G. Hçrner et al.
[43]
ÀC
of 5-mJpulseÀ1 or 7-mJpulseÀ1, respectively. Transient decays were re-
corded at individual wavelengths by the step-scan method with a step dis-
tance of 5 nm in the range of 300 to 800 nm and obtained as the mean
signals of 6 to 16 pulses. Spectral resolution was in the range of Æ3 nm.
Samples for LFP were rigorously deoxygenated by flushing with analyti-
cal-grade nitrogen in a circulating flow system (55-mm Suprasil quartz
cell) for 20 min prior to and kept under nitrogen during measurement.
known spectrum of bp was used in the regression. The tyrosyl radical
C
Tyr(O ) was represented in the regression analysis by a spectrum mea-
sured in water by pulse radiolysis.[44a] The LFP spectra in our study were
recorded at substantially lower resolution, which leads to dampening of
C
the very narrow absorption feature of Tyr(O ) at 405 nm. Thus, the molar
C
absorption coefficient reported in the cited work for Tyr(O ) (eTyr
(405 nm)=3200mÀ1 cmÀ1) appeared to be inadequate. A value of eTyr
(405 nm)=1900mÀ1 cmÀ1 for acetonitrile solution, which is in accord with
Synthesis: Chemicals and solvents (Sigma–Aldrich and BACHEM) for
synthesis were of highest available analytical grade and were used with-
out further purification. Synthesis of the dyads followed the routines of
carbodiimide-induced amide-coupling (for details of procedures and char-
acterization, see Supporting Information). The identity and purity of the
[44b]
C
literature data for a protein-bound Tyr(O ),
was extracted from bimo-
lecular quenching experiments of bp with N-Boc-Tyr-OMe, based on
C
C
equimolar formation of Tyr(O ) and bpH .
Computational methods: The statistical distribution of the distances
(pair-distribution function), rO···O, between the carbonyl oxygen atom of
the bp moiety and the Tyr hydroxylic oxygen was calculated from the po-
1
dyads were studied by H and 13C NMR and combustion analysis. The ob-
tained NMR spectra were in accord with the molecular structures of 1a–
d. Combustion analysis gave slight deviations from ideal stoichiometry
for the benzamide 1b due to inclusion of residual solvent (diethyl ether,
ethyl acetate) in the crystalline foams, which could not be removed even
on extended evacuation. Attempts to produce the dyads as crystalline
material were not successful. However, because HPLC analysis proved
the absence of contaminants absorbing light with l>220 nm in all cases,
the dyads were used in this study without further work-up.
tential of mean force, w
(rO···O), by using Equation (14).[45]
ACHTREUNG
gðrOÁÁÁOÞ ¼ expfÀwðrOÁÁÁOÞ=kBTg
ð14Þ
These calculations were accomplished with umbrella sampling,[46] done in
conjunction with Langevin dynamics (LD)[47–49] and the CHARMM[50] all-
atom empirical potential. In the LD no explicit solvent molecules were
used, but the usual LD frictional drag of the solvent was factored in by
using a collision frequency for all heavy atoms equal to approximately
20 psÀ1, which reflects the viscosity of acetonitrile. We set the sampling
Spectral analysis of LFP intermediates: Quantum yields for the forma-
tion of the ith transient, Fi, were obtained by using relative actinometry
with benzophenone solutions of matched optical density in acetonitrile,
CH3CN [Eq. (12)]. The absorbed light intensity Ia is expressed as the re-
sulting triplet-state concentration in the actinometer solution with the
measured DAT at 525 nm. The known values of molar absorption coeffi-
windows at intervals of 0.1 and a force constant for the umbrella po-
tential of 20 kcalmolÀ1
(83.7 kJmolÀ1 À2). Each window simulation
À2
was run with a 1.5-fs time step for 50 ps, preceded by 9 ps of heating
from 0 to 300 K and 10 ps of equilibration. For the CHARMM27 force-
field calculations, we used version 7 of the HyperChem PC molecular-
modeling package.[51] To suppress unrealistic over-representation (see
above) of short distances, rO···O, with carbonyl and hydroxyl in hydrogen
bonding, the atom charges of all the atoms of the molecules were set to
zero which, in practice, is the equivalent of setting the dielectric permit-
tivity equal to infinity.
cient eT
ACHTREUNG
(525 nm)=6500mÀ1 cmÀ1 and triplet quantum yield FT(bp)=1.00
were also used in Equation (12).[31]
DAðljÞ
eðljÞ
ci
Ia
FTðbpÞ Â eTð525 nmÞ
DATð525 nmÞ
Fi ¼
¼
Â
ð12Þ
Here, DA(lj) and e(lj) denote the measured change in optical density
after laser pulsing of the sample solution, and the molar absorption coef-
ficient of the transient at the wavelength lj, respectively. The procedure
summarized in Equation (12) is limited to cases in which wavelengths
exist that are characteristic for a single transient. In the more common
case of convoluted spectra, a multi-regression analysis has to be done on
the optical transient spectra resulting from pulsed irradiation in order to
extract the individual transient concentrations ci. Within any time
window, following the excitation pulse, the absorbance of the signal is re-
lated to the concentrations and molar absorption coefficients of the tran-
Acknowledgements
This work was supported by the Research Training Network SULFRAD
(HPRN-CT-2002-00184) and by COST Chemistry CM0603. The authors
thank Prof. O. Brede and Dr. R. Hermann (University Leipzig, Germa-
ny) for access to the LFP equipment and for technical support. The com-
putation was performed employing the computation resources of the In-
terdisciplinary Centre for Mathematical and Computation Modelling of
the Warsaw University (G-24-13) and the Albigowa Biotechnology
Centre of the Rzeszow University of Technology. This paper is Document
No. NDRL-4751 from the Notre Dame Radiation Laboratory. G.L.H.
was a Fulbright Scholar at AMU.
sients through Beers Law DA=logCAHTREU(GN I0/I).
n
X
DAðljÞ ¼
ci  eiðljÞ Â l
ð13Þ
i¼1
In the regression analysis of the experimental spectra by Equation (13)
the concentrations of the individual transients times the optical path-
length, lci, are the regression parameters to be fit.[42] The sets of ei(lj)
are the reference spectra of the underlying transients enumerated by the
i-th subscript. The uncertainties for the ci are computed from the square
roots of the diagonal matrix elements of the covariance matrix for each
linear regression.
b) C. W. Hoganson, C. Tommos, Biochim. Biophys. Acta 2004, 1655,
116–122.
[2] For representative examples, see: a) G. W. Burton, K. U. Ingold,
D. A. Hrovat, J. L. Thomas, W. T. Borden, J. Am. Chem. Soc. 2002,
124, 11142—11147; d) M. Sjçdin, S. Styring, H. Wolpher, Y. Xu, L.
Sun, L. Hammarstrçm, J. Am. Chem. Soc. 2005, 127, 3855–3863;
e) I. J. Rhile, T. F. Markle, H. Nagao, A. G. DiPasquale, O. P. Lam,
11918; g) M. Sjçdin, T. Irebo, J. E. Utas, J. Lind, G. Merenyi, B.
Akermark, L. Hammarstrçm, J. Am. Chem. Soc. 2006, 128, 13076–
13083; h) F. Thomas, O. Jarjayes, H. Jamet, S. Hamman, E. Saint-
Reference spectra for the excited triplet states of the bp[Tyr dyads 1a–d
were obtained by LFP of diluted solutions of the model compounds 2a–c
in CH3CN and dichloromethane, CH2Cl2. Molar absorption coefficients
were obtained by comparison of the transient absorptions DA
ACHTER(UGN lmax) and
DATA(525 nm) of the actinometer solution at time delays for which no sig-
CHTREUNG
nificant decay has taken place, and under the assumption of unity triplet
yield.[31] Spectra of radical species relevant to this study were obtained by
bimolecular quenching of the respective triplet states of 2a–c in CH3CN
with methanol, MeOH, or 2-propanol. Spectra of the resulting ketyl radi-
C
cals (bpH , also: hemipinacol) were corrected by scaling with known
ÀC
molar absorption coefficients. Because ketyl anion radicals (bp ) turned
out to be of minor importance in this study, no attempts were made to es-
tablish a set of reference spectra for these species. If needed, a literature-
7928
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Chem. Eur. J. 2008, 14, 7913 – 7929