Supplemental Material: Coherences Observed in
vivo in Photosynthetic Bacteria Using TwoDimensional Electronic Spectroscopy
Peter D. Dahlberg1, Graham J. Norris2, Cheng Wang2, Subha Viswanathan2, Ved P. Singh2, and
Gregory S. Engel2,*
1. Graduate Program in the Biophysical Sciences, Institute for Biophysical Dynamics, and
the James Franck Institute, The University of Chicago, Chicago, IL 60637
2. Department of Chemistry, Institute for Biophysical Dynamics, and James Franck
Institute, The University of Chicago, Chicago, IL, 60637
* Corresponding Author E-mail: [email protected]
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Supplemental Figures:
Figure S1: Linear absorption spectra taken in 1 mm path length cuvette of isolated LH2 (black) and R. sphaeroides grown in H2O (blue) and 30% D2O (green) growth media, showing peaks at 800 nm and 850 nm resulting from rings of bacteriochlorophyll a known as B800 and B850. The cellular samples are strongly affected by Raleigh scattering and so the optical density of the samples at 800 nm was lowered to attain an optimal signal‐to‐noise ratio. Raleigh scattering has been removed from the whole cells’ absorption spectra. Figure S2: Phased 2D spectra at T=50 fs from isolated LH2 (left), cells cultured in 30% D2O (middle), and cells cultured in H2O (right). Data was phased to separately acquired pump‐probe spectra. 2
Figure S3: Bottom Row: Power spectral density at 1000 cm‐1 represented as a percentage of the normalized, integrated power spectrum from the absolute value data. Middle Row: Detail of the power spectrum at the 800‐850 nm upper cross peak boxed in the bottom row. Top Row: Phase of the 1000 cm‐1 oscillations over the same region, with the saturation determined by the power spectral density from the middle row. 3
Figure S4: In analogy to Figure 3, lifetime maps of coherences at the 800‐850 nm upper cross peak for isolated LH2 and R. sphaeroides grown in H2O and 30% D2O growth media. Lifetimes were calculated by fitting an exponentially decaying sinusoid to the residual of the bi‐
exponential fit to waiting time traces at each point, and are indicated by color. The saturation of each point is determined by the power spectral density of that point (see Figure 3). 4
Figure S5: The complete power spectra of the waiting time traces shown in figure 4 normalized to the integral of the power spectra. The 1σ error on the mean was calculated from the average of 16 scans. 5
Figure S6: A. Black diamond indicates the location of waiting time trace analyzed (λt= 795 nm λτ=850 nm) in B‐E. B. The raw waiting time from 0‐2800 fs before the subtraction of a bi‐
exponential. C. Residual from the bi‐exponential fit performed on panel B. D. The power spectrum of the residual from 0‐2800 fs. The broad Lorentzian from ~600‐1000 cm‐1 is attributed to the vibronic coherence at early waiting times. E. The power spectrum of the residual from 200‐2800 fs. Despite the larger noise floor on the edge of the spectra the 2 largest features are at 90 cm‐1, and 730 cm‐1, which are all well known vibrational modes of bacteriochlorophyll a. 6
Figure S7: A. Black diamond indicates the location of waiting time trace analyzed (λt= 792 nm λτ=845 nm) in B‐E. B. The raw waiting time from 0‐2800 fs before the subtraction of a bi‐
exponential. C. Residual from the bi‐exponential fit performed on panel B. D. The power spectrum of the residual from 0‐2800 fs. The broad Lorentzian from ~400‐800 cm‐1 is attributed to the vibronic coherence at early waiting times. E. The power spectrum of the residual from 200‐2800 fs. The 4 largest features are at 90 cm‐1, 190 cm‐1, 730 cm‐1, and 900 cm‐1 are all well known vibrational modes of bacteriochlorophyll a. 7
Details of Fitting Algorithms:
The fits to the data were obtained using a trust-region-reflective algorithm contained within
MATLAB’s lsqcurve fit function. The data, which extends to 2.8 ps in waiting time (T), was
initially fit to bi-exponential decays of the form
.
The residual from this fit was used to isolate quantum beating signals. The residual from T = 0200 fs, was also fit to an exponentially damped sine wave of the form:
sin
.
The power spectrum and phase of this oscillatory function from 0-200 fs is plotted in figure 3.
The lifetime from this fit is shown in figure S4 above.
Comment on Relative Noise Between Samples:
The noise in the H2O data set is slightly larger than that of the D2O sample. The authors attribute
this difference to the lower optical density of the H2O sample as compared to the D2O sample as
well as possible bacterial contamination present in the H2O sample leading to higher scatter.
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