| 1. |
- Burzykowski, T, et al.
(author)
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Analysis of photon count data from single-molecule fluorescence experiments
- 2003
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In: Chemical Physics. - 0301-0104. ; 288:2-3, s. 291-307
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Journal article (peer-reviewed)abstract
- We consider single-molecule fluorescence experiments with data in the form of counts of photons registered over multiple time-intervals. Based on the observation schemes, linking back to works by Dehmelt [Bull. Am. Phys. Soc. 20 (1975) 60] and Cook and Kimble [Phys. Rev. Lett. 54 (1985) 1023], we propose an analytical approach to the data based on the theory of Markov-modulated Poisson processes (MMPP). In particular, we consider maximum-likelihood estimation. The method is illustrated using a real-life dataset. Additionally, the properties of the proposed method are investigated through simulations and compared to two other approaches developed by Yip et al. [J. Phys. Chem. A 102 (1998) 7564] and Molski [Chem. Phys. Lett. 324 (2000) 301].
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| 2. |
- Bäck, A, et al.
(author)
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Investigation of quantum effects on vibrational excitation of CF3Br scattering from graphite
- 2002
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In: Chemical Physics. - 0301-0104. ; 285:2-3, s. 233-244
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Journal article (peer-reviewed)abstract
- Mixed quantum–classical molecular dynamics simulations of vibrational excitation of CF3Br in collisions with graphite have been carried out. The quantum problem is made numerically manageable by a reduced dimensionality treatment of the internal degrees of freedom including only the C–Br stretch and the umbrella motion. These two coordinates are treated quantum mechanically as a 2D wavepacket whereas the translational and rotational degrees of freedom and the surface atoms are treated classically. A 3D wavepacket scheme where the distance to the surface is included among the quantum degrees of freedom is also considered as well as purely classical trajectories. It is found that the total vibrational excitation is quite low. Excitation of the C–Br stretch dominates with only a very small fraction of the excitation energy going into the umbrella motion. The 2D wavepacket calculations and the classical trajectories (initiated without zero point energy) give nearly identical results for the total excitation but the 2D wavepacket model excites the umbrella motion to a lesser extent. The 3D wavepacket method shows a considerable dependence on the initial width of the wavepacket due to the underlying mean-field approximation. All methods show a linear increase in vibrational excitation with increasing surface temperature, in agreement with previous experimental results.
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| 3. |
- Cacciani, P, et al.
(author)
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Predissociation of the 4p pi L-1 Pi Rydberg state of carbon monoxide
- 2002
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In: Chemical Physics. - 0301-0104. ; 282:1, s. 63-73
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Journal article (peer-reviewed)abstract
- Time-domain and frequency-domain spectroscopic experiments have been performed on the (4ppi)L(1)Pi, v = 0 Rydberg state in three isotopomers of carbon monoxide. Accurate values for the excited state lifetimes of the f-parity components have been determined: tau((CO)-C-12-O-16) = 1.08 +/- 0.05 ns, tau((CO)-C-13-O-16) = 72 +/- 10 ps and tau((CO)-C-13-O-18) = 29 +/- 6 ps. The spectral resolution in the frequency-domain experiment goes as far as the limit imposed by the natural lifetime; Q-branch lines, or f-parity components of the heavier isotopes, are resolved for the first time. Highly accurate transition frequencies are determined in a molecular beam experiment using comparison and interpolation with a saturated iodine reference standard. The results reveal a number of perturbations and predissociation mechanisms, displaying a high degree of complexity in the energetic region of the 4p Rydberg states of CO with strong isotopic effects. (C) 2002 Elsevier Science B.V. All rights reserved.
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| 4. |
- Dahlgren, T., et al.
(author)
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Electronic spectra of dithieno analogues of phenanthrene
- 1979
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In: Chemical Physics. - : Elsevier BV. - 0301-0104. ; 40:3, s. 397-404
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Journal article (peer-reviewed)abstract
- The magnetic circular dichroism (MCD) spectra of some dithieno analogues of phenanthrene: benzo [2,1-b;3,4-b′] dithiophene (I) benzo [1,2-b;4,3-b′] dithiophene (II), benzo [1,2-c;3,4-c′] dithiophene (III) and benzo [1,2-b;3,4-b′] dithiophene (IV) are reported. For I–III the spectra corresponding to two different transition moment directions could be obtained from low-temperature linear dichroism spectra. The results compare well with theoretical energies, oscillator strengths, moment directions and MCD B-terms which were obtained from semi-empirical quantum mechanical calculations in the π-electron approximation.
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| 5. |
- Davidsson, A., et al.
(author)
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A method for determination of the refractive index in a region of absorption. Anomalous dispersion of CS2 in the UV range
- 1975
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In: Chemical Physics. - : Elsevier BV. - 0301-0104. ; 8:1-2, s. 223-230
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Journal article (peer-reviewed)abstract
- A method is described for determining the refractive index of, e.g., a liquid solution, within an absorption band by studying the linear dichroism generated by different reflections at inclined optical incidence. The method requires a sensitive differential photometric technique, such as that accomplished in a circular dichroism spectrometer.The refractive index of CS2 is reported in the region 260–450 mm. and the result compared to that obtained from a Kramers-Kronig integration on the 320 nm absorption band. Though this band is fairly isolated the experimentally gained result was found more reliable. This was due to difficulties in obtaining an accurate absorption coefficient of liquid CS2 as well as to the fact that the integration had to be restricted to a finite spectral range.
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| 6. |
- Engdahl, Anders, et al.
(author)
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The Binary Complex Between Hydrogen Peroxide and Ozone: A Matrix Isolation Study.
- 2003
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In: Chemical Physics. - 0301-0104. ; 293:2, s. 203-209
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Journal article (peer-reviewed)abstract
- The interaction between hydrogen peroxide and ozone has been studied in argon matrices using infrared spectroscopy. The spectra show that hydrogen peroxide forms a weak hydrogen bond to one of the end oxygens of ozone. A comparison is made with other ozone complexes.
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| 7. |
- Feyziyev, Yashar, et al.
(author)
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Electron transfer from cytochrome b559 and tyrosineD to the S2 and S3 states of the water oxidizing complex in photosystem II
- 2003
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In: Chemical Physics. - 0301-0104. ; 294:3, s. 415-431
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Journal article (peer-reviewed)abstract
- We have investigated the electron transfer from reduced tyrosine YD (YDred) and cytochrome b559 to the S2 and S3 states of the water oxidizing complex (WOC) in Photosystem II. The EPR signal of oxidized cyt b559, the S2 state multiline EPR signal and the EPR signal from YD@? were measured to follow the electron transfer to the S2 and S3 states at 245 and 275 K. The majority of the S2 centers was reduced directly from YDred but at 245 K we observed oxidation of cyt b559 in about 20% of the centers. Incubation of the YDredS3 state resulted in biphasic changes of the S2 multiline signal. The signal first increased due to reduction of the S3 state. Thereafter, the signal decreased due to decay of the S2 state. In contrast, the YD@? signal increased with a monophasic kinetics at both temperatures. Again, we observed oxidation of cyt b559 in about 20% of the PSII centers at 245 K. This oxidation correlated with the decay of the S2 state. The complex changes can be explained by the conversion of YDredS3 centers (present initially) to YD@?S1 centers, via the intermediate YD@?S2 state. The early increase of the S2 state multiline signal involves electron transfer from YDred to the S3 state resulting in formation of YD@?S2. This state is reduced by cyt b559 resulting in a single exponential oxidation of cyt b559. Taken together, these results indicate that the electron donor to S2 is cyt b559 while cyt b559 is unable to compete with YDred in the reduction of the S3 state in the pre-reduced samples. We also followed the decay of the S2 and S3 states and the oxidation of cyt b559 in samples where YD was oxidized from the start. In this case cyt b559 was able to reduce both the S2 and the S3 states suggesting that different pathways exist for the electron transfer from cyt b559 to the WOC. The activation energies for the YDredS2->YD@?S1 and YDredS3->YD@?S2 transformations are 0.57 and 0.67 eV, respectively, and the reason for these large activation energies is discussed.
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| 8. |
- Garding, L., et al.
(author)
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Simple formulas for rotation averages of spectroscopic intensities
- 1979
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In: Chemical Physics. - : Elsevier BV. - 0301-0104. ; 41:3, s. 431-437
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Journal article (peer-reviewed)abstract
- We give a self-contained exposition of the “ensemble method”, a rule for calculating rotation averages of spectroscopic absorption intensities. The rule is mathematically exact and conceptually simple and applies to rotation averages for several axes of rotation occurring in helical and superhelical symmetry. A measure of dichroism, DI, is introduced which has a simple multiplicative property relative to axes of rotation. There are several applications to linear dichroism spectroscopy.
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| 9. |
- Giertz, A., et al.
(author)
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Vibrationally resolved photoelectron spectra of the carbon 1s and nitrogen 1s shells in hydrogen cyanide
- 2002
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In: Chemical Physics. - 0301-0104. ; 277:1, s. 83-90
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Journal article (peer-reviewed)abstract
- Vibrational structures of the C1s and N1s photoelectron spectra of gas-phase HCN have been investigated using monochromated third-generation synchrotron radiation. Both spectra exhibit resolved fine structure associated with several vibrationally excited states. In the C1s spectrum a single vibrational progression is observed, while the N1s spectrum is more complex. High-level ab initio calculations were performed to simulate the spectra and the agreement with the experimental results is good. Based on the calculations, the C1s ionisation is found to induce vibrations solely in the C≡N stretching mode with an energy of 280 meV, while the N1s ionisation generates vibrations also in the C-H stretching mode with an energy of about 387 meV, as well as combinations of these two modes.
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| 10. |
- Kropacheva, Tatyana N, et al.
(author)
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Spin conversion of cytochrome b559 in photosystem II induced by exogenous high potential quinone
- 2003
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In: Chemical Physics. - 0301-0104. ; 294:3, s. 471-482
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Journal article (peer-reviewed)abstract
- The spin-state of cytochrome b559 (Cyt b559) was studied in photosystem II (PSII) membrane fragments by low-temperature EPR spectroscopy. Treatment of the membranes with 2,3-dichloro-5,6-dicyano-p-benzoquinone (DDQ) converts the native low-spin (LS) form of Cyt b559 to the high-spin (HS) form characterized with the g= 6.19 and g= 5.95 split signal. The HS Cyt b559 was pH dependent with the amplitude increasing toward more acidic pH values (pH 5.5-8.5). The HS state was not photochemically active upon 77 and 200 K continuous illumination under our conditions and was characterized by a low reduction potential (=<0 V). It was also demonstrated that DDQ treatment damages the oxygen evolving complex, leading to inhibition of oxygen evolution, decrease of the S2-state EPR multiline signal and release of Mn2+. In parallel, studies of model systems containing iron(III) protoporphyrin IX chloride (FeIIIPor), which is a good model compound for the Cyt b559 prosthetic group, were performed by using optical and EPR spectroscopy. The interaction of FeIIIPor with imidazole (Im) in weakly polar solvent results in formation of bis-imidazole coordinated heme iron (FeIIIPor Im2) which mimic the bis-histidine axial ligation of Cyt b559. The reaction of DDQ with the LS FeIIIPor Im2 complex leads to its transformation into the HS state (g@?=5.95, g@?=2.00). It was shown that the spin conversion occurs due to the donor-acceptor interaction of coordinated imidazole with this high-potential quinone causing the displacement of imidazole from the axial position. The similar mechanism of DDQ-induced spin change is assumed to be valid for the native membrane Cyt b559 in PSII centers.
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