Article
Inorganic Chemistry, Vol. 48, No. 22, 2009 10563
3
All CD data sets were averaged together in the overlapping
spectral regions.
Electrochemical data were obtained on a Princeton Applied
Research PARSTAT 2273 potentiostat using a standard three-
electrode cell (pyrolytic graphite edge working electrode, Pt disk
auxiliary electrode, SCE reference electrode). Concentrations of
refinements are based on Fourier Filtered k (χ) data over the
-
1
˚
energy range of k = 2.0-12.5 A and back-transformed from
0
˚
r = 1.0-2.5 A.
Electronic Structure, Excited State, and EPR Calculations. All
electronic structure calculations were performed using Neese’s
3
6
software package ORCA version 2.6.35. Geometry optimized
(GO) structures were generated from minimized NiSOD active-
sites on oxidized forms, and used convergence criteria (in au) of
root-mean-square (rms) and maximum forces of 0.0003 and
0.0001, respectively, and rms and maximum gradients of 0.002
and 0.001, respectively. The group attached to the N(ε) of the
II
M1
{
Ni (SOD -Im-X)} in 50 mM NEM buffer were ∼0.7-1.0
mM, and NaCl was used as the supporting electrolyte (100 mM).
The solutions were sparged with Ar prior to recording the data.
Square wave voltammograms were recorded with a pulse height
of 15 mV at a frequency of 5 Hz. The oxidation and reduction
waves were then extracted from the background capacitance by
applying a cubic spline function before and after the oxidation/
reduction peaks. Peak positions were then determined by taking
the first derivatives of these data.
III
Me
His(1) imidazole ring was varied between Me (Ni (SOD )), H
)), and -SO H
III
(Ni (SOD )), 2,4 dinitrophenyl (Ni (SOD
H
III
DNP
2
III Tos
(Ni (SOD )). GO calculation on all species utilized the local
3
density approximation of Vosko, Wilk, and Nusair, the
7
3
8-40
41,42
EPR spectra were recorded using ∼0.05 mM solutions of
gradient correction of Becke
VWN), the TZVP
aug-TZVPP
and Perdew
for all non-ligating atoms, and the
basis set for Ni, S, and all ligating N atoms.
(BP86/
III
M1
43-45
{
of I in EtOH) as 1:1 mixtures of buffer/glycerol (buffer =
Ni (SOD -Im-X)} (generated by the addition of 0.5 equiv
4
3-47
2
5
0 mM NEM pH 7.4) in quartz EPR tubes. The spectra were
Frequency calculations on all GO structures were performed
using the Becke’s three parameter hybrid functional for ex-
change with the Lee-Yang-Parr functional for correlation
recorded at 77 K in a quartz EPR finger dewar on a Varian E4
EPR spectrometer interfaced to a PC through a Scientific Soft-
ware Services EWWIN system. Data were averaged over 40
scans. The following experimental parameters were used: micro-
wave frequency = 9.07-9.12 GHz; microwave power =
4
8,49
(the B3LYP hybrid functional),
two sided displacements,
4
3-45
43-47
the TZVP for all non-ligating atoms, the aug-TZVPP
basis set for Ni, S, and all ligating N atoms, a 434 point Lebedev
-
7
angular mesh, and convergence criteria of 10 E in energy. In
2
1
.5-5.0 mW; modulation amplitude = 10 G; time constant =
0 ms; conversion time = 10 ms; gain = 2 ꢀ 10 .
h
4
addition, vibrational frequencies were also obtained using
5
0
III
Me
III
Gaussian 03 for Ni SOD , Ni SOD
DNP
III
, Ni SOD
Tos
Resonance Raman data were obtained using a modified Jobin
to
provide input-files for Lehnert’s program for performing the
Yvon U1000 high resolution double monochromator employ-
ing 1800 groves/mm gratings and a PMT detector. The gratings
were driven by a microstepper motor (50 nm/step resolution)
attached to the cosecant bar, and the output from the PMT was
recorded using a DATAQ DI-158 data acquisition module. The
microstepper motor and data acquisition module were con-
trolled by a PC using in-house written software in C++. The
monochromator was calibrated using the Hg emission lines
from a low-pressure Hg(Ar) lamp. Excitations were provided
with a 405 nm solid state diode laser (bandwidth ∼5 nm)
provided by Opto Engine LLC with ∼30 mW of laser power
at the sample. The light from the laser was passed through a
monochromator containing a 2400 grooves/mm holographic
grating (for selecting λex = 405.0 nm) and then focused onto the
sample. Data were collected at room temperature in quartz
fluorescence cuvettes or in NMR tubes in a quartz EPR finger
dewar at 77 K using a 135° backscattering geometry. Samples
were recorded in 1:1 mixtures of buffer/glycerol with concentra-
3
2,51-53
QCA-NCA.
As these calculations were to provide for
an initial set of force constants as input for the QCA-NCA
3
8-42
programs, we utilized the BP86/VWN functional
TZVP basis set on all atoms.
and
4
3-45
EPR g-values and superhyperfine coupling constants were
calculated by solving the coupled-perturbed SCF (CP-SCF)
5
4,55
equations.
tional,
These calculations utilized the B3LYP func-
basis-set for all non-ligating atoms,
basis set for Ni and S, and Kutzelnigg’s
4
8,49
43-45
the TZVP
4
3-47
the aug-TZVPP
NMR/EPR basis set (IGLO-III) for all ligating N atoms. All
5
6
orbitals from -100 to 100 E of the HOMO/LUMO gap were
h
considered for the EPR calculations, with the center of electro-
nic charge defined as the origin of the g-matrix.
(36) Neese, F. In ORCA, An Ab Initio, Density Functional, and Semi-
empirical Program Package, 2.6.35 ed.; Universitat Bonn: Bonn, Germany,
2008.
III
tions ranging between 1-5 mM. All Ni species were generated
by adding concentrated I dissolved in EtOH to the reduced Ni
2
II
(37) Vosko, S. H.; Wilk, L.; Nusair, M. Can. J. Phys. 1980, 58, 1200–1211.
(
38) Becke, A. D. J. Chem. Phys. 1986, 84, 4524–4529.
metallopeptides. All spectra were independently calibrated by
using an internal standard of acetaminophen. Force constants
were obtained initially from DFT calculations (vide infra) and
then subsequently refined using the Quantum Chemistry As-
sisted Normal Coordinate Analysis (QCA-NCA) procedure of
(39) Becke, A. D. Phys. Rev. A: Gen. Phys. 1988, 38, 3098–3100.
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41) Perdew, J. P. Phys. Rev. B: Condens. Matter Mater. Phys. 1986, 33,
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(
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2
Lehnert and Tuczek.
Ni K-edge X-ray absorption data were collected on beamline
X3b at the National Synchrotron Light Source (Brookhaven
National Laboratories; Upton, NY) as previously described.
2577.
(
44) Ahlrichs, R.; coworkers unpublished.
2
4
(45) Neese, F. unpublished results.
(
46) Balabanov, N. B.; Peterson, K. A. J. Chem. Phys. 2005, 123, 64107.
III/II
M1
Samples of ∼0.7-3 mM of {Ni
(SOD -Im-X)} (50 mM
(47) Woon, D. E.; Dunning, T. H., Jr. J. Chem. Phys. 1993, 98, 1358–
NEM buffer, pH 7.4) were injected between windows made from
Kapton tape in aluminum sample holders, and quickly frozen in
liquid nitrogen. All spectra represent the average of 5 to 10
data sets. Data were analyzed using the software packages
1371.
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(
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34,35
EXAFS123 and FEFF 8.2
as previously described. All
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006, 45, 2795–2811.
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580.
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(
(
32) Lehnert, N.; Tuczek, F. Inorg. Chem. 1999, 38, 1659–1670.
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2
005.
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(
(55) Neese, F. Curr. Opin. Chem. Biol. 2003, 7, 125–135.
(56) Kutzelnigg, W.;Fleischer, U.;Schindler, M.The IGLO-Method: Ab-initio
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(