)
0.5363608)
0.50753(25)
0.36205(20)
0.6879506)
0.6214802)
0.4910102)
0.5350209)
0.5925803)

0.3512 ( 3)
0.2951 ( 3)
0.2746(3)
0.30858(24)
0.37104(24)
0.2808 ( 3)
0.0969 ( 3)
0.0256 ( 3)
0.0907 ( 3)
0.1997 ( 3)
0.2702 ( 3)
0.2702 ( 3)
0.0969 ( 3)
-0.0029 ( 3)
0.0540 ( 4)
0.1634 ( 3)
-0.0825 ( 3)
0.2661 ( 4)
0.2419 ( 3)
0.0571609)
0.3708608)
0.26306(21)
0.10340(21)

0.26961(7)
0.25414( 8)
0.22066 ( 7 )
0.20266 ( 7 )
0.21839( 7 )
0.15661 ( 7)
0.15819( 7)
0.14707( 8)
0.15122( 9)
0.13208( 8)
0.14426( 7)
0.09585( 8)
0.08750 ( 7 )
0.11068( 8)
0.05245( 9)
0.08684( 7)
0.1670801)
0.1366802)
0.07700( 8)
0.16892( 6)
0.14487( 6)
0.08102( 6)
0.09106( 7)

4.8908)
5.2609)
4.3906)
3.1703)
3.1603)
3.3903)
3.6505)
4.3606)
5.3909)
4.6006)
3.7604)
4.9507)
4.1905)
4.7207)
6.48(21)
4.4307)
7.23(25)
7.9(3)

8.7909)
5.2201)
5.0502)
6.0104)
6.3005)

 

86

 

 

Table III-2 (cont'd) ZnNKAP
x y z Biso

Zn 0.21688(4) 0.99502(3) 0.20191706) 3.083( 15)
N1 0.11388(24) 0.9541709) 0.2832800) 2.8801)
N2 0.0500(3) 1.11057(20) 0.1704101) 3.4501)
N3 0.3400(3) 1.0692409) 0.1272300) 3.3201)
N4 0.40098(25) 0.9112409) 0.2393300) 2.9000)
N5 0.1902(3) 0.48962(20) 0.3352202) 4.0603)
C1 0.1654(3) 0.89152(23) 0.3356902) 2.8303)
C2 0.0498(3) 0.88513(25) 0.3815703) 3.40(14)
C3 -0.0699(3) 0.9397(3) 0.3553004) 3.6006)
C4 -0.0291(3) 0.98464(24) 0.2947303) 3.2504)
C5 -0.1199(3) 1.0558(3) 0.2549405) 3.8606)
C6 -0.0847(3) 1.1161(3) 0.1987004) 3.7505)
C7 -0.1797(4) 1.1981(3) 0.1613005) 4.5207)
C8 -0.1016(4) 1.2410(3) 0.1112705) 4.7608)
C9 0.0432(4) 1.1849(3) 0.1167204) 3.9805)
C10 0.1560(4) 1.2010(3) 0.0745604) 4.2906)
C11 0.2947(4) 1.14885(25) 0.0788103) 3.7505)
C12 0.4119(4) 1.1659(3) 0.0335604) 4.3107)
C13 0.5266(4) 1.0963(3) 0.0550703) 3.9306)
C14 0.4799(3) 1.03586(25) 0.1137303) 3.5204)
C15 0.5648(3) 0.9549(3) 0.1514403) 3.5504)

 

Table 111-2 (cont'd)

87

 

C16
C17
C18
C19
C20
C21
C22
C23
C24
C25
C26
C27
C28
C29
C30
C31
C32
C33
C34
C35
C36
C37
C38

0.5295(3)
0.6269(3)
0.5576(3)
0.4146(3)
0.3075(3)
0.0503(4)
-0.2181(4)
-0.2310(5)
-0.3346(4)
-0. 1479(4)
-0.1186(7)
0.4033(5)
0.4659(6)
0.6736(4)
0.7755(3)
0.7703(4)
0.6201(3)
0.3538(3)
0.4298(3)
0.4734(4)
0.4324(4)
0.3508(3)
0.2993(4)

0.89722(24)
0.81650(24)
0.78370(24)
0.84476(22)
0.83959(22)
0.8331(3)
0.9552(3)
1.0607(4)
1.2298(3)
1.3353(3)
1.4562(4)
1.2453(3)
1.3622(4)
1.0808(3)
0.7798(3)
0.6845(4)
0.6948(3)
0.78687(24)
0.86005(24)
0.8287(3)
0.7246(3)
0.6471(3)
0.5436(3)

0.2087002)
0.2449803)
0.2983902)
0.2954102)
0.3412902)
0.4463605)
0.3837006)
0.40887(20)
0.1781009)
0.0604508)
0.06808(24)
-0.02657(15)

-0.03040(23)

0.0256205)
0.2253404)
0.1921007)
0.3483304)
0.4021402)
0.4266503)
0.4842304)
0.5183103)
0.4963203)
0.5345705)

3.1203)
3.1803)
3.0403)
2.7303)
2.6702)
5.1808)
4.8409)
6.98(24)
6.24(22)
6.53(22)
10.4(3)

5.95(21)
10.6(3)

5.29(20)
3.8205)
5.59(20)
3.9606)
2.8703)
3.3304)
4.0906)
4.1606)
3.6104)
5.1409)

 

Table 111-2 (cont'd)

88

 

C39 0.2183(5) 0.4688(3) 0.5149606) 5.99(21)
C40 0.1941(4) 0.4887(3) 0.45534( 16) 5.4009)
C41 0.2428(4) 0.58623(25) 0.4158503) 3.7105)
C42 0.3166(3) 0.67258(24) 0.4365902) 3.0403)
C43 0.2259(4) 0.59858(25) 0.3512904) 4.1106)
C44 0.0492(4) 0.4801(3) 0.3160905) 4.2707)
C45 0.0224(4) 0.3774(3) 0.2900205) 4.3307)
C46 0.1110(4) 0.2726(3) 0.3219907) 5.36(20)
C47 0.2729(4) 0.2989(3) 0.3152207) 5.1509)
C48 0.3036(4) 0.4064(3) 0.3373805) 4.7007)
C49 0.3226(4) 0.3252(3) 0.2507209) 5.89(22)
C50 0.2364(4) 0.4235(3) 0.2105806) 4.8709)
C51 0.0725(4) 0.4051(3) 0.22488(16) 4.8609)
C5 2 0.2734(5) 0.4187(4) 0.1465609) 7.6(3) .
C53 0.2788(4) 0.5458(3) 0.2124806) 5.38(20)
C54 -0.1416(4) 0.3536(3) 0.2960409) 6.27(23)
C55 0.3629(5) 0.1949(3) 0.34799(23) 8.6(3)
C56 0.0918(6) 0.8678(4) 0.1113708) 8.3(3)
01 0.1305(3) 0.8571108) 0.1679000) 5.1902)
02 -0.0425(3) 0.55350(20) 0.3196002) 5.9504)
03 0.4216(3) 0.42435(20) 0.3539901) 5.8304)
04 0.4203(3) 0.55604(24) 0.2200404) 7.8508)
05 0.1949(3) 0.62726(20) 0.2050303) 7.2406)
H01 0.159(4) 0.798(3) 0.1842(15) 8.400) .

 

89

Table III-3. Selected Bond Distances (A) and Angles (deg) and Their
Estimated Standard Deviations for N KAP and ZnNKAP.

 

 

 

NKAP ZnNKAP
Dime};
Zn-Nl 2.0482(24)
Zn-N2 2.063(3)
O(1)-HO(5) 201(3) Zn-N3 2.063(3)
Zn-N4 2.0578(24)
Zn-O 2.1587(24)
O(4)-HO(5) 1 .65 7(3)
Angles
N 1-Zn-N2 91.3600)
N1-Zn-N4 8745(9)
O(5)-HO(5)-0(1) 173(4) N2-Zn-N3 87.4400)
N3-Zn-N4 9063(9)

O(4)-HO(5)-O(5) 159(4)

 

90

naphthalene connector. Not only is the C20-C33-C42 angle at 126.54(25)°
larger than 123.5(6)° found in the parent naphthoic acid, but the porphyrin
plane also bends outwardly by as much as 9° from the C20-C33 axis
(Figure III-1c), resulting in a bigger “bite” than otherwise possible.
Laterally, the C20-C33 bond deviates from the naphthalene plane by tilting
about 6° in the C5 direction and is supplemented by further distortions at
C20 (the C19-C20-C33 angle of 117.57(25)° is larger than the C1-C20-C33
angle of 115.06(25)°), to displace the porphyrin core to the right (Figure
III-lb), presumably to achieve the best alignment with the water proton.
Despite this, it is significant that the imide-to-naphthalene linkage retains its
near perfect alignment and C2 symmetry (with only a slight rotation along
the C43-N5 bond). Undoubtedly, much of this rigidity arises from the
nonbonding interaction between the C43 methylene and the porphyrin

whereby the substituent at C43 obtains a predictable conformation.

The zinc complex of N KAP crystallized from methylene chloride
solution layered with methanol has a methanol molecule as axial ligand
with the O-Zn distance of 2.1587(24) A (Figure III-2a). The methanolic
proton is H-bonded to the carbonyl group of the Kemp's acid with a
distance of 1.98(3) A. In order to accommodate this H-bond, the
superstructure is twisted off center (Figure 2b). The naphthalene spacer
and the porphyrin ring also distort severely from the ideal C20-C33 axis
(Figure 2c). The "jaw-opening" observed in ZnNKAP is even greater than
that in the free base N KAP.

In both structures, the porphyrin skeleton remains essentially

unchanged. The X-ray structures clearly indicate that the NKAP system is

91

ideal for binding small, preferably monoatomic substrates. By inference
supported by molecular modeling, the AKAP compounds with a greater
porphyrin to acid distance should serve as good receptors for larger

substrates.
2. Substrate Binding Studies

The magnitude of molecular inclusion is followed by 1H NMR

studies, UV-vis spectroscopy and differential scanning calorimetry.
a) Substrate Binding of Metal-free Systems

The magnitude of molecular inclusion was followed by 1H NMR
titration cam'ed out in CDC13. Upon stepwise addition of guest molecules
into the porphyrin solution, all the protons of the Kemp's acid
superstructure exhibited downfield shift due to less diamagnetic ring
current. This downfield shift suggested that upon binding of the guest
molecule, a "jaw-opening" motion occurred at the porphyrin-spacer I
conjunction. On the other hand, along this motion, the naphthyl proton on
C34 experienced an upfield shift due to the tilting of naphthalene, bringing
this proton closer to the porphyrin. A similar shift was also observed for
the corresponding proton on anthracene in AKAP. The binding constants
were derived from the chemical shift of naphthyl or anthryl methylene
protons as well as by distinctive shifts of other protons during the titration

process.

For studying the H20 binding to NKAP, it is crucial that all reagents
and the NMR tube are as anhydrous as possible. The binding of water to I
N KAP is strong enough that the saturation point can be reached before the

92

solubility of water in CDC13 becomes a problem.7 Figure III-3 displays
1H NMR spectra showing the chemical shift of the naphthyl methylene

proton at varying concentrations of water.

The DSC (differential scanning calorimetry) analysis was also
applied to the solid crystals of NKAP-H20. The DSC (Figure III-4)
showed two endothermic peaks, with the first one attributable to
dehydration and the second peak coinciding with the melting of the
compound. Continuous heating led to decomposition. The heat flow
associated with the first peak is 18.76 J g'l, indicating that the water
binding energy is about -15 i 1 k1 mol'l.

For the AKAP binding of imidazole or purine, the interaction
presumably relies on multipoint recognition as depicted by the computer
model (Figures 111-6, 7). The titration (Figure III-5) data give a 1:1
complex with binding constants of 2550 and 2600 M"1 for imidazole and
purine, respectively. As purine is a weaker base than imidazole (Table III-
4), the comparable binding strength of the two bases suggests that the
intrinsic basicity is not the determining binding force. In our systems, 1t-1t
interactions between the guest and host molecules need not to be
considered. Therefore, the attractive forces solely come from the H-

bonding network.

93

 

 

 

 

d: 0.047 M .

1
c: 0.037 M

1
b: 0.022 M .
“CHIN/
a: 0.000 M ' \
("W

4.2 4.0 3.8 3.6 3.4 3.2 Ppm

[NKAP] = 3mM

Figure III-3. 1H NMR titration of H20 into NKAP. [NKAP] = 3 mM,
[H20] in a: 0.000; b: 0.022; c: 0.037; d: 0.047 M.

94

cow

.onEoo $33-3 Z We 32:23on UmQ .35 2an

omm . cam

68 838388.

93

P p

0%

02

OS

 

 

 

¢

$8.8

83.02:

 

 

(film) mom 19911

95

-m C .2803: w=m3o=£

05 E :32? 8 65225.3 :6 .5on .Eqn v.o_-c.o 5
V2836- .88 3.3 a
w 6333.88 thoM so £585 .83 m.~..o.o E Amt—mom 93an 3883
.2 Emmd 6 ”2 $86 no
”2 $86 ”a ”E 9806 ”a E 35.2 0586
"$53 .652 8 888:. 882E 8 ”:22 m. .2: 8:me

97

 

 

0.5
C
_ LO
_ . 1'.—~ (.3.3: . 4. ‘ \. ‘(.‘.-’
0.1 l \
. O . ..

 

 

0.0 1.1.1....1....1....1....1..1.1....1
0.0 0.5 1.0 1.5 2.0 2.5 3.0 3.5
[Im]x10-2

Figure III-6. Schematic structure of AKAP-imidazole and plot of the anthryl

methylene protons as a function of concentration of imidazole

in CDCl3.

98

0.20 .—
015 b

0.10 '

A5 ppm

0.05 h

 

 

 

0.0 0.2 0.4 0.6 0.8 1.0 1.2
[Purine] x 10-2

Figure III—7. Schematic structure of AKAP-Purine and plot of the anthryl

methylene protons as a function of concentration of purine.

99

 

com 8.. 88 E 65:5 6.8.02

 

cm H ommm 0.5 2082:: EU?
3 H co 7 ONE A<MZ
3.3: «M «Mm 393 68:35 aoaooom

 

.moaabmnsm 2:3 532 98 m<M Z Sm £52350 £85838. 4i: 2an

100

b) Substrate Binding of Zinc Porphyrins

In order to estimate how much stabilization energy the C-clamp acid
group can impart to metalloporphyrin-ligand binding, we examined the
zinc porphyrin as a model. The same protocol of 1H NMR titration as
mentioned previously was used for the C-clamp zinc porphyrin systems. A
typical NMR titration of ZnNKAP-MeOH is shown in Figure III-8. For
the control study using ZnOEP (octaethylporphyrin) whose guest-host
interactions cannot be easily followed by 1H NMR, UV-vis spectroscopy
was used to monitor ligand binding. The binding constants of these systems
are listed in Table III-5.

Methanol ligation to zinc porphyrin has been well studied.3k
ZnNKAP binds MeOH stronger than the unfunctionalized ZnOEP (AAG =
3.1 k] mole-1) due to the additional binding force derived from the H-
bonding clearly shown in the crystal structure.

DMF is often employed as solvent for heme model studies and
knowledge of DMF binding would be useful. However, DMF titration of
ZnNKAP monitored by either 1H NMR or UV-vis failed to show any
evidence for enhanced binding. This may be due to both steric and
electronic factors. DMF coordination to metalloporphyrin through the
oxygen lone pair would induce the N-methyl groups to bump into the
pendant acid group; coordination to zinc also reduces the electron density
on the amide oxygen for which H-bonding must compete. The binding
constants of ZnOEP and ZnNKAP are practically the same as DMF can
bind to zinc from the unhindered side.

101

 

 

Figure III-8. 1H NMR titration of methanol to ZnNKAP.
[ZnNKAP] = 0.014M and [MeOH] in a: 0.000;
b: 0.013; c: 0.032; d: 0.064; c: 0.132; f: 0.395 M.

102

«W.

L

M!“

 

 

 

 

J beu .

 

LL

 

 

 

 

ll
, ll
JUL L JJUL

Jam
“Mug

 

If
. 1.5ppm

 

 

103

 

~o~o§5-m.~; as we

 

 

 

 

 

 

Emofi 3 mm 82 H 253 3 aoafiéfi m<M<=N
ESHEAHJ E 2 cu H 8m 3 o_o§E+.m._ mmofi
Emofi m5 3 E H 88 3 2333-3; SEN
cm H o: 3 0833-3; mmofi
H H m l ”:5 325
a H w E29 .503
mmofi 22H. m H mm - moo: .hlmfizfi
a H h - moo: .505
A12: 3503 9.3: «M «Ma ovam oambmnsm Banana
3:55 9a :00: 55

matznaoaéN no 353280 :ouamoomm< .mA: Bash

104

The most dramatic effect in molecular inclusion has been seen in the
case of triazoles. 1,2,4-Triazole, being a weaker base (pKa 2.3)8 than
imidazole, is normally not a strong ligand for metalloporphyrins. But
ZnAKAP maximizes the binding by a three-point contact as depicted in the
schematic structure (Figure 111-9). The binding constant is 21,000 i 1000
M4, with a free energy gain of 9.9 U mol'l. 1H-l,2,3-triazole, capable of
only a two-point interaction, displays a significant decrease in binding
energy (AAG 4.8 k] mol'l). The binding of 1,2,4-triazole was conducted
by adding aliquots of concentrated CD3OD solution of the base to the zinc
porphyrin dissolved in CDC13 due to insolubility of the base in pure
CDC13. The 1,2,3-triazole study was measured in pure CDC13, and the
energy gain is 9.4 k] mol-l, even in the presence of small amount of
methanol employed to improve solubility. However, the 1H—1,2,3-triazole,
capable of only a two point interaction, displays a significant decrease in
binding energy (AAG 4.5 k] mol'l). The binding of l,2,3,-triazole was
tested in the condition of dissolve all reagents in CDC13, as well as in the
condition that very concentrated 1,2,3-triazole in CD3OD titrated to zinc
porphyrin CDC13 solution. Both experiments gave the same binding
constant within the margin of experimental error. The CD3OD actually
acts more as solvent than binding competitor due to its relative small
binding constant. The binding selectivity of ZnAKAP over different

tn'azoles may be a useful way to separate such heterocyclic bases.

105

.2§E-n~.§§<§ 3V asafiéfidfig 3 .3: 2:5

I r/IIVJNM m. N ,Imhmll
" /. n F
S _.
z / y
m. 2-2
I” Hm I aw.“
O I
Jxo @ 04mg

106

3. Discussion

The X-ray structure of the NKAP-H20 complex allows a rare
opportunity to examine the geometry of the acid-H20 interface. Ab initio
calculations of benzoic acid monohydrate predict two possible
conformations, syn and anti, with the syn being the more stable form.9
The optimized geometric distances and angles are shown in Figure 111-10.
The salient feature is that the H-bond COH---O is slightly shorter and less
bent than the C=O---H bond. The NKAP-H20 clearly displays a syn
conformation with a slightly shorter and near linear COH----O and a more
bent H-bonding for the carbonyl group. The agreement between our
structure and the theoretical model seems excellent given the other

constraints that the water has to meet within this artificial molecular cleft.

Molecular inclusion in C-clamp porphyrins is brought about by
multiple H-bonding. It is always interesting to identify the contribution of
each individual hydrogen bond within the overall free energy of
complexation. Selective removal of certain H-bonding participants from
either the receptor or the substrate has been an important tactic in
addressing this question. However, H-bond obliteration studies of this type
must be treated with caution since other changes in the molecular
properties, such as basicity and conformation, may contribute to the
differences in binding energy. A comparison of ZnOEP vs ZnAKAP
binding of 1,2,3-tn'azole provides an estimation of the magnitude of H-
bonding strength of acid C=O---H. The energy difference here is 7.8 It]
mol'l. This AAG may be compared to the 3.1 kJ mol'1 observed in MeOH
binding to ZnNKAP vs ZnOEP. The difference clearly has something to
do with the acidity of the proton (NH vs OH). Another useful comparison

107

.oNHHHHfiHz ..Ho 2325... H530 0H?” 3-x 3H5 He

.moHHHHHHEoHHoE Eon F3 hHo 0.58:5 333030 3 .oTE Eswfi

H 6::

oodi .

       

  

. oN.mNH
I EH.

SH

E?

I

. . 0
H232: H.... NH: ow.2H-o~.mmH

1.52%.? H_H. ...,H. RH .33 H
0

%. va

108

is the 3-point (1,2,4-tn'azole) vs 2-point (1,2,3-tn'azole) contact. The AAG
value of 4.8 kJ mol-1 arises from more than just the extra H-bond. The
basicity difference of the two triazoles has significantly influenced the Zn-
N bond (2.7 k] mol'l) whereas its effect on the NH---O=C is possibly very
small.

D. Conclusion

In conclusion, the functionalized porphyrin receptors, NKAP, AKAP
and their zinc complexes, are capable of binding and recognizing various
small neutral molecules. The shape and rigidity of the superstructure
porphyrin make possible some very effective complexation of substrates
through multipoint recognition. The selectivity demonstrated by ZnAKAP
suggests possible applications for the separation of heterocyclic bases. It is
also possible to further modify the overhanging carboxyl group to effect

more sophisticated substrate binding and recognition.

109

E. References

1. Ciba Foundation Symposium, "Host-Guest Molecular Interactions:

From Chemistry to Biology", 1991, John Wiley & Sons.
2. Momenteau, M.; Reed, C. A. Chem. Rev. 1994, 94, 659-698.

3. a) Lindsey, J. S.; Kearney, P. C.; Duff, R. J.; Tjivikua, P. T.; Rebek,
J., Jr. J. Am. Chem. Soc. 1988, 110, 6575-6577.
b) Aoyama, Y.; Yamagishi, A.; Asagawa, M.; Toi, H.; Ogoshi, H. J.
Am. Chem. Soc. 1988, 110, 4076-4077.
c) Ogoshi, H.; Hatakeyama, H.; Yamamura, K.; Kuroda, Y. Chem.
Lett. 1990, 51-54.
(1) Imai, H.; Nakagawa, S.; Kyuno, E. J. Am. Chem. Soc. 1992, 114,
6719-6723.
e) Slobodkin, G.; Fan, B.; Hamilton, A. D. New J. Chem. 1992, 16,
643-645.
D Hayashi, T.; Miyahara, T.; Hashizume, N.; Ogoshi, H. J. Am. Chem.
Soc. 1993, 115, 2049-2051.
g) Mizutani T.; Ema, T.; Tomita, T.; Kuroda, Y.; Ogoshi, H. J. Am.
Chem. Soc. 1994, 116, 4240-4250.
h) Kuroda, Y.; Ogoshi, H.; Synlett. 1994, 319-324.
i) Kuroda, Y.; Kato, Y.; Ito, M.; Hasegawa, J .; Ogoshi, H. J. Am.
Chem. Soc. 1994, 116, 10338-10339.
j) Shipps, G., Rebek, J. Tetrahedron Lett. 1994, 35, 6823-6826. .
k) Bonar-Law, R. P.; Snaders, J. K. M. J. Am. Chem. Soc. 1995, 117,
259-271.

110

Chang, C. K., Liang, Y.; Avilés, G.; Peng, S.-M. J. Am. Chem. Soc.
1995, 117, 4191-4192.

Liang, Y.; Chang, C. K. Tetrahedron Lett. 1995, 36, 3817-3820.

a) Wilcox, C. S. in "Frontiers in Supramolecular Organic Chemistry
and Photochemistry", Schneider, H.-J., Durr, H., Eds.; VCH:
Weinheim, Germany, 1990, 122-143.

b) Wilcox, C. S., Cowart, M. D. Tetrahedron Lett. 1986, 27, 5563-
5566.

Staverman, A. J. Reel. Trav. Chim. 1941, 60, 836-841.

Albert, A. "Heterocyclic Chemistry", 2nd Ed., Oxford University
Press: New York, 1968, 441.

Nagy, P.; Durant, G. J .; Smith, D. A. in "Modeling the Hydrogen
Bond", Smith, D. A., Ed., American Chemical Society, Washington,
DC, 1994, 60-79.

111

Chapter IV

Conformational Control of Intramolecular Hydrogen Bonding
in Heme Models: Maximal Co(II)-()2 Binding in

Naphthalene Kemp's Acid Porphyrin

A. Introduction

Hydrogen bonding plays a crucial role in heme protein reactions. In
myglobin (Mb) and hemoglobin (Hb), the interaction between the distal
histidyl proton and the heme-bound 02 has been identified as the most
significant factor controlling 02 binding.1 In catalase and peroxidase, H-
bond polarizes the peroxy group to facilitate a heterolytic O-O bond
cleavage.2 Likewise, in cytochrome a3, the presence of proton donor is an
integral part of 02 reduction.3 The study of H-bonding effects, therefore,
is always a focal point in heme model chemistry. In early times, such
studies were mainly confined to intermolecular interactions such as Solvent
effects, but more recently, synthetic models equipped with intramolecular

proton donors have emerged.4-8 While these models clearly established the

112

positive effect of enhancing 02 affinity, they did not permit a closer look at
how structural and steric perturbations made by the proton donor would
influence the heme-substrate reactions. For example, from X-ray9 and
neutron diffraction10 data, it has been noted that the H-bonding between the
distal histidine and Fe-02 in Mb and Hb is an oblique one,7 raising
possibilities that the proton could interact with both 01 and 02. Most
model systems available to date, as exemplified by the naphthoic acid
porphyrin (NAP),5 have the H-bond at O; in a stretched-out, coplanar Fe-
Ol-Ozu-H. Model NAP also has a fatal fault as it undergoes an unusual
ring degradation giving rise to an oxaporphyrin.11 In an effort to address
the H-bond conformation issue and to sidestep the metabolism of NAP,
NKAP and AKAP12 were designed and synthesized in which the proton

donor is overhanging above the heme binding site.

The result of 02 binding affinity of Co(II)NKAP will be compared
with that of Co(II)AKAP and Co(II)NAP in this chapter. Conformational
information then can be obtained about H-bonding effect on 01, or 02
which affects the 02 affinity for heme proteins. Additional information
from 15N N MR of Fe(CN)2 porphyrins provides further support to our
conclusion about H-bonding effect.

B. Experimental
(1) Cobalt insertion

The synthesis of the naphthalene Kemp's Acid Porphyrin (NKAP)
and its derivatives is described in Chapter 11. Cobalt ion was inserted into
the porphyrins by heating a methanol solution of cobaltous chloride

together with a dichloromethane solution of the free-base porphyrin

113

containing a trace amount of sodium acetate. Co(II) complexes were
precipitated by graduate evaporation of dichloromethane. Water was
added and CHzClz was used to extract the cobalt porphyrin. Pure cobalt
porphyrin was then obtained after the solvent was removed by rotary

evaporation under aspirator vacuum.
(2) 02 Binding studies

The dioxygen binding experiments were conducted by using fresh
inserted Co-complexes. The Co-porphyrins (0.5 mg) were dissolved in
CH2C12 (5 ml) and the solution was degassed by passing argon through it
for 30 min. The solution was then transferred to a gas-tight syringe
containing a degassed solution of sodium dithionite in water. The reduced
Co(II) porphyrins were injected to a 60 ml tonometer and redissolved in
freshly distilled DMF (4 ml) The mixture was degassed 3-7 times by

freeze-pump-thaw cycles at around 10'5 torr.

Oxygenation was monitored spectrophotometrically at several
temperatures. The low temperatures were achieved by immersing the
tonometer in a dewar filled with liquid propane (b.p. -42°C), liquid Freon
12 (b.p. -30°C), slush bath of benzyl alcohol (-l7°C) or water/crushed ice
(0°C). The dioxygen adducts were stable at -42°C but underwent auto
oxidation rapidly at room temperature (t1 /2 at 0°C in most cases were about
4 min). The dioxygen affinities were determined by direct titration of
Co(II)porphyrin with pure 02 or fresh air, using a standard
spectrophotometn'c procedure used by Halpem and coworkers. 13 A typical
titration spectrum is shown in Figure IV-l. After each injection of pure

oxygen or fresh air, the solutions were allowed to stand for about

114

Figure IV-l. Typical 02 titration spectra of Co(II)porphyrins.

 

 

 

 

 

 

A/nm

116

2 minutes to reach equilibrium before the spectra were measured. The
solubility of 02 in DMF at low temperature is not determined and all the
equilibrium constants are calculated at the standard state of 1 torr. The
titration curves typically had correlation coefficients of 0.990 to 0.999 and
varied between experiments by less than 15%. The equilibrium constants
shown in Table IV-l are the average of 2-4 runs. Since the UV-vis
spectrum of the oxygenated complexes is very similar with that of the
oxidized Co(III) complex, the solution of 02 complex was pumped again
after the titration in order to obtain the original spectrum of Co(II)

porphyrin. This process also proved that no oxidation had taken place

during the 02 titration.
(3) Iron insertion

The typical ferrous sulfate method was used for Fe(III) insertion.”
Free base porphyrin (10 mg) was dissolved in 30 ml mixed solvent of
acetic acid: pyridine (20:1). This porphyrin solution was placed in a pear-
shaped flask with a gas inlet tube. Argon was passed through the gas inlet
to the solution and the mixture was heated on a steam bath to 80°C. A
saturated aqueous solution of ferrous sulfate was added by a syringe into
the reaction system through the gas outlet side arm. The temperature was
then raised to 90°C for half an hour. The argon flow was terminated and
the mixture was allowed to cool down to room temperature. A stream of
air was introduced upon the cooling to allow the auto oxidation of the
unstable Fe(II) porphyrin complex. Water was added and the porphyrin
was extracted by CH2C12. Purification from column gave the u-oxo dimer
which was then washed with 5% HCl solution to generate Fe(III) porphyrin

chloride.

117

(4) 15N NMR studies

The 15N NMR measurement was performed by dissolving 3-5 mM
high-spin ferric porphyrins in 0.75 ml DMSO-d6. A 10-fold excess of
KC15N (98%, Icon Inc.) was added to this porphyrin DMSO solution and
color change was observed instantly. The 15N NMR was collected on a
Varian VXR 500 spectrometer. The sweepwidth for a normal 15N
spectrum is 100 MHz. A 200 [is delay prior to acquisition serves to
diminish acoustic probe ringing. At room temperature, spectra of Fe(CN)2
porphyrins usually require 30,000 to 80,000 scans. The chemical shift of
the Fe bound C15N was recorded with excess KC15N as the reference peak
set at -100 ppm.

C. Results and Discussion
1. Oxygen Binding

To measure 02 binding, both Co(II) and Fe(II) have been tested, but
Fe(II)NKAP proves to be too labile even at -42°C. The 02 adduct of
Co(II)NKAP is much more stable with DMF serving as solvent and weak
trans-ligand.15 Appreciable auto oxidation does not occur below -20°C
and W2 at 0°C is about 4 minutes. Reversible Oz binding of Co(II)NKAP
was studied spectrosphotometrically in a tonometer at several temperatures
(-42°C, -30°C, -17°C and 0°C). Thermodynamic parameters (AH and AS)
were then derived from the van't Hoff plot (Figure IV-2). Table IV-l
summarizes the 02 binding parameters of several relevant models,

including NKAP, AKAP, NAP and equine myoglobin.18

118

.AQHQCHHA m> .5: mo 83 to: H.§> .~->~ ostE

pa no: .5
3. 3 Ne He 4 m.m m.m E Q».

—dqdu—-dq4—.4—qfiu——-—1fi_-1—H-u——__dfi.—~ddd o

 

 

LJlllLllllllllJlll1111111

m
.3 m H 9.- u 2 HHOEHHSVH NH H EH- u :<

119

 

 

 

 

 

 

 

ow. m. H H- hm mm 23:33.: £200
8% $1 .32 a. .392 Ho 52m 0:
86 c
on- WE- vmd 5.
god NV-
md H in NV.
H8 8
omo H wmd o
mHov. ~.HHv.HH- NodHHHd 2.
wood H wNod 0m-
Hood H mood NV.
3.83 2858534 9.8.5 Sm 60:. HHHHHHoHHEoU

 

.EHSHeoHHHHHVou 2 eoHoEaanH $6ch No .3: 22$

120

The Oz affinity was evaluated by P1/2. As shown in Figure IV-3, for
the equilibrium of the 02 binding, the binding constant is described in
equation I. When half of the Co(II) porphyrin is coordinated, the pressure
of 02 added is termed as P1 /2. The binding constant is then derived as
reversely proportional to P1 /2. The lower the P1 /2 is, the higher the Oz
affinity will be.

The P1/2 obtained at -42°C from Co(II)NKAP is an all-time record
for Co(II) porphyrin models. It is at least three times better than that of
Co(II)NAP reported previously.5 The 5x104-fold enhancement from the
ester to acid is truly dramatic. The affinity is even higher if a stronger
trans ligand is present.16 In the anthracene case, the enhancement is less
impressive. The increase from ester to acid is only about 102,
demonstrating the importance of the distance and geometry of the proton
donor. This difference may be due to a mismatch of the geometry and/or
increased motion of the pendent group. The difference between the
Co(II)NKAP and Co(II)NAP at first seems hard to reconcile. Even if the
previous P1/2 of Co(II)NAP at 0°C is given a tenfold reduction,17 the
adjusted AH and AS are still much more negative than Co(II)NKAP. We
believe that the disparity is caused by the mode of H-bonding. In
Co(II)NAP, the coplanar and inflexibile Fe-O-OmH has the highest gain in
AH but suffers the highest loss in AS.

As already discussed in Chapter ID, the C-clamp NKAP is ideal for
biting a monoatomic ligand. Therefore, in Co(II)NKAP, the H-bond
would aim at 01, which may not be good for best gain in AH but is
conformationally less restrictive for the chelated 02. Thus, the smaller

121

.Q—& .«o :OEGQQU 05 93 mamas NO 2939/2 mo comuwzvo 2E. .mnz ouswmnm

 

 

 

 

 

MHHHHHHHHHHEAHSH n HEEEOHHNOHSH

335280 HHHHEEon—ou 05 we be: :23?

 

 

 

a 8H HHHHHEHWoHoB u M
HEEEOAHHNQSH
:tzseeA—ANOVHHU NO + 5.39.530

v—

122

loss in AS is apparently more than enough to compensate for the enthalpic

loss to afford large binding constants throughout the temperature range.4a
2. Further information from 15N NMR

To lend further support to our contention that NKAP disfavors the
open end of diatomic ligands, 15N-NMR was used to probe the ligand
environment.19 H-bonding is known to cause a large upfield shift of the
15N signal for (C 15N)2Fem porphyrins, due to reduced spin transfer from
iron to cyanide.20 The 15N chemical shift of the iron cyano porphyrins is
tabulated in Table IV-2. Typical porphyrin complexes such as OEPhemin
(Table IV-2), in DMSO containing tenfold excess of KC15N, exhibit one
single peaks around 8 720. With the anthracene AKAP, which should
clamp down a CEN well if the acid group is in place, biscyano-FeAKAP
has two peaks at 5 622 and 490. When the -C02H is reduced to -CH20H,
the corresponding peaks become 5 701 and 657. The more upfield signal is
due to the H-bonded CN which weakens the axial ligand field and
simultaneously shifts the trans ligand signal. The spread between the two
signals becomes smaller as the H-bond becomes weaker. With NKAP, the
(C15N)2FeNKAP shows two peaks at d 715 and 670, suggesting a quite
ineffective H-bond to this cyano nitrogen. Using Figure IV-4 as a model,
an iron-bound CN would place the N at X - a very awkward position to
align with the proton. Replacing the linear CN by a bent O=O would not
give a better OZmH-O alignment without first requiring severely twisting
the acid group off center (estimated C43-N5 rotation of at least 40° for an
optimum H-bond). While such rotation may still happen, the more likely

H-bond in our model is an oblique interaction toward the n-bond or both

Table IV-2. 15N NMR chemical shift of Fe(CN)2porphyrins

 

FePorphyrin

 

8 (ppm)

720

x=coon 622, 490
X=CH20H 701,657

715, 670

124

 

.
/ 121.810
('0
..
o

 

Figure IV-4. Side-view of N KAP-HzO complex.

125

01 and 0;, if the X-ray structure is any indication.
D. Conclusion

This study demonstrates conformational control of the distal H-
bonding effect in the heme-02 reaction; it highlights the fact that due to the
entropic factor, a high 02 binding constant is not necessarily the result of
an ideal Fe-O-O---H interaction. Rather, the binding is always enhanced
with less restrictive H-bond(s). The CoNKAP is an attractive
electrocatalyst for 02 reduction. The preferential H-bonding with
monoatomic ligand also makes N KAP an excellent model for studying

ferryl heme intermediates. These results will be discussed in Chapter V.

126

E. References

1. (a) Mims, M. P.; Porras, A. G.; Olson, J. S.; Noble, R. W.; Peterson,
J. A. J. Biol. Chem. 1983, 258, 14219-14232.
(b) Rohlfs, R. J .; Mathews, A. J .; Carvert, T. B.; Olson, J. S.;
Springer, B. A.; Egeberg, K. D.; Sligar, S. G. J. Biol. Chem. 1990,
265, 3168-3176.

2. Poulos, T. L.; Kraut, J. J. Biol. Chem. 1980, 255, 8199-8205.
3. Babcock, G. T.; Wikstrom, M. Nature, 1992, 356, 301-309.

4. (a) Momenteau, M.; Reed, C. A. Chem. Rev. 1994, 94, 659-698 and
references therein.
(b) Jameson, G. B.; Ibers, J. A. Comments Inorg. Chem. 1983, 2, 97-
126.

5. (a) Chang, C. K.; Traylor, T. G. Proc. Natl. Acad. Sci. USA. 1975,
72, 1166-1170.
(b) Chang, C. K.; Ward, B.; Young, Y.; Kondylis, M. P. J. Macromol.
Sci-Chem. 1988, A25, 1307-1312.
(c) Chang, C. K.; Kondylis, M. P. J. Chem. Soc. Chem. Commun.
1986, 316—318.

6. Momenteau, M.; Mispelter, J .; Loock, B.; Lhoste, J .-M. J. Chem. Soc.
Perkin Trans. I 1985, 61-69 and 221-231.

7. Wuenschell, G. B.; Tetreau, C.; Lavalette, D.; Reed, C. A. J. Am.
Chem. Soc. 1992, 114, 3346-3355.

10.

11.

12.

13.

14.

15.

16.

127

Collman, J. P.; Zhang, X.; Wong, K.; Brauman, J. I. J. Am. Chem.
Soc. 1994, 116, 6245-6251.

(a) Shaanan, B. Nature( London ) 1982, 296, 683-684.
(b) Condon, P. J .; Royer, W. E. J. Biol. Chem. 1994, 269, 25259-
25267.

Phillips, S. E. V.; Schoenborn, B. P. Nature(London) 1981, 292, 81-
82.

Chang, C. K.; Avilés, G.; Bag, N. J. Am. Chem. Soc. 1995, 116,
12127-12128.

Avilés, G. “Interaction of Intermoleculaar Carboxylic Acid with

Heme-02 Complex”, Ph.D. Dissertation, Michigan State University,
1991.

Marzilli, G. L.; Marzilli, P. A.; Halpem, J. J. Am. Chem. Soc. 1971,
93, 1374-1378.

Chang, C. K.; DiNello, R. K.; Dolphin, D. Inorg. Chem. 1980, 20,
147-155.

Brinigar, w. 3.; Chang, C. K. J. Am. Chem. Soc. 1974, 96, 5595-
5597.

Due to complications involving 6-coordinate competition and technical
problems in measuring such small P1 /2 (requiring proportionally
larger tonometer) at low temperature, only the DMF results are

presented.

17.

18.

19.

20.

128

The 02 affinity of Co(II)NAP at 0°C is subject to a high degree of
uncertainty due to additional complications brought about by the

catabolic reaction.11 During re-examination, the P1 /2 at 0°C could be

as low as 5-10 torr which is included in Table IV-l.

Spilburg, C. A.; Hoffman, B. M.; Petering, D. H. J. Biol. Chem.
1972, 247, 4219-4223.

Avilés, G.; Chang, C. K. J. Chem. Soc. Chem. Commun. 1992, 31-32.

(a) Behere, D. V.; Gonzalez-Vergara, E.; Goff, H. M. Biochim.
Biophys. Acta 1985, 832, 319-323.

(b) Morishima, 1.; Inubushi, T. J. Am. Chem. Soc. 1978, 100, 3568-
3574.

129

CHAPTER V

Structural and Vibrational Character of H-bonded Vanadyl
Porphyrins. Models of H-Bonded Ferryl Heme

A. Introduction

Ferryl heme, or oxoiron(IV) porphyrin, is an important
intermediate in the enzymatic cycles of dioxygen activation and reduction.
The Fe(IV)=O species is known as Compound 11 of catalases and
peroxidasesl. Its presence has also been demonstrated in cytochrome P450
and related oxygen transfer process2 as well as in cytochrome c oxidase3
and cytochrome d.4 Extensive studies have been devoted to understanding
the nature of the iron-oxo bond in proteins as well as in model
compounds. In particular, resonance Raman studies on peroxidase
Compound II5, ferryl myoglobin5, and heme model complexes7have
given much insight on how the Fe-O bond is influenced by ligand and
polarization effects. The reported Fe-O stretching frequency falls in the

range between 750-810 cm“1 for proteins and 807-852 cm"1 for various 5-

130

or 6-coordinate porphyrin models. One dominating factor that tends to

reduce VFe-O comes from the trans-ligand which competes with the oxo
group for metal (1 orbitals.7a Another often suggested factor that may
lower VFe-O is hydrogen-bonding, although the importance or the
magnitude of this effect in various heme proteins remains largely a subject

of speculation.3a4.5

In the course of studying the properties of oxoiron(IV) porphyrins,
other oxometalloporphyrin complexes of the third row transition metals,
including titanium3, vanadium9, chromiumlo, and manganese11 have been
reported. Vanadyl porphyrins with a stable VO bond, can serve as a

convenient model for the more reactive ferryl porphyrins.

Even though vanadium has not been shown to be present in
mammalian systems, they do occur as natural products.12 To date, the
best evidence for a biological role of vanadium is from bacteria (nitrogen
fixation in Azotobacter species) and from plants (haloperoxidases in
marine algae). Significant amounts of vanadium in a biological system
were first discovered in 1911 by the German physiologist M. Henze in the
blood of the ascidian Phallusia mammillate.13 The ascidians have a
striking physiological feature in accumulating vanadium effectively from
the surrounding seawater. A two step reduction process is proposed from
V(V) to V(III) with V(IV) as intermediate.14 Most of the peroxidases
have been reported to be heme-containing enzymes and divided into three
families: plant peroxidases, animal peroxidases and catalases.15 However,
peroxidases isolated from brown algae belonging to F ucales and
Laminariales are vanadium-dependent haloperoxidases.16 Additionally,

the degradation of chlorophyll and other biologically active porphyrins is

131

thought to be the source of vanadyl porphyrins in petroleum.17
Therefore, vanadium chemisz has always been interesting and useful in

understanding biological systems.

In the study of vanadyl porphyrins,18 Spiro and coworkers have
examined solvent effects, including H-bonding, axial ligand interactions
and radical cation formation on the stretching frequency of the V-O bond
by resonance Raman spectroscopy. They have shown a linear correlation

between vv-o and the solvent acceptor number.19 Although H-bonding

was implied,l8 no direct spectroscopic evidence has been reported.

Our success in synthesizing the C-Clamp porphyrins, especially the
Naphthalene Kemp's Acid Porphyrin (NKAP) and its amide derivative
NKAmideP,20 has provided us the opportunity to probe intramolecular H-

bonding effect on oxo species.
B . Experimental
1. Reagents

All reagents used in this work were purchased from Aldrich
Chemical Co. except as noted below. HOAc (glacial) was from EM
Science and NaOAc (anhydrous) was purchased from J. T. Baker. CHzClz
was freshly distilled over CaH2 before use. NKAP, N KAmideP and NAP

were synthesized by previously discussed methods in Chapter 11.20
2. VO Insertion

a) NKAP(VO). NKAP 10 mg (0.01 mmol), acetic acid 15ml, sodium

acetate 450 mg and VO(acac)2 100 mg were placed in a round-bottom

132

flask fitted with a ground glass joint connected to a reflux condenser. The
mixture was refluxed under argon and the progress of the reaction was
monitored by UV-vis spectroscopy (Figure V-l). When a sample,
withdrawn with a pipette, indicated that no more complex was being
formed (>95% conversion), the reaction was quenched by adding 15 ml of
water. The mixture was allowed to stand overnight to crystalize. The
product was collected by filtration and washed with water until the filtrate
was colorless. The crude compound was purified by running it over a
short column of silica gel with methylene chloride as solvent to give the
pure red solid product. Yield: 9.9 mg (92%). FABMS: m/e, 920. UV-
vis: hmax nm (relative intensity): 417.0 (10.4), 540.0 (1.0), 578.0 (1.2).
The IR spectra showed a strong absorption band at 978 cm'1 characteristic

of a vanadyl vibration.

b) NKAmideP(VO), NAP(VO) and OEP(VO). These were prepared
by similar protocol to that for NKAP(VO). The purification of the
crude products from the vanadyl Naphthalene Kemp’s Amide Porphyrin,
NKAmideP(VO), and vanadyl Naphthoic Acid Porphyrin, NAP(VO),
gave two compounds, one as major product and another as a minor

portion.
3. Instrumentation
a) Spectroscopy

UV-vis spectral measurements were carried out on a Cary 219 .or a
Shimadzu 160 spectrophotometer, with samples dissolved in CH2C12 or 1-
Melm. Infrared spectra were obtained by either layering the vanadyl
porphyrin complex on a NaCl plate or by placing the CH2C12 solution of

133

.3 Z 8 H8985 33:3, .H-> 0.5me

\. / <

 

 

134

the V0 porphyrins in a liquid cell; spectra were then recorded on a
Nicolet IR/42 spectrometer. FABMS (fast atom bombardment mass
spectra) were recorded on a JEOL HX-llO HF double focusing
spectrometer operating in the positive ion detection mode. Resonance
Raman (RR) studies were carried out by Dr. Einhard Schmidt.21

b) X-Ray Determination

Crystals of NKAmideP(VO) and NAP(VO) suitable for single-
crystal X-ray diffractometry were obtained by diffusion of methanol into
a sample solution in CH2C12 followed by slow evaporation. Data
collection was performed on a Nonius CAD4 diffractometer at room
temperature using graphite-monochromated Mo K; radiation. The crystal
used for analysis were of approximate dimensions 0.30 x 0.40 x 0.40 mm
for NKAmideP(VO) and 0.05 x 0.10 x 0.20 mm for NAP(VO). The unit
cell parameters were determined by a least squares fit of 25 machine-
centered reflections having 26 values in the ranges of 41.62-57.14° for
NKAmideP(VO) and 12.00-17.70° for NAP(VO). The intensity data were
reduced and corrected for Lorentz and polarization factors using the
applied programs. The crystal structures were solved by direct methods
using the NRCVAX program package. All non-hydrogen atoms were
refined anistropically. The protons on N6 were located from a difference
Fourier map and positionally refined. All the rest of the hydrogen atoms
were placed at calculated positions with fixed isotropic thermal

parameters. Other crystallographic parameters are listed in Table V-l.

135

Table V-1. Crystallographic Data for NKAmideP(VO) and NAP(VO)

 

 

NKAmideP(VO) NAP(VO)
Formula C5 5N604H60V C43N4O3H42V
fw 928.05 713.76
cryst syst Monoclinic Triclinic
space group C 2/0 pl
a, 19.72902) 11.367(9)
b, A 12.021906) 13.3690)
c, A 41.280(5) 14.5790)
0t, deg 90 106.97(5)
0, deg 10130700) lOO.56(7)
'y,deg 90 113.70(6)
V, A3 9600.3(20) 1822.5(20)
z 8 2
Q(calc), gcm-3 1.284 1.301
p, cm-1 21.318 0.031
scan speed, deg min-1 2.06-8.04 1.37-8.24
scan width, deg 2(0.65 + 0.35tan0) 2(0.65+ 0.35mi»
no. of measd reflns 6064 4766
no. of obsd reflns 4246 (I>20(I)) 1979(I>20’(I))
no. of refined params 606 461
Rf, Rw 0.055, 0.055 0.047, 0.048
Gof 2.33 1.35

 

NOte: Rf = ZIFO'Fcl/ZlFol
RW = (2(W(F0'Fc))2/Z(WF02))1/2
Gof = (2(w(Fo-Fc))2/(# reflns-# params))1/2

136

C. Results and Discussion

Four vanadyl compounds have been studied in this work. They are
NKAP(VO), NKAmideP(VO), NAP(VO) and vanadyl octaethyl
porphyrin, OEP(VO). Among these four systems, OEP(VO) is used
basically as a reference. In all other systems, the V0 moiety potentially
has two possible orientations, one toward the acid or amide (as "cis"); and

the other has the opposite orientation (as "trans" isomer).
1. H-Bonding for 5-Ligated VO-porphyrins

IR spectroscopy studies were recorded for all the four vanadyl
systems. The results are listed in Table V-2. Previous studies of vanadyl
porphyrins have established that the V0 stretching frequency is in the
1000 cm“1 region, therefore we assigned the peak at 99lcm"l observed in
IR spectrum of OEP(VO) as the stretching of the V0 bond.18 In the
spectra of N KAP(VO), a peak at 971 cm'1 was detected instead (Figure V-
2). The 20 cm'1 shift to lower energy is due to the intramolecular H-
bonding provided by the carboxylic acid proton. In order to prove that
this shift is exclusively caused by H-bonding, further resonance Raman
(RR) studies were carried out. After deprotonation with a bulky base,
1,5-diazabicyclo[4.3.0]non-5-ene (DBN), the V0 absorption band of
NKAP(VO) shifted to 991cm'1. The porphyrin core vibrations were not
affected during this process. DBN could not coordinate to the vanadium
as a sixth ligand as OEP(VO) vibrations were also unaffected by DBN.
Thus, the 20 cm'1 vibrational shift is solely caused by intramolecular H-

bonding.

137

 

 

- as an 6.35 6522
end 56 an 8.88 AOBEMZ
- Km AO>E<MZ
wmm 5a SEA—mo
780 .8085?898 Ou>9 7:8 .GQmEEooo-nv Ou>s €233

 

8:298 525/ .8 38 E .~-> 633.

138

Figure V-2. IR Spectrum of NKAP(VO).
The sample was layered on NaCl plate.

 

139

a . Dram IDZM><3 h . mmmn
. _ owe . _ _ 0J3 _ _ _ fidmm . . _ cm: _ . “Jud b _ _ emu“

\

 

«w.wm

lode

BBWLS

 

SL'SUI
SS'VBQI

VE'SSH
l
O
.;
m

 

 

l
BONVllIHSNVHl X

 

 

 

 

 

 

 

 

140

Figure V-3 shows the IR spectra of the major and minor products
of NKAmideP(VO). The major product has a 987 cm“1 absorption, a 4
cm'1 shift to lower wavenumber. This implies a relatively weak
intramolecular H-bonding from the amide proton to the vanadyl oxygen.
The minor product of NKAmideP(VO) displayed a 991 cm'1 vibration,
with no H-bonding effect and thus corresponding to a "trans" isomer with
reference to the IR of OEP(VO).

However, the major product of NAP(VO) showed a 991 cm-1
vibration while the minor compound had the vibration at 972 cm'l. This
implies the major product is a "trans" isomer and the minor is a "cis"

isomer.
2. H-Bonding for 6-Ligated VO-porphyrins

The amide of NKAmideP(VO) cannot be deprotonated by nitrogen
base, such as pyridine or 1-methylirnidazole(1-Melm), thus allowing the
opportunity to detect the H-bonding effect for 6-coordinated vanadyl
porphyrins. However, 6-ligated species cannot be fully achieved even in
pure l-MeIm (Figure V-4). Two Soret peaks at 436 nm and 418 nm
indicated a mixture of 5- and 6-coordinated species (Table V-3). This
phenomenon can be explained by the strong electron donation from the
oxo ligand which reduces the effective positive charges on the V(IV)
center. The out of plane geometry of V0 is another contributing factor.22

IR studies of OEP(VO) in pure l-MeIm showed two absorption
bands; one at 987 cm‘1 is from the remaining 5-coordinated species while
the other is shifted to 958 cm'l, reflecting the 6-coordinated complex. The
A1) is 28 cm'l. As for NKAmideP(VO), we detected a peak at 954 cm'l.

141

Figure V-3. IR Spectrum of NKAmideP(VO).
a) Major product;
b) Minor product.

The samples were layered on NaCl plates.

 

 

142

m.mvn

 

 

 

 

mmmm232w><3 m . ova“
o a
. L. lib. a $40“ _ _ _ OJwa. p. . . 0qu _ p ._ OJmu . _ _ omnu
«mwnn.mm
Ev
......
on: .
.7
o«vm«.mm
m««m«.mm
% 3
IL
.m.
mmvoo.mv

 

 

w4n1<m hdzmwc

143

Figure V-4. The optical spectra of N KAmideP(VO) in
a) CH2C12; b) pyridine; c) l-MeIm

 

 

 

144

 

 

 

 

 

 

 

SAHPz REF:
+2.509 7* ' ‘ '
> 1
(a) , .
0.500
(A/DIU.)
*0.000 . __. NH
300.0 100.0(NH/DIU.) 000.0
:2 30 6/08 '94 L 000.000 0.001;]

 

(1)5AUE (2)EXP.(3)PE9K (4)0ERIU.25)PRIHT No.‘
+0.90“ ' ' ' ' T

(b)

 

 

 

1

 

 

+8.08“ 4 A —

 

 

 

 

 

 

 

 

 

NH
300.0 100.0(NH/OIU.) 000.0
12:34 6/08 '94 L_§00.0NH 0.001fl
snap: REF:
+1.100 ' ' ‘ '
> 1
0 200
(C) (n/OIU.) ’ J
. 1
. n . , -
‘6 0° 1 T H"
300.0 - 100.0(NH/DIU.) 000.0

 

19:19 6/08 '94 [7000.000 -0.033m

145

 

 

8.: 3% H3.: :00 30: :5... 5.0: :9. 58 2600362; 6>Emo
3.: BE ”8.: 2% Ge: 39. m 5N5 63mm:
8.: BR ”8: 2% A3: 3? ”SN: 3:. 58 6002.502; 63%252
6.: 3% ”a: 3mm 00: Gem... x3 : SE. 58 602% 6:062ng
2.: RR é: 3mm 3.33.: m 505 8>E§0§z
a: 3% é: 3% as: 3:. m 506 8>E<M2
30 .0: Ea: .630: 30 .0: 00: seem .080 -20 06:8 05808

 

$55398 Enaca> 3.3% «c Sun 358% 5:985. Bongo 2? .m-> 035.

146

The hydrogen bonding effect brought 4 cm'1 red shift for V0 stretching
mode which is of the same magnitude of the 5-ligated complex.

3. X-Ray Single Crystal Structure of NKAP(VO) and NAP(VO)

Attempts to grow crystals of NKAP(VO) were unsuccessful due to
its poor solubility. Crystals for NKAmideP(VO) and NAP(VO) were
grown from the major product of the vanadyl insertion. Table V-4 lists
the atomic coordinates of non-hydrogen atoms of NAP(VO), and Table V-
5 lists the atomic coordinates of non-hydrogen atoms and the two protons
on N6 of N KAmideP(VO). A listing of selected bond distance and angles
for both compounds is given in Table V-6.

For NKAmideP(VO), the crystal was monoclinic and its ORTEP
structure is shown in Figure V-Sa. The oxo ligand is in the expected
orientation towards the amide, a "cis" structure, as predicted by R and
IR. The four porphyrin nitrogens are coplanar within the standard error.
H-bonding distance is 2.04(5) A from the amide proton to the vanadyl
oxygen. The angle of the N(6)-HN(6)-Ol is 16l(4)°. The average V-N
bond distance is 2.067 A and the V-O bond length is 1.590(3) A. A side
view of this structure (Figure V-Sb) shows that the naphthalene ring plane
is tilted from the 90° angle to the porphyrin mean plane in order to bring
the amide proton to the best alignment to the vanadyl oxygen. This
torsion also brings the amide proton closer to the vanadyl oxygen since the

vertical distance of the naphthalene ring is shortened along the tilting.

The crystal obtained from the major isomer of NAP(VO), contrary
to what we got for NKAmideP(VO), has the oxo pointing on the opposite

147

Table V-4. Atomic Parameters x, y, z and Biso. for NAP(VO)

with E. S. Ds. refer to the last digit printed.

 

 

x y z Biso
V 0.7308702) 0.14775(11) 0.26545( 9) 2.47( 7)
N1 0.9403 (5) 0.2400 (5) 0.3392 (4) 2.6 (3)
N2 0.7645 (5) 0.2131 (5) 0.1550 (4) 2.7 (3)
N3 0.5401 (5) 0.1357 (5) 0.2202 (4) 2.4 (3)
N4 0.7214 (5) 0.1803 (5) 0.4109 (4) 2.7 (3)
C1 1.0074 (7) 0.2369 (6) 0.4267 (5) 2.8 (4)
C2 1.1452 (7) 0.2609 (6) 0.4280 (5) 3.0 (4)
C3 1.1627 (7) 0.2922 (6) 0.3489 (5) 3.0 (4)
C4 1.0330 (7) 0.2772 (6) 0.2920 (5) 2.8 (5)
C5 1.0110 ( 7) 0.2929 ( 7) 0.2040 ( 5) 3.4 ( 5)
C6 0.8877 (7) 0.2661 (6) 0.1387 (5) 3.0 (5)
C7 0.8636 (7) 0.2774 (7) 0.0436 (5) 3.4 (5)
C8 0.7279 ( 7) 0.2292 ( 7) -0.012 ( 5) 3.4 ( 5)
C9 0.6658 ( 7) 0.1897 ( 6) 0.0677 ( 5) 3.0 ( 4)
C10 0.5276 ( 7) 0.1383 ( 6) 0.0521 ( 5) 3.2 ( 5)
C11 0.4665 ( 7) 0.1129 ( 6) 0.1229 ( 5) 2.8 ( 4)
C12 0.3224 ( 7) 0.0674 ( 6) 0.1093 ( 5) 3.0 ( 5)
C13 0.3101 ( 7) 0.0642 ( 6) 0.1986 ( 5) 2.7 ( 4)
C14 0.4453 ( 7) 0.1088 ( 6) 0.2685 ( 5) 3.0 ( 5)
C15 0.4794 ( 7) 0.1321 ( 7) 0.3702 ( 5) 3.3 ( 5)
C16 0.6076( 7) 0.1721 ( 7) 0.4386 ( 5) 3.4 ( 5)
C17 0.6402 ( 7) 0.2040 ( 7) 0.5462 ( 5) 3.6 ( 5)
C18 0.7697 ( 7) 0.2244 ( 7) 0.5835 ( 5) 3.7 ( 5)
C19 0.8203 ( 7) 0.2086 ( 6) 0.4987 ( 5) 2.9 ( 5)
C20 0.9511 ( 6) 0.2234 ( 6) 0.5023 ( 5) 2.6 ( 4)

 

Table V-4 (cont'd)

148

 

C21
C22
C23
C24
C25
C26
C27
C28
C29
C30
C3 1
C32
C33
C34
C35

C36

C37
C38
C39
C40
C41
C42
C43
01

02

03

1.2524 ( 7)
1.2925 ( 7)
1.3654 (10)
0.9759 ( 8)
0.6495 ( 8)
0.6255 (11)
0.2153 ( 7)
0.1999 ( 9)
0.1820 ( 7)
0.5477 ( 7)
0.4581 (10)
0.8454 ( 8)
1.0380 ( 7)
1.0094 ( 8)
1.0905 ( 9)
1.2025 ( 9)
1.2385 ( 8)
1.3598 ( 9)
1.3980 ( 9)
1.3164 ( 9)
1.1977 ( 7)
1.1545 ( 7)
1.1119 ( 8)
0.7006 ( 5)
0.9991 ( 5)
1.1712 ( 5)

0.2550
0.3417
0.4751
0.3328
0.2198
0.3221
0.0357

( 7)
( 8)
(9)
( 9)
( 8)
(10)
(7)

0.1415 (9)
0.0228 (7)
0.2225 ( 8)
0.1114 ( 9)
0.2669 ( 9)
0.2289 ( 6)
0.1231 ( 7)
0.1149 ( 8)
0.2126 ( 8)
0.3274 ( 7)
0.4299 ( 8)
0.5387 ( 8)
0.5482 ( 7)
0.4537 ( 6)
0.3369 ( 7)
0.4804 ( 6)
0.0137 ( 4)
0.4676 ( 5)
0.5225 ( 5)

0.4992 (6)
0.3252 ( 6)
0.3682 ( 9)
0.0043 ( 7)
-0.1007( 6)
-0.0911( 7)
0.0126 ( 5)
0.0075 ( 7)
0.2241 ( 6)
0.6057 ( 6)
0.6090 ( 8)
0.6941( 6)

0.5965 ( 5)
0.6045 ( 6)
0.6826( 7)

0.7553 ( 6)
0.7531 ( 6)
0.8237 ( 6)
0.8191 ( 7)
0.7428 ( 7)
0.6727 ( 5)
0.6727 ( 5)
0.6018 (6)
0.2166 ( 4)
0.6031 ( 4)
0.5432 ( 4)

4.0
4.4
9.1
5.7
4.7
7.5
3.7

(6)
(6)
(9)
(7)
(6)
(8)
(5)

6.5 (7)
4.3 (5)
4.6 (6)
7.4 (8)
5.5 ( 7)
3.0 ( 5)
4.6 ( 5)
5.3 ( 6)
5.2 ( 6)
4.4 ( 6)
5.9 ( 6)
6.8 ( 6)
6.3 ( 6)
3.6 ( 5)
3.3 ( 5)
3.8 ( 5)
3.4 ( 3)
4.7 ( 4)
5.2 ( 4)

 

Biso is the Mean of the Principal Axes of the Thermal Ellipsoid.

Table V-S. Atomic Parameters x, y, z and Egg for N KAmideP(V O)
with E.S.Ds. refer to the last digit printed.

 

 

x y z Beq
V 0.56932( 4) 0.416840) 0.087358(21) 2.75( 4)
N1 0.56751(19) 0.4745 (3) 0.13440 ( 9) 2.86(19)
N2 0.47465(18) 0.4921(3) 0.07188( 9) 2.70(18)
N3 0.53869(18) 0.3102(3) 0.04801( 9) 2.67(19)
N4 0.62916(18) 0.2885(3) 0.11131( 9) 2.69(18)
N5 0.85156(19) 0.5428(3) 0.155 19( 10) 3.13(20)
N6 0.74863(22) , 0.6254(4) 0.08617(12) 5.3 ( 3)
Cl 0.61567(24) 0.4551(4) 0.16312(12) 2.94(23)
C2 0.6049( 3) 0.5368(4) 0. 18832(12) 3.6 ( 3)
C3 0.5508(3) 0.6019(4) 0.17429(12) 3.5 ( 3)
C4 0.52783(25) 0.5636(4) 0. 14107( 12) 3.4 ( 3)
C5 0.4722(3) 0.6092(4) 0.1 1967(12) 3.6 ( 3)
C6 0.44646(24) 0.5759(4) 0.08760(12) 3.2( 3)
C7 0.3889(3) 0.6271(4) 0.06590(13) 3.6( 3)
C8 0.38224(24) 0.5756(4) 0.03616(12) 3.06(24)
C9 0.43545(23) 0.4915(4) 0.0397402) 3.98(15)
C10 0.44645(24) 0.4201(4) 0.01519(12) 3.02(24)
C11 0.49383(24) 0.3355(4) 0.01911(12) 2.94(24)
C12 0.5001(3) 0.2555(4) -0.00666(12) 3.15(25)
C13 0.5491(3) 0.1808(4) 0.00723(12) 3.4( 3)
C14 0.57335(24) 0.2163(4) 0.04149(12) 3.04(24)
C15 0.6233(3) 0.1631(4) 0.06369(12) 3.4( 3)
C16 0.64876(24) 0.1946(4) 0.09619(12) 3.3(3)
C17 0.7007(3) 0.1346(4) 0.11858(13) 3.6(3)
C18 0.7132(3) 0.1910(4) 0.14772(12) 3.4(3)

 

Table V-5 (cont'd)

 

C19
C20
C21
C22
C23
C24
C25
C26
C27
C28
C29
C30
C3 1
C32
C33
C34
C35

C36 .

C37
C38
C39
C40
C41
C42
C43
C44
C45
C46
C47
C48

0.66811(24)
0.66289(24)
0.6458(3)
0.5167(3)
0.4566(4)
0.3469(3)
0.3293(3)
0.2687(3)
0.4579(3)
0.3884(4)
0.5754(3)
0.7323(3)
0.7012(3)
0.7654(3)
0.69999(25)
0.6618(3)
0.6840(3)
0.7452(3)
0.7879(3)
0.851 1(3)
0.8952(3)
0.8760(3)
0.81412(24)
0.76635(24)
0.79791 (24)
0.8431(3)
0.8974(3)
0.9661(3)
0.9603(3)
0.9068(3)

0.2880(4)
0.3669(4)
0.5553(5)
0.6921(5)
0.6537(7)
0.7222(5)
0.5964(5)

0.5209(8) .

0.2551(5)
0.1992(6)
0.0846(5)
0.0260(5)

-0.0734(6)

0.1542(5)
0.3447(4)
0.2835(5)
0.2595(6)
0.3015(5)
0.3636(5)
0.4019(5)
0.4578(6)
0.4794(5)
0.4459(4)
0.3854(4)
0.4731(4)
0.6580(4)
0.731 1(5)
0.6692(5)
0.5598(5)
0.4886(5)

0.1433302)
0.1672702)
0.22254(14)
0.1899504)
0.20348(17)
0.07522(14)
0.0053603)
0.0032107)

-0.04105(13)
-0.04347(16)
-0.00912(13)

0.1112904)
0.1264507)
0.1770206)
0.2023802)
0.2200803)
0.2534704)
0.2694203)
0.2528503)
0.2699703)
0.2550704)
0.2211203)
0.2024702)
0.2179802)
0.1656302)
0.1564902)
0.1451403)
0.1513104)
0.1326204)
0.1447603)

3.03(24)
2.95(24)
5.2( 3)
5.0 ( 3)
8.3(5)
5.2(3)
4.6(3)
8.8(5)
4.5( 3)
7.7(4)
5.1(3)
5.0(3)
6.9(4)
6.2(4)
3.17(24)
4.7 ( 3)
5.8( 4)
53(3)
4.0(3)
5.1(3)
5.4(3)
4.5(3)
3.20(24)
3.09(24)
3.3( 3)
3.7(3)
4.1(3)
5.2(3)
4.5( 3)
3.9(3)

 

Table V-5 (cont'd)

 

C49
C50
C5 1
C52
C53
C54
C55
01
02
O3
()4
H30
H3b

0.9375(3)
0.871 1(3)
0.8748(3)
0.8651(3)
0.8080(3)
0.9026(4)
1.0281(3)
0.6218006)
0.7939909)
0.9098509)
0.81122(21)
0.7138(23)
0.7494(23)

0.5833(5)
0.6520(4)
0.7536(5)
0.6903(6)
0.5771(5)
0.8406(5)
0.4991(7)
0.4976(3)
0.6963(3)
0.3887(3)
0.4770(3)
0.579(4)

0.696(4)

0.09578(13)
0.0856302)
0.1079504)
0.04986(14)
0.0841002)
0.1643806)
0.1388909)
0.07424(8)
0.16600(9)
0.1464000)
0.07966( 10)
0.0869(1 1)
0.0887(1 1)

4.7(3)
3.7(3)
4.2(3)
5.7(3)
3.9(3)
6.8(4)
8.1(5)
3.62( 17)
5.13(21)
5.41(22)
5.80(25)
6.6(14)
6.3(14)

 

Beq is the Mean of the Principal Axes of the Thermal Ellipsoid.

152

 

 

 

ddaasw $24192 8:55 $2.102
282.52 $2-182 3:862 $2-102
23.3.32 62-262 ABE-.3 624182
232$ $2-032 2222.2 32$-82
288.20: 624032 8:32 €2$-€2
3:33 Adz-$-82 3:25 $2.032
233.82 80-102 6:82: €0$-§2
$83.82 804102 0:382 504192
0:02: ave-$-02 6:92: 80-252
€38.82 €0$-€2 0:32: €o$2:2
€22 2:96:22-sz
020.3
622 €22-30
@280 202$ €380 82$
6:33 62$ €83 62$
6:680 52$ €33 02$
6:83 82$ €03 32$
€32 30$ 682 80$
gamma
5.3.22 85.030522

 

33.22 20 632620.422 .0 880.62
080% Began-2 22:. Be 203 805. 20 a: 66505 082 80628 .e$ ess-

153

Figure V-5. (a) ORTEP structure of N KAmideP(VO).

154

.2
as ..w

0.
Eu .0:

    

08 .807

  

08 . .
’71" .. ...; ONO
"\ ‘lfl. a
305 . . 7..» a. 7 On
... 8 93 .... 88
... 8 N8 2

155 ‘

 

Figure V-5. (b) Sideview of N KAmideP(VO).

156

porphyrin side of the carboxylic acid, a "trans" isomer in agreement with
the IR results (Figure V—6). The average V-N bond length is 2.069 A and
the V-O bond distance is 1.583(5) A. From the unit cell structure (Figure
V-6b), we observe dimer formation of NAP(VO). Two molecules of
NAP(VO) come together through two intermolecular hydrogen bonds
between the two carboxylic acids. The "trans" configuration is most likely

the result of such acid pairing, blocking the “cis” site.
4. Orientation of the V0 Directed by H-Bonding

From the results of X-ray determination and IR studies, we
conclude that the oxo orientation is determined by hydrogen bonding.
The strong hydrogen bonding present in NKAP(VO) induces a single “cis”
isomer either by formation of COOH-~O=V(acac)2 prior to the metal

insertion; or by equilibrium of the two isomers after the V=O insertion.

For NKAmideP(VO), since the amide group constitutes a weaker
hydrogen bond than the acid, most of the oxo goes to the amide side
(“cis”) and only a minor proportion goes to the opposite side to form the
“trans” isomer. As for NAP(VO), due to the dimer formation, the acid
proton is unavailable for hydrogen bonding. The oxo rather picks the less
sterically hindered side of the porphyrin to give mostly the “trans”

isomer.

157

.6>E<z 26 8025... 200.06 02.2 3 .e$ 800-2

 

158

       

r»... -

“(C-Icing

.0
tempu- fitfi C- o .-

 

Figure V-6. (b) Unit cell structure of NAP(VO).

159

D. Conclusion

The hydrogen bonding effect on the 5- and 6-coordinated vanadyl
porphyrin as observed in NKAP(VO) and NKAmideP(VO) gives a Auv=o
of 4 cm'1 to 20 cm’1 depending on the relative strength of their hydrogen
bonds. In comparison, the magnitude of the hydrogen bonding strength of
HRP II is almost a 10 cm'1 shift to lower energy.5a This H-bond
presumably plays a central role in HRP II activity. In cytochrome c
peroxidase, there is proposed strong H-bonding from distal arginine (Arg
48) and trytophan (Trp 51) to the ferry] heme causing the Fen/=0 shift to

753 cm'l, a very low frequency in the 750-810 cm"1 range for proteins.

H-Bonding to V=O and Fe=O reduces the oxygen to metal 11
interactions and shift the M=O vibration to lower energy. The lower
energy absorption indicates a weaker V0 bond and sometimes longer bond
length. Table V-7 shows some crystal structures of vanadyl porphyrins.
The relative longer V0 bond of (cis)NKAmideP(VO) [1.590(3)] vs
(trans)NAP(VO) [1.583(5)] observed by X-ray analysis could be the result
of hydrogen bonding. It is comparable with the intermolecular hydrogen
bonding brought about by quinol adducts or by water molecules in the
solid state.18 Even though when comparing NKAP(VO) with OEP(VO)23
and etioPorphyrin(VO) [ETP(VO)], the latter two compounds24 have
longer V=O bond length than the H-bonded N KAmideP(VO). We suspect
that the C-clamp porphyrin may clamp down on the oxo group and in

effect push the V=O toward the porphyrin plane.

With the soret electronic excitation, the vanadyl VO stretching

mode is strongly enhanced in resonance. H-bonding weakens the V0 bond

160

02002095283504.“ mo 202030.590 "Dam:

 

 

mm Eb.~ 2:0: 8:30; 505-£5395:
mm wam 2:00.: Gian; 83um
mm :30 mm.: 6330.2 532%.
nvm wt: wvd A30 2 c. 2 83¢me
00a Nomm mvmd Adamo; AO>EmO
0:03 mood Amvmumd Amvmwmg AO>E<Z
£5 SQN Amvvomd 93302 5320252
002020002 < .z-> 0w020>0 < .0203 .«o 28$ < .Ou> 0:209:00

 

02509200 3228> ~000>0m 00 025 ansbm .>-> 0302.

161

due to reduced oxygen to V(IV) electron donation. Removal of this H—
bond allows the electron density to localize to the V0 moiety. The
stronger the H-bonding to vanadyl, the lower the stretching energy of V0
will be. This has been proven by intramolecular H-bonding studies of
both NKAP(VO) and NKAmideP(VO) systems. The coordination by a
sixth ligand causes the vibration energy to drop more than 30 cm'1 due to

electron donation from the sixth ligand to vanadium.

The 20 cm‘1 uV=0 shift observed due to H-bonding provides a
benchmark for H-bonded M=O species. Any shift greater than 25 cm'1
cannot be accounted for by H-bonding alone, in which case trans-ligand

coordination probably also plays a role.

162

E. References

1. a) Hewson, W. 0.; Hager, L. P. in The Porphyrins; Dolphin, D.,
Ed.; Acdemic: New York, 1979; Vol VII, Chapter 6.
b) Reczek, C. M.; Sitter, A. J .; Turner, J. J. Mol. Struct. 1989, 214,
27-35.

2. a) Watanabe, Y.; Groves, J. T. in The Enzymes, Sigman, D. S. Ed.;
Academic: New York, 1992; Vol XX, Chapter 9 and references
therein.

b) There is another proposed intermediate which is isoelectronic to
the Fe=O species but in the form of Fe(III)porphyrin N-oxide, see

Weber, L.; Home], R.; Behling, J .; Haufe, G.; Hennig, H. J. Am.

Chem. Soc. 1994, 116, 2400-2408.

3. a) Varotsis, C.; Babcock, G. T. Biochem. 1990, 29, 7357-7362.
b) Ogura, T.; Takahashi, S.; Hirota, S.; Shinzawa—Itoh, K.;
Yoshikawa, S.; Appelman, E. H.; Kitagawa, T. J. Am. Chem. Soc.
1993, 115, 8527-8536.

4. a) Kahlow, M. A.; Zuberi, T. M.; Gennis, R. B.; Loehr, T. M.
Biochem. 1991, 30, 11485-11489.
b) Ozawa, S.; Watanabe, Y.; Nakashima, S.; Kitagawa, T.;
Morishima, I. J. Am. Chem. Soc. 1994, 116, 634-641.

5. a) Sitter, A. J .; Reczek, C. M.; Terner, J. J. Biol. Chem. 1985, 260,
7515-7522.
b) Hashimoto, S.; Tatsuno, Y.; Kitagawa, T. Proc. Natl. Acad. Sci.
U.S.A. 1986, 83, 2417-2421.

10.

163

c) Hashimoto, S.; Teraoka, J .; Inubushi, T.; Kitagawa, T. J. Biol.
Chem. 1986, 261, 11110-11118.

a) Sitter, A. J .; Reczek, C. M.; Temer, J. Biochim. Biophys. Acta
1985, 828, 229-232.

b) Fenwick, C.; Marmor, S.; Govindaraju, K.; English, A. M.;
Wishart, J. F.; Sun, J. J. Am. Chem. Soc. 1994, 116, 3169-3170.

a) Kean, R. T.; Oertling, W. A.; Babcock, G. T. J. Am. Chem. Soc.
1987, 109, 2185-2187.

b) Oertling, W. A.; Kean, R. T.; Babcock, G. T. Inorg. Chem. 1990,
29, 2633-2645.

a) Latour, J. M.; Gallunb, B.; Marchon, J .-L. J. Chem. Soc. Chem.
Commun. 1979, 570-571.

b) Woo, L. K.; Hays, J. A.; Goll, J. G. Inorg. Chem. 1990, 29, 3916-
3917.

a) Pettersen, R. C.; Alexander, L. E. J. Am. Chem. Soc. 1968, 90,
3873-3876.

b) Buchler, J. W.; Puppe, L.; Rohbock, K.; Schneehage, H. M. Ann
N. Y. Acad. Sci. 1973, 206, 116-121.

c) Macor, K. A.;Czernuszewicz, R. S.; Spiro, T. G. Inorg. Chem.
1990, 29, 1996-2000.

(1) Lin, M.; Lee, M.; Yue, K. T.; Marzilli, L. G. Inorg. Chem. 1993,
32, 3217-3226.

a) Nill, K. H.; Wasgestian, F.; Pfell, A. Inorg. Chem. 1979, 18,
564-567.

164

b) Groves, J. T.; Kruper, W. J.; Jr.; Haushalter, R. C.; Butler, W. M.
Inorg. Chem. 1982, 21, 1363-1368.

c) Penner-Hahn, J. B.; Benfatto, M.; Hedman, B.; Takahash, T.;
Sebastian, D.; Groves, J. T.; Hodgson, K. O. Inorg. Chem. 1986, 25,
2255-2259.

11. Stern, M. K.; Groves, J. T. in "Manganese Redox Enzymes", V. L.
Pecoraro, Ed.; VCH, 1992, Chap. 11 and references therein.

12. Vanadium and its Role in Life, in "Metal Ions in Biological Systems",
Vol. 31. Sigel, H. and Sigel, A., Ed.; Marcel Dekker, New York,
1995.

13. Henze, M. Hoppe-Seyler's Z. Physiol. Chem, 1911, 72, 494-496.
14. Michibata, H. Adv. Biophys. 1993, 29, 105-109.

15. Welinder, K. G. in Molecular and Physiological Aspects of Plant

Peroxidases, University of Geneva, 1986, l.

16. Vilter, H.; Glombitza, K.-W.; Grawe, A. Bot. Mar. 1983, 26, 331-
337.

17. a) Nagy., B. Chemistry 1966, 39, 9-14.
b) Rosscup, R. J.; Pohlman, H. P. Polym. Prep., Am. Chem. Soc.,
Div. Petrol. Chem, 1967, 12, A-103-104.

18. Su, Y. 0.; Czemuszewicz, R. S.; Miller, L. A.; Spiro, T. G. J. Am.
Chem. Soc. 1988, 110, 4150-4157.

19.

20.

21.

22.

23.

24.

25.

165

a) Mayer, U.; Gutmann, V.; Gerger, W. Monatash. Chem. 1975,
106, 1235--l239.

b) Gutmann, V. Electrochem. Acta. 1976, 21, 661-672.

c) Gutmann, V. The donor-Acceptor Approach to Molecular

Interactions, Plenum: New York, 1978.

a) Chang, C. K.; Kondylis, M. P. J. Chem. Soc. Chem. Commun.
1986, 316-318.
b) Liang, Y.; Peng, S.-M.; Chang, C. K. J. Molecular Recognition

in press.

Schmidt, E. “ Ligand Binding Properties of Metalloporphyrins, Factors
That Influence Their Chemical Properties and Relationships to
Biological Proteins“, Ph.D. Dissertation, Michigan State University,
1995.

Ozawa, T.; Hanaki, A. Inorg. Chim. Acta. 1988, 141, 49-51.
Poulos, T. L.; Finzel, B. C. Pept. Protein Rev. 1984, 4, 115-118.

a) Molinaro, F. S., Ibers, J. A. Inorg. Chem. 1976, 15, 2278-2283.
b) Pettersen, R. C. Acta Crystallogr., Sect. B, 1969, 25, 2527-2539.

Drew, M. G. B.; Mitchell, P. C. H.; Scott, C. E. Inorg. Chim. Acta.
1984, 82, 63-68.

166

Chapter VI

Structural and Vibrational Properties of RuCO and FeCO

C-Clamp Porphyrin and Derivative

A. Introduction

The binding of small substrates to porphyrins that model the heme
active site has drawn considerable attention of bioinorganic chemists. In
order to provide insights into structure/function relationships, factors like
steric interaction, substituent effects on porphyrin and trans ligand effects
have been studied for 02, CO and NO binding.1 CO binding, in particular,
has been studied in exploring the nature of the heme binding site and in
evaluating cis and trans ligand effects.2 Crystallographic studies of carbon
monoxy hemoglobins and myoglobins3 have shown that the CO ligand
exhibits a bent or tilted configuration with respect to the heme plane. This
stereochemical feature of the hemeproteins is associated with nonbonding

interactions of the axial ligand with nearby amino acid residues in the

167

ligand-binding pocket. These interactions are thought to lower the CO
affinities in the proteins and protect the organisms from C0 poisoning.4
However, for non-constrained heme derivatives, the bonded CO appears in
near linear geometry. There are many factors affecting CO bonding and
they are usually hard to evaluate practically with high degree of reliability.
Generally, ligands capable of influencing the dn orbitals and hence the
1t(Fe)-1t*(CO) back-bonding are predicted to affect the CO bonding as well
as the CO stretching frequency. Goedken has reported several examples to
illustrate the sensitivity of Fe(H)-CO bonding.5

In comparing properties of oxy and carboxy heme, the Fe-CO
overlap density is greater than the Fe-02 overlap density, according to
theoretical calculations.1 This is in agreement with the greater affinity of
CO. One influence caused by this stronger overlap is that the CO bonding
is more sensitive to the ligand field strength of the trans ligand on Fe(II).1
Iron monocarbonyl heme models with different trans ligands, such as
THF,6 pyridine7 and mercaptan,8 have provided strong evidence of this
kind of sensitivity. Here, we have conducted research to show how a fine-
tuned trans ligand environment can shift the CO vibration in the C-clamp
porphyrin N KAP and its derivative NKAmideP.

B. Experimental
1. Preparation of RuCOporphyrins

Ru3(CO)12 was allowed to react with free base porphyrin under the
conditions reported by Collen and coworkers.9 11.6 mg of NKAP in
freshly distilled toluene was heated on an oil bath under argon. A small

amount (3 mg) of triruthurium dodecacarbonyl [Ru3(CO)12] was added.

168

After each additional 8 hours, a small amount (3 mg) of RU3(CO)12 was
added. The reaction was monitored by UV-Vis and by TLC. When the

metal insertion was completed (~ 48 h), the reaction was stopped by adding
1 ml of methanol.

The product was purified on the TLC plate using methylene chloride
as the eluent. The first band was yellowish brown, and proved to be
Ru3(CO)12 by mass spectrometry and UV-Vis. The second band was
orange colored showing the properties of ruthenium inserted porphyrin.
The UV-vis spectrum of the product was consistent with formation of
RuCO-porphyrin. The product is a monocarbonyl complex as identified by
Ibers.9 For RuCONKAP: MS, m/e (relative intensity) 983 (M+, 1.0); IR
CO vibration at 1931 cm'l; UV-Vis hmax nm (relative intensity) 397.5 nm
(12.8); 521.0 (1.0); 533.0 (1.1). For RuCONKAmideP: MS, m/e (relative
intensity) 982 (M+, 2.0); IR: CO vibration at 1927 cm'l; UV-Vis hmax nrn
(relative intensity) 399.5 nm (12.7); 522.0 (1.0); 553.5 (1.1).

2. Preparation of FeCOporphyrins

A solution of sodium dithionite was introduced to a methylene
chloride solution of Fe(III) porphyrin under argon. CO gas was then
added to this Fe(II)porphyrin solution and the color of the solution changed
instantaneously. An IR cell was first flushed with argon to eliminate air
and the methylene chloride solution of Fe(II)COporphyrin was introduced
to this liquid IR cell through a cannula; IR measurement was then

conducted.

169

3. Instrumentation
a) Spectroscopy

UV-vis spectral measurements were carried out on a Shimadzu 160
spectrophotometer, with samples dissolved in methylene chloride. Infrared
spectra were obtained by either layering the RuCOporphyrin complex on a
NaCl plate or by measurement of the CH2C12 solution of FeCOporphyrin
in a liquid IR cell. Spectra were recorded on a Nicolet IR/42 spectrometer
at a resolution of 1 cm'l. Mass spectra were measured from a benchtop
VG Troi-l mass spectrometer using the DCI (Desorption Chemical

Ionization) probe for sample inlet.
b) X-Ray Structure Determination

Crystals of RuCONAKP(MeOH) and RuCONKAmideP(MeOH)
suitable for single-crystal X-ray diffractometry were obtained by diffusion
of methanol into the sample solution in CH2C12 followed by slow
evaporation. Crystallographic data are listed in Table VI-l. Data
collection was performed on a Nonius diffractometer at room temperature
using graphite-monochromated Mo K; radiation. The crystals used for
analysis were of approximate dimensions 0.05 x 0.22 x 0.25 mm for
RuCONKAP(MeOH) and 0.40 x 0.40 x 0.50 mm for RuCONKAmideP
(MeOH). The unit cell parameters were determined by a least squares fit
of 25 machine-centered reflections having 20 values in the ranges of 9.40-
20.22° for RuCONKAP(MeOH) and 15.48-23.66° for RuCONKAmideP
(MeOH). The intensity data were reduced and corrected for Lorentz and
polarization factors using the applied programs. The crystal structures

were solved by direct methods using the NRCVAX program package. All

170

Table VI-l. Crystallographic Data of RuCONKAP(MeOH) and

 

 

RuCONKAmideP(MeOH)
RuCONKAP RuCONKAmideP

Formula RuC57N5O6H63 RuC57N605H54
fw 1015.21 1014.23
cryst syst monoclinic monoclinic
space group p 21 /c P 2No
a,A 10.706(3) 10.650(3)
b,A 25.999(3) 26.071(8)
c, A 18.760(3) 18.842(8)
B. deg 103.002(22) 103.13(3)
v, A3 5087.7(17) 5095(3)
z 4 4
Q(calc), gcm’3 1.325 1.322
“cm-1 3.515 3.525
transm coeff 0967-1000 0.926- 1 .000
scan speed, deg min'l 2.06-8.24 2.06-8.24
scan width. deg 2(0.60 + 0.351010) 2(0.60+ 0.351010)
no. of measd reflns 6639 6648
110- 0f obsd reflns 2639 (1)260» 4516(I>20'(I))
no. of refined params 6639 6648
Rf, Rw 0.0045, 0.044 0.042, 0.041
Gof 1.13 2.12

NOtC: Rf = :lFo-Fci; :iFoi

 

Rw =(EXW(1::0'Fc))2/£(WFOZ))1,2

Gof = (2(w(Fo-Fc))2/(# reflns-# params))1/2

171

non-hydrogen atoms were refined anisotropically. All the hydrogen atoms
were placed at calculated positions with fixed isotropic thermal parameters.
The highest difference Fourier peaks were 0.320 eA'3 for
RuCONKAP(MeOH) and 0.420 eA'3 RuCONKAmideP(MeOH),

respectively.
C. Results and Discussion

1. X-Ray Single Crystal Structures of RuCONKAP(MeOH) and
RuCONKAmideP(MeOH)

The orange colored crystals obtained were in the shape of long
needles. Table VI-2 lists the atomic coordinates of non-hydrogen atoms of
RuCONKAP(MeOH) and Table VI-3 lists that of RuCONKamideP(MeOH).
A listing of selected bond distance and angles for both compounds is given
in Table VI-4.

For RuCONKAP(MeOH), the crystal is monoclinic and its ORTEP
structure is shown in Figure VI-l. The CO is on the opposite side from the
Kemp's acid with one molecule of solvent methanol bound trans. Just like
the methanol inclusion in ZnNKAP, the methanol hydroxy proton is H-
bonded with the Kemp's acid carbonyl oxygen. The methanol oxygen is
coordinated to ruthenium as an axial ligand with an Ru-O distance of
2.202(6). In RuCONKAmideP(MeOH) (Figure v1-2), the Ru-O(MeOH)
distance is 2.205(4) and the methanol hydroxy proton is H-bonded with
Kemp's amide carbonyl oxygen. In both crystal structures, the COappears
in almost linear geometry with Ru-C-O angles 177.5(8)° for RuCONAKP

172

Table VI-2. Atomic Parameters x, y, z and Biso for

RuCONKAP(MeOH) with E.S.Ds. refer to the last digit printed.

 

 

X y 2 Biso
Ru 0.33672( 8) 0.13948( 3) 0.15460( 4) 2.50( 3)
C 0.2763 ( 9) 0.1960 ( 3) 0.1887 ( 5) 3.1 ( 5)
0 0.2338 ( 7) 0.2330 ( 3) 0.2084 ( 4) 5.5 ( 4)
01 0.4061 ( 6) 0.07065 (23) 0.1070 ( 3) 3.8 ( 3)
02 0.2069 ( 7) -0.1106 ( 3) 0.1494 ( 4) 5.4 ( 4)
03 0.4443 ( 7) -0.0707 ( 3) 0.3728 ( 4) 5.8 ( 4)
04 0.4539 ( 8) -0.0286 ( 3) 0.1497 ( 4) 7.3 ( 5)
05 0.5843 ( 8) -0.0135 ( 3) 0.2545 ( 5) 8.0 ( 6)
N1 0.1644( 6) 0.1023 ( 3) 0.1421 ( 3) 2.6 ( 4)
N2 0.2877( 6) 0.1678( 3) 0.0501( 4) 2.4( 4)
N3 0.5173( 6) 0.1691( 3) 0.1630( 4) 2.7( 3)
N4 0.3915( 6) 0.1043( 3) 0.2546( 4) 2.3 ( 3)
N5 0.3324( 7) -0.0890( 3) 0.2585( 4) 3.3 ( 4)
C1 0.1165( 8) 0.0761( 3) 0.1947( 5) 2.8 ( 5)
C2 -0.0160( 9) 0.0611 ( 4) 0.1623( 5) 3.6 ( 5)
C3 -0.0426( 8) 0.0787 ( 4) 0.0918( 5) 3.4 ( 5)
C4 0.0694( 8) 0.1046( 3) 0.0803( 5) 2.7 ( 4)
C5 0.0739( 8) 0.1305 ( 4) 0.0157( 4) 3.5 ( 5)
C6 0.1718(8) 0.1610(3) 0.0027( 5) 2.9 ( 5)
C7 0.1691( 9) 0.1908 ( 4) -0.0635(5) 3.5(5)
C8 0.2830( 8) 0.2153 ( 3) -0.0547(5) 3.0(5)
C9 0.3605( 9) 0.2012 ( 3) 0.0178 ( 5) 3.1(5)

 

Table VI-2 (cont'd)

 

C10
C11

C12
C13
C14
C15
C16
C17
C18
C19
C20
C21
C22
C23
C24
C25
C26
C27
C28
C29
C30
C31

C32
C33

0.4837( 8)
0.5579( 8)
0.6907( 9)
0.7309( 9)
0.6222( 8)
0.6136( 8)
0.5124( 8)
0.5145( 8)
0.3928( 8)
0.3150( 8)
0.1877( 9)
-0.1 102(10)
-0.1636(10)
-0.l727(l4)
0.0579(10)
0.3224(10)
0.2666(13)
0.7718(1 1)
0.8554 (16)
0.8615(10)
0.6309( 9)
0.6577(1 1)
0.3559( 9)
0.1120( 8)

0.2152 ( 4)
0.2002 ( 3)
0.2125 ( 4)
0.1889 ( 4)
0.1612 ( 3)
0.1332 ( 4)
0.1080 ( 3)
0.0841 ( 3)
0.0678 ( 3)
0.0799 ( 3)
0.0644 ( 3)
0.0329 ( 5)
0.0715 ( 4)
0.0238 ( 5)
0.1924 ( 5)
0.2537 ( 4)
0.3062 ( 5)
0.2510 ( 5)
0.2244 ( 7)
0.1889 ( 5)
0.0812 ( 4)
0.1294 ( 6)
0.0434 ( 4)
0.0448 ( 4)

0.0468 ( 5)
0.1136 ( 5)
0.1411 ( 5)
0.2057( 5)
0.2190 ( 5)
0.2810( 5)
0.2991( 4)
0.3684( 4)
0.3677( 4)
0.2952( 5)
0.2651( 5)
0.1949( 6)
0.0353( 6)
-0.0053( 8)
-0.1280( 6)
-0.1051( 5)
-0.1002( 7)
0.1091( 6)
0.0728 ( 8)
0.2573( 6)
0.4299( 5)
0.4752( 6)
0.4315( 5)
0.3189( 4)

3.1 (5)
3.0 ( 5)
4.2 ( 5)
4.1 ( 6)
3.0 ( 4)
3.5(5)

2.6 ( 4)
2.6 ( 4)
2.5 ( 4)
2.5 (5)
2.9 ( 5)
6.3 ( 7)
5.3 ( 6)
10.8 (10)
5.9 ( 7)
4.5 ( 6)
8.1 ( 9)
6.6 ( 7)
11.6(12)
6.0 ( 7)
4.7(6)

8.6(9)

3.9(5)

2.9(5)

 

Table VI-2 (cont'd)

 

C34
C35
C36
C37
C38
C39
C40
C41
C42
C43
C44
C45
C46
C47
C48
C49
C50
C51
C52
C53
C54
C55
C56

0.0562( 9)

-0.0247(10)

-0.0507( 9)
0.0039( 9)
-0.0318( 9)
0.0216(10)
0.1 106(10)
0.1488( 9)
0.0897( 8)
0.2537( 9)
0.3036( 9)
0.3984( 9)
0.4603(10)
0.5262( 9)
0.4340( 9)
0.6342( 9)
0.5944( 9)
0.5035( 9)
0.7150(1 1)
0.5356(10)
0.3305(12)
0.5852(12)
0.4742(13)

0.0813 ( 4)

0.0691 ( 4)

0.0198 ( 4)

-0.0209( 4)
-0.0725 ( 4)
-0.1109 ( 4)
-0.0999 ( 4)
-0.0509 ( 4)
-0.0088 ( 3)
-0.0439 ( 4)
-0.1187 ( 4)
-0.1592 ( 4)
-0.1815 ( 4)
-0.l407 ( 4)
-0.0970 ( 4)
-0.1 181 ( 4)
-0.0964 ( 4)
-0.1352 ( 4)
-0.0899 ( 4)
-0.0427 ( 4)
-0.2018 ( 4)
-0.1621 (4)
0.0702 ( 5)

0.3538( 5)
0.4008( 6)
0.4106( 5)
0.3781( 5)
0.3859( 6)
0.3570( 6)
0.3145( 5)
0.3027( 5)
0.3313( 5)
0.2610( 5)
0.1952( 5)
0.1866( 5)
0.2616( 6)
0.3122( 5)
0.3182( 5)
0.2799( 6)
0.2020( 5)
0.1539( 5)
0.1716( 7)
0.1985( 6)
0.1350( 6)
0.3880( 6)
0.0529( 7)

36(5)
47(6)
46(6)
32(5)
45(6)
54(6)
5J(6)
39(5)
28(5)
35(5)
38(5)
43(6)
49(7)
43(5)
38(5)
47(6)
38(5)
50(6)
71(8)
55(7)
66(7)
10(7)
7.8(9)

 

Biso is the Mean of the Principal Axes of the Thermal Ellipsoid.

RuCONKAmideP(MeOH) with E.S.Ds. refer to the last digit printed.

175

Table VI-3. Atomic Parameters x, y, z and Biso for

 

 

x y Z Biso
Ru 0.33981( 4) 0.140072(l8) 0.15862( 3) 2.615(20)
C 0.2778 ( 5) 0.19604 (22) 0.1925 ( 3) 3.5 ( 3)
0 0.2346 ( 4) 0.23267 (17) 0.21175(24) 5.9 ( 3)
()1 0.4131 ( 4) 0.07161 (14) 0.11243(20) 3.91(21)
02 0.1978 ( 4) -0.10710(l7) 0.14887(24) 6.0 ( 3)
03 0.4524 ( 5) -0.07l25(17) 0.36910(23) 6.2 ( 3)
04 0.4447 ( 5) -0.02750(l6) 0.1474 ( 3) 6.6 ( 3)
N1 0.1670 ( 4) 0.10256 (17) 0.14508(22) 2.8l(21)
N2 0.2931( 4) 0.16825(16) 0.05388(22) 2.75(21)
N3 0.5211( 4) 0.17013(17) 0.16766(23) 3.06(22)
N4 0.3927( 4) 0.10596(16) 0.25927(23) 2.72(2l)
N5 0.3284( 5) -0.08760(l8) 0.2571( 3) 4.0 ( 3)
N6 0.5838( 6) -0.00936(21) 0.2490( 3) 6.8 ( 4)
C1 0.1181 ( 5) 0.07708(22) 0.1969( 3) 3.2 ( 3)
C2 -0.0161( 5) 0.06255(23) 0.1639( 3) 4.0 ( 3)
C3 -0.0411( 5) 0.07893 (23) 0.0942( 3) 4.1 ( 3)
C4 0.0707( 5) 0.1043l(2l) 0.0824( 3) 3.2 ( 3)
C5 0.0787( 5) 0.12996(22) 0.0191( 3) 3.5 ( 3)
C6 0.1773( 5) 0.16062(21) 0.0055( 3) 3.2 ( 3)
C7 0.1754( 5) 0.18932(22) -0.0602(3) 3.4 ( 3)
C8 0.2891( 5) 0.21465(22) -0.0508(3) 3.4(3)
C9 0.3635( 5) 0.20053(21) 0.0214 ( 3) 3.0(3)

 

Table VI-3 (cont'd)

176

 

C10
C11

C12
C13
C14
C15
C16
C17
C18
C19
C20
C21
C22
C23
C24
C25
C26
C27
C28
C29
C30
C31

C32
C33

0.4897( 5)
0.5641( 5)
0.6973( 5)
0.7343( 5)
0.6228( 5)
0.6171( 5)
0.5139( 5)
0.5145( 5)
0.3941( 5)
0.3167( 5)
0.1873( 5)
-0.1114( 6)
-0.l637( 6)
-0.l750( 9)
0.0643( 6)
0.3287( 6)
0.2753( 8)
0.7779( 6)
0.8639(10)
0.8654( 6)
0.6306( 6)
0.6519( 7)
0.3557( 9)
0.1118( 5)

0.21510(21)
0.20060(22)
0.21431(23)
0.19071(23)
0.16390(21)
0.13605(23)
0.11115(21)
0.08685(21)
0.06879(20)
0.08081(20)
0.06718(20)
0.0361 ( 3)
0.0721 ( 3)
0.0229 ( 4)
0.1910 ( 3)
0.2514 ( 3)
0.3039 ( 3)
0.2500 ( 3)
0.2245 ( 4)
0.1921 ( 3)
0.0848( 3)
0.1343 ( 4)
0.04255(24)
0.04631(21)

0.0518 ( 3)
0.1187 ( 3)
0.1477 ( 3)
0.2131( 3)
0.2260 ( 3)
0.2874( 3)
0.3048( 3)
0.3731( 3)
0.371 1( 3)
0.2980( 3)
0.2688( 3)
0.1986( 4)
0.0376( 4)
-0.0006( 5)
-0.1250( 3)
-0.1011( 3)
-0.0970( 4)
0.1127( 4)
0.0795( 5)
0.2649( 4)
0.4365( 3)
0.4808( 4)
0.4330( 3)
0.3206( 3)

3.5 ( 3)
3.4 ( 3)
4.0 ( 3)
3.9 ( 3)
3.3 ( 3)
35(3)

2.9 ( 3)
3.0 ( 3)
2.8 ( 3)
2.8 ( 3)
2.7 ( 3)
6.9 ( 4)
6.3 ( 4)
11.8 ( 6)
5.5 ( 4)
4.5 ( 3)
7.4 ( 5)
6.1 (4)
11.5( 8)
6.4 ( 4)
4.5 ( 3)
8.7 ( 5)
4.2(3)

3.0(3)

 

Table VI-3 (cont'd)

177

 

C34
C35
C36
C37
C38
C39
C40
C41
C42
C43
C44
C45
C46
C47
C48
C49
C50
C51
C52
C53
C54
C55
C56

0.0569( 5)
-0.0234( 6)
-0.0534( 6)
0.0005( 5)

-0.0332( 6)

0.0171( 7)
0.1083( 7)
0.1463( 6)
0.0888( 5)
0.2509( 6)
0.2981( 6)
0.3923( 6)
0.4525( 6)
0.5256( 6)
0.4338( 6)
0.6333( 6)
0.5909( 6)
0.4959( 6)
0.7071( 7)
0.5333( 6)
0.3193( 7)
0.5854( 8)
0.4775( 8)

0.08251(23)
0.0707 ( 3)
0.0206 ( 3)
-0.01872(23)
-0.0709 ( 3)
-0.1092 ( 3)
-0.09885( 4)
-0.04994(23)
-0.00747(22)
-0.04177(22)
-0.l 1602(23)
-0.15685(22)
-0.18093(23)
-0.l4075(25)
-0.09777(23)
-0.1 1908(24)
-0.09476(22)
-0.13189(24)
-0.0885 ( 3)
-0.04l75(24)
-0.1976 ( 3)
-0.1643 ( 3)
0.0712 ( 3)

0.3564( 3)
0.4027( 4)
0.4110( 3)
0.3777( 3)
0.3869( 4)
0.3552( 4)
0.3146( 4)
0.3033( 3)
0.3328( 3)
0.2624( 3)
0.1927( 3)
0.1819( 3)
0.2534( 4)
0.3061( 3)
0.3156( 3)
0.2723( 4)
0.1972( 3)
0.1485( 3)
0.1638( 4)
0.1979( 3)
0.1285( 4)
0.3793( 4)
0.0577( 4)

39(3)
49(4)
50(4)
39(3)
53(4)
6J(4)
55(4)
30(3)
32(3)
42(3)
42(3)
40(3)
49(4)
40(3)
45(4)
5J(3)
4J(3)
40(3)
67(5)
47(4)
64(4)
73(5)
7.6(5)

 

Biso is the Mean of the Principal Axes of the Thermal Ellipsoid.

178

Table VI-4. Selected Bond Distance (A) and Angle (deg) and Their
Estimated Standard Deviations for RuCONKAP(MeOH) and

 

 

 

RuCONKAmideP(MeOH).
RuCONKAP RuCONKAmideP
Distance (A)
Ru-N 1 2.050(7) Ru-Nl 2.049(4)
Ru-N2 2.050(7) Ru-N2 2.058(4)
Ru-N3 2.054(7) Ru-N3 2.055(4)
Ru-N4 2.051(6) Ru-N4 2.054(4)
Ru-C 1.781(9) Ru-C 1.779(6)
C-O 1.160(11) C-O 1.154(7)
Ru-O(MeOH) 2.202(6) Ru-O(MeOH) 2.205(4)
Angle (deg)

Ru-C-O 177.5(8) Ru-C—O 177.3(6)
O(MeOH)-Ru-C 177.1(3) O(MeOH)-Ru-C l77.83(20)
Nl-Ru-C(O) 92.3(4) Nl-Ru-C(O) 9230(22)
N2-Ru-C(O) 90.6(3) N2-Ru-C(O) 91 .29(22)
N3-Ru-C(O) 94.3(4) N3-Ru-C(O) 94.34(22)
N4-Ru-C(O) 95.3(3) N4-Ru-C(O) 9403(22)
O(MeOH)-Ru-N1 87.0(3) O(MeOI-D-Ru-Nl 87.3006)
O(MeOI-D-Ru-NZ 86.6504) O(MeOID-Ru-NZ 8659(16)
O(Me0H)-Ru-N3 86.5(3) O(MeOH)-Ru-N3 8607(16)
O(MeOH)-Ru-N4 87.47(24) O(MeOH)-Ru-N4 8808(16)
Nl-Ru-N2 91.7(3) N l-Ru-N2 9208(16)
N1-Ru-N3 173.4(3) N1-Ru-N3 173.3608)
N1-Ru-N4 87.7(3) N1-Ru-N4 87.6206)
N2-Ru-N3 88.4(3) N2-Ru-N3 8778(17)
N2-Ru-N4 174.1(3) N2-Ru-N4 174.6707)
N3-Ru-N4 91.5(3) N3-Ru-N4 91.9006)

 

179

Ru .Afiw

\0

08 W

1‘

.A300EE<V_ZOU=M 00 0:50:50 awn-EEO 43> 053%

D...
Naumao L“.— V

8025‘ \v a 08 i...
94,.
03 o on
‘ [Id W
3%.!» No 0 Vs

2 .thfl
98.0 9.8 8

\. \
\ )v 30 SJ 9 ova

P
$0
$0 .
\v «x
03.3...) iv .0.
as sew/7,070.

\ui - 9
NB fir H8 63 3.8 05

 

.Eoozzfiefiioué 06 8525... $55 .~-_> 050$

 

0
610.
l.
NHU ...\~
4 .
03 ‘. . 08 s -
29 s a
who mz
02 ‘W‘ .\\
332.8 «a 0.86:; o“ 8
'f’.‘ \‘l’ ‘0
V. 30 .. .u .04 m5
mno .'
040 60
Ono): H1 28‘.
'....>«' r’//..w.n.111.mu.' 01‘“ ll/w. “no
\flJH \. .0 ‘ 3'3. ’\
«3 W.» Go 03 5 03

181

and 177.3(5)° for RuCONKAmideP, which agree with those found in other
RuCO or FeCO porphyrins (Table VI-5).

The average Ru-N(porphyrin) distances of RuCONKAP(MeOH) and
RuCONKAmideP(MeOH) are 2.054(4) and 2.051(7), respectively. These
results agree within experimental error with those found for other
RuCOporphyrins (Table VI-S). The deviations from planarity of the
porphyrin mean plane are 0.2A, comparable with those found in other

metalloporphyrins.
2. IR studies of RuCOporphyrins

Table VI-6 lists the results of infrared spectroscopic studies of the C-
O vibration of RuCOporphyrins. Literature results from RuCOporphyrins
having various trans ligands are included in Table VI-6 as well. According
to the reported uco range of 1920-1960 cm'l, the CO vibration for
RuCONKAP is characterized at 1931 cm'1 and for RuCONKAmideP, at
1927 cm'l. Both RuCOporphyrins exhibit a very strong and sharp CO
vibration. Since in both compounds methanol is a trans ligand, the
difference must be brought about by H-bonding on methanol, perturbing
the electron density on methanol oxygen and causing the shift in C-O

vibration.

3. IR Studies of FeCOporphyrins

Table VI-7 lists the C-0 vibrations of FeCOporphyrins. In~ analogy
to the ruthenium system, the FeCO complexes of NKAP and NKAmideP
most likely have a water molecule (from aqueous dithionite solution)

trapped between the metal and the Kemp’s acid and acting as the sixth

182

 

 

8.0 820 $6: €02 3:: 680 89300800".
3.0 6002 8:; €05 $83 a 3-283060065006833
28 $53 83: 64:2 68: 65 885088388
03 $502.0 $3: 6:2; 63: 648.0 moNEeomoooovéaové
523 $83 63E 8:3: 53: 508.0 2330088
c 680 So: 60: 3:2 663.0 efiosmzfioué
one @020 6;: 39.2 623 3480 8” 053268098805
€83 $2.: 2:8: 555 SE: 8062:5288
$83 603: 6%: 6025 $480 5002000085288
vaswwm 33.: 3030-068 200.0 $0 0.2 202.: >6 85.888

 

.mctEBoméS0E 0033:3000 @0000_0m .«o 2000308800 R03 29?. EB 30 0053me 28m 6.; 030,—.

 

183

2 Que EACOU—E

 

S Re zavsméamovoosm

2 one fieggxfieoeooé
x83 £5 33 Eoozvnzmzouni
x83 as 82 Eooziogegooé
oocosmom 7:8 009 mccsomfioo

 

mcfizeaové é 22:25 0-0 .95 Ba.

184

 

 

an 82 Exmmboufi

an 2.2 Evasoeooom

o 32 EEQBEQUE
is» as one 8£E§zoo£
#53 as $2 6£E8€<M28£
cog—Bowed :5 co 9 3:23:80

 

manageaouom § 88%; 0-0 .E> Ba.

185

ligand to iron. The result of such H-bonding would cause a increase in
electron density on the water oxygen, and therefore make it a stronger

ligand comparing to a non-bonded water molecule.

4. Trans Ligand Effect in Affecting CO Vibration in M-
COporphyrins

CO bonding has been recognized as being highly sensitive to its trans
ligand strength.5'3’10'15 The existence of trans ligand shifts the CO
stretching frequency to lower energy (Table VI-6); RuCOTPP has CO
vibration at 1945 cm“1 without any trans ligand. As shown in Table VI-S
of selected carbonylated metalloporphyrins, the geometry of
carbonylmetalloporphyrins varies due to different trans ligands. In the
case of RuCOporphyrins, as ethanol being a weaker ligand than pyridine, a
longer C-O bond and a shorter Ru-C distance in RuCOTPP(EtOH) are
observed as compared to RuCOTPP(py). Similar correlation exists in
FeCOporphyrins. For the RuCONKAP(MeOH) and RuCONKAmideP
(MeOH), there are slight differences between them. RuCONKAP(MeOH)
has a shorter Ru-O(MeOH), longer Ru-C and longer C-O distance as well.
CO vibration from IR studies displayed that CO is 4 cm'1 stronger in
RuCONKAP(MeOH). The same magnitude of CO frequency shift has been
observed for FeCONKAP(H20) comparing to FeCONKAmideP(H20), as
shown in Table VI-7. The higher uco detected for the NKAP complexes
suggests a higher bond order for the coordinated CO ligand and hence, a
weaker trans ligand effect. Since the difference affecting the trans ligand

field comes solely from the H-bonding between the methanolic proton and

186

the carbonyl oxygen of the Kemp’s acid versus amide, it is good evidence

that amide C=O is a better electron donor than the acid C=O.

D. Conclusion

The FeCO and RuCO complexes of NKAP and NKAmideP have
been synthesized and investigated by X-ray crystallography and IR
spectroscopy. The CO ligand in the ruthenium complexes is located at the
site opposite from the Kemp's acid or the amide cap with a metal-bound
methanol serving as the trans ligands to CO. The CO stretching vibration
is found to be 4-5 cm'1 stronger in the NKAP complex comparing to that
of N KAmideP. The same magnitude is also detected for the FeNKAP
versus FeNKAmideP, arguing strongly that a H20 molecule, instead of
MeOH, is present as the trans ligand in the iron systems. The fact that CO
prefers the opposite coordination site from the proton donor indicates that
there is little stabilization of the CO ligand by H—bonding in the Fe- and

Ru-porphyrin complexes.

187

E. Reference

1. “Iron porphyrin” Part I. Eds: Lever, A. B. P. and Gray, H. B.;
Addison-Wesley, London, 1982.

2. (a) Caughey, W. S.; Barlow, C. H.; O'Keeffe, D. H.; O'Tode, M. C.
Ann. N. Y. Acad. Sci. 1972, 206, 296-309.
(b) Buchler, J. W.; Kokisch, W. B.; Smith, P. D. Struc. Bonding
(Berlin) 1978, 34, 79-134.

3. (a) Huber, R.; Epp, 0.; Formanek, K. J. Mol. Biol. 1970, 52, 349-
354.
(b) Heidner, E. J .; Ladner, R. C.; Perutz, M. F. J. Mol. Biol. 1976,
104, 707-712.
(c) Norvell, J. C.; Nunes, A. C.; Schoenborn, B. P. Science 1975,
190, 568-570.
(d) Tucker, P. W.; Phillips, S. E. V.; Perutz, M. F.; Houtchens, R. A.;
Caughey, W. S. Proc. Natl. Acad. Sci. USA 1978, 75, 1076-1080.
(e) Steigemann, W.; Weber, E. J. Mol. Biol. 1979, 127, 309-338.
(f) Baldwin, J. M. J. Mol. Biol. 1980, 136, 103-128.

4. Collman, J. P. Acc. Chem. Res. 1977, 10, 265-172.

5. Goedken, V. L.; Peng, S.-M.; Molin-Norris, J .; Park, Y. J. Am.
Chem. Soc. 1976, 98, 8391-8400.

6. Scheidt, W. R.; Haller, K. J .; Fons, M.; Mashiko, T.; Reed, C. A.
Biochem. 1981, 20, 3653-3657.

7. (a) Peng, S.-M.; Ibers, J. A. J. Am. Chem. Soc. 1976, 98, 8032-8036.

10.

11.

12.

13.

14.

15.

188

(b) Alben, J. 0.; Caughey, W. S. Biochem. 1968, 7, 175-183.

Caron, C.; Mitschler, A.; Riviére, G.; Ricard, L.; Schappacher, M.;
Weiss, R. J. Am. Chem. Soc. 1979, 101, 7401-7402.

Collen, D.; Jun, E. M. J. Chem. Soc. Chem. Commun. 1972, 584-585.

Bonnet, J. J.; Eaton, S. S.; Eaton, G. R.; Holm, R. H.; Ibers, J. A. J.
Am. Chem. Soc. 1973, 95. 2141-2149.

Slebodnick, C.; Kim, K.; Ibers, J. A. Inorg. Chem. 1993, 32, 5338-
5342.

Little, R. G.; Ibers, J. A. J. Am. Chem. Soc. 1973, 95, 8583-8590.

Tsutsui, M.; Ostfeld, D.; Francis, J. N. J. Coord. Chem. 1971, I, 115-
1 19.

Eaton, G. R.; Eaton, S. S. J. Am. Chem. Soc. 1975, 97, 235-236.

Chow, B. C.; Cohen, 1. A. Bioinorg. Chem. 1971, I, 57-63.

"llllllllllllllllli“