Research Projects
:: Catalysis of Phosphate Diester Hydrolysis by Metal Ion Complexes
Studies on catalysis of RNA-hydrolysis by metal-ion complexes have
identified many active catalysts, but have provided only limited insight
into the relationship between the catalyst structure and the activity
towards cleavage of phosphate diesters. Consequently, the results from this
work allow qualitative comparisons of the activity for different catalysts,
but do not provide the type of data needed to formulate a mechanism for the
stabilization of the catalyst-bound transition state. Our aim is to develop
systematic methods for quantitative analyses of the catalytic activity of
these metal ion complexes, in order to rationalize why different catalytic
activities are observed for structurally related catalysts. This question
is of considerable intellectual interest, and its resolution will provide
insight into reaction mechanisms that can be used in the design of
catalysts with enhanced activity. Our work on these problems studies have
produced results which provide a detailed description of the catalytic
reaction mechanism along with interesting leads that will guide the design
of new catalysts.
(1) We have shown that the two metal-ion centers in Zn2(L2O) function
cooperatively in the cleavage of simple phosphodiesters and RNA. This
conclusion follows directly from the comparison of the relative catalytic
activities of a series of dinuclear catalysts of HpPNP cleavage at pH 7.6
and 25 C (Scheme 1). This Scheme shows that the total activity of several
dinuclear catalysts [Zn2(L5), Zn2(L6) and Zn2(L7)] is generally not much
greater than the sum of their parts [Zn(L1)]. By comparison, the dinuclear
catalyst Zn2(L2O) shows a catalytic activity that is 120-times greater than
observed for Zn(L1), or 60-fold greater than the activity expected for a
complex in which the tethered macrocycles react independently. See
Inorganic Chemistry, 42, 7737-7746 (2003).
(2) We have shown that the pendant hydroxyl group of Zn(L1OH) is protonated
at pH 7, but that the linker hydroxyl group at Zn2(L2O) is ionized at
neutral pH. Two lines of evidence provide support for this conclusion: (A)
Potentiometric titrations show that there is a pKa of < 6 for an acidic
oxygen in the formation of Zn2(L2O), but not for Zn(L1OH). 1H NMR spectra
show that the chemical shift of the signals for the protons closest to the
relevant hydroxyl groups of Zn2(L2O) and Zn(L1OH) remain fixed as the pH is
increased from = 7-10. (B) The X-ray structure of
[Zn2(L2O)(Cl)(H2O)2](ClO4)2 for a crystal obtained at pH 6 features a
bridging alkoxide that forms a chelate to the two Zn(II) ions. The two
Zn(II) ions have different coordination numbers and geometries in spite of
the symmetry of the ligand L2OH. This highlights the structural flexibility
of Zn(II). By comparison, the crystal structure of [Zn(L1OH)(Br)](Br)
obtained at pH 9.1 confirms that a neutral alcohol group is coordinated to
Zn(II). These data show that the bridging alkoxide group of Zn2(L2O)
shields the electrostatic interactions between the Zn(II) ions, and allows
the cations to be drawn close together in a complex of greatly enhanced
activity (Figure 1). This high density of positive charge at Zn2(L2O) is
ideal for providing electrostatic stabilization of the transition state for
cleavage of phosphodiesters relative to the reactant state, because there
is a net unit increase in negative charge on proceeding from the reactant
to transition state. See
Journal of the American Chemical Society, 125,
1988-1993 (2003).
(3) We have characterized the substrate specificity of Zn2(L2O) for
cleavage of nitrophenyl phosphate diesters. A comparison of the observed
first-order rate constants for hydroxide ion-catalyzed cleavage, and the
second-order rate constant for Zn2(L2O)-catalysed cleavage at pH of 7.0
shows that the rate acceleration from catalysis by 1 M of Zn2(L2O) is
50-fold larger for cleavage of HpPNP (9.8 x 106-fold) than for cleavage of
UpPNP (1.8 x 105-fold). This corresponds to 9.3 kcal/mol stabilization of
the transition state for cleavage of the minimal substrate HpPNP by
interaction with Zn2(L2O) (Scheme 3, S = HpPNP) and a smaller 7.1 kcal/mol
stabilization of the transition state for cleavage of the nucleoside
substrate UpPNP. The observation that the transition state for cleavage of
HpPNP is more strongly stabilized (tightly bound) by Zn2(L2O) than for
cleavage of UpPNP is surprising and revealing because, while the
opportunity for development of binding interactions to the nucleoside
substrate UpPNP transition state is greater than that for the minimal
substrate HpPNP, the observed interactions are significantly weaker.
Intramolecular tethering of the metal ions at the macrocyclic ligands
across the bridging alkoxide ion of Zn2(L2O) has the effect of generating a
highly charged core of unusual catalytic activity. These results provide
evidence for the notion that a significant drawback of this array is that
access to the catalytic core is restricted, so that HpPNP may bind closely
to the cationic core to achieve stabilization of the anionic transition
state, while the interaction of UpPNP with the catalyst is not as
effective, perhaps due to steric interactions between the catalyst and
nonreacting portions of this substrate. See
Journal of the Chemical
Society, Chemical Communications, 2832-2833 (2003).
(4) We have determined the effect of changing the metal cation on the
activity of dinuclear complexes of L2OH towards cleavage of HpPNP. The
relative reactivity of dinuclear Zn(II), Cu(II) and Cd(II) complexes of
L2OH have been rationalized by a consideration of the different geometric
preferences of complexes of the metal cations, and the relative Lewis
acidities of their complexes. A comparison of the X-ray crystal structures
Zn2(L2O) and Cu2(L2O) provides evidence that the difference in the
catalytic activity of these two complexes (Figure 4) is due to the larger
number of open coordination sites in the active Zn(II) complex compared to
the Cu(II) complex for interaction with the substrate. The subtle
differences in the catalytic properties of the dinuclear Cd(II) and Zn(II)
complexes are a consequence of the higher Lewis acidity of Zn(II) bound
water compared to Cd(II) bound water. See
Inorganic Chemistry
43, 1743-1750 (2004).
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