Low-energy chlorophyll states in the CP43 antenna protein complex: simulation of various optical spectra. II

The CP43 protein complex of the core antenna of higher plant photosystem II (PSII) has two quasidegenerate "red" absorption states. It has been shown in the accompanying paper I (Dang, N. C., et al. J. Phys. Chem. B 2008, 112, 9921.) that the site distribution functions (SDFs) of red-states A and B are uncorrelated and the narrow holes are burned in subpopulations of chlorophylls (Chls) from states A and B that are the lowest-energy pigments in their particular CP43 complexes and cannot further transfer energy downhill. In this work, we present the results of a series of Monte Carlo simulations using the 3.0-A structure of the PSII core complex from cyanobacteria (Loll, B., et al. Nature 2005, 303, 1040.) to model absorption, emission, persistent, and transient hole burned (HB) spectra. At the current structural resolution, we found calculated site energies (obtained from INDO/S calculations) to be only suggestive because their values are different for the two monomers of CP43 in the PS II dimer. As a result, to probe the excitonic structure, a simple fitting procedure was employed to optimize Chl site energies from various starting values corresponding to different A/B pigment combinations to provide simultaneously good fits to several types of optical spectra. It is demonstrated that the shape of the calculated absorption, emission, and transient/persistent hole-burned spectra is consistent with experimental data and our model for excitation energy transfer between two quasi-degenerate lowest-E states (A and B) with uncorrelated SDFs discussed in paper I. Calculations revealed that absorption changes observed near 670 nm in the non-line-narrowed persistent HB spectra (assigned to photoconversion involving Chl-protein hydrogen-bonding by Hughes (Biochemistry 2006, 45, 12345.) are most likely the result of nonphotochemical hole-burning (NPHB) accompanied by the redistribution of oscillator strength due to modified excitonic interactions. We argue that a unique redistribution of oscillator strength during the NPHB process helps to assign Chls contributing to the low-energy states. It is demonstrated that the 4.2 K asymmetric triplet-bottleneck (transient) hole is mostly contributed to by both A and B states, with the hole profile described by a subensemble of pigments, which are the lowest-energy pigments (B s- and A s-type) in their complexes. The same lowest-energy Chls contribute to the observed fluorescence spectra. On the basis of our excitonic calculations, the best Chl candidates that contribute to the low-energy A and B states are Chl 44 and Chl 37, respectively.     

Frequency-domain spectroscopic study of the PS I-CP43' supercomplex from the cyanobacterium Synechocystis PCC 6803 grown under iron stress conditions

Absorption, fluorescence excitation, emission, and hole-burning (HB) spectra were measured at liquid helium temperatures for the PS I-CP43' supercomplexes of Synechocystis PCC 6803 grown under iron stress conditions and for respective trimeric PS I cores. Results are compared with those of room temperature, time-domain experiments (Biochemistry 2003, 42, 3893) as well as with the low-temperature steady-state experiments on PS I-CP43' supercomplexes of Synechococcus PCC 7942 (Biochim. Biophys. Acta 2002, 1556, 265). In contrast to the CP43' of Synechococcus PCC 7942, CP43' of Synechocystis PCC 6803 possesses two low-energy states analogous to the quasidegenerate states A and B of CP43 of photosystem II (J. Phys. Chem. B 2000, 104, 11805). Energy transfer between the CP43' and the PS I core occurs, to a significant degree, through the state A, characterized with a broader site distribution function (SDF). It is demonstrated that the low temperature (T = 5 K) excitation energy transfer (EET) time between the state A of CP43' (IsiA) and the PS I core in PS I-CP43' supercomplexes from Synechocystis PCC 6803 is about 60 ps, which is significantly slower than the EET observed at room temperature. Our results are consistent with fast (< or =10 ps) energy transfer from state B to state A in CP43'. Energy absorbed by the CP43' manifold has, on average, a greater chance of being transferred to the reaction center (RC) and utilized for charge separation than energy absorbed by the PS I core antenna. This indicates that energy is likely transferred from the CP43' to the RC along a well-defined path and that the "red antenna states" of the PS I core are localized far away from that path, most likely on the B7-A32 and B37-B38 dimers in the vicinity of the PS I trimerization domain (near PsaL subunit). We argue that the A38-A39 dimer does not contribute to the red antenna region.     

New Insight into the Water‐Soluble Chlorophyll‐Binding Protein from Lepidium virginicum

This study describes new recombinant water‐soluble chlorophyll (Chl)‐binding proteins (WSCP) from Lepidium virginicum (LvWSCP). This complex binds four Chls (i.e. two dimers of Chls) per protein tetramer. We show that absorption, emission, hole‐burned (HB) spectra and the shape of the zero‐phonon hole (ZPH) action spectrum are consistent with the presence of uncorrelated excitation energy transfer between two Chl dimers. Thus, there is no need to include slow protein relaxation within the lowest excited state (as suggested in a previous analysis of cauliflower WSCP [Schmitt, F.‐J. et al. (2008) J. Phys. Chem. B, 112, 13951; Pieper, J. et al. (2011) J. Phys. Chem. B, 115, 4053]) in order to explain the large shift observed between the maxima of the ZPH action and emission spectra. Experimental evidence is provided which shows that electron exchange between lowest energy Chls and the protein may occur, i.e. electrons can be trapped at low temperature by nearby aromatic amino acids. The latter explains the shape of nonresonant HB spectra (i.e. the absence of antihole), demonstrating that the hole‐burning process in LvWSCP is largely photochemical in nature, though a small contribution from nonphotochemical hole burning (in resonant holes) is also observed.     

Advanced theory of excitation energy transfer in dimers

Previously, we developed a unified theory of the excitation energy transfer (EET) in dimers, which is applicable to all of the cases of excitonic coupling strength (Kimura, A.; Kakitani, T.; Yamato, T. J. Phys. Chem. B 2000, 104, 9276). This theory was formulated only for the forward reaction of the EET. In the present paper, we advanced this theory so that it might include the backward reaction of the EET as well as the forward reaction. This new theory is formulated on the basis of the generalized master equation (GME), without using physically unclear assumptions. Comparing the present result with the previous one, we find that the excitonic coupling strengths of criteria between exciton and partial exciton and between hot transfer and hopping (F?rster) mechanisms are reduced by a factor of 2. The critical coherency eta c is also reduced significantly.     

How solvent controls electronic energy transfer and light harvesting: toward a quantum-mechanical description of reaction field and screening effects

This paper presents a quantum-mechanical study of electronic energy transfer (EET) coupling on over 100 pairs of chromophores taken from photosynthetic light-harvesting antenna proteins. Solvation effects due to the protein, intrinsic waters, and surrounding medium are analyzed in terms of screening and reaction field contributions using a model developed recently that combines a linear response approach with the polarizable continuum model (PCM). We find that the screening of EET interactions is quite insensitive to the quantum-mechanical treatment adopted. In contrast, it is greatly dependent on the geometrical details (distance, shape, and orientation) of the chromophore pair considered. We demonstrate that implicit (reaction field) as well as screening effects are dictated mainly by the optical dielectric properties of the host medium, while the effect of the static properties is substantially less important. The empirical distance-dependent screening function we proposed in a recent letter (Scholes, G. D.; Curutchet, C.; Mennucci, B.; Cammi, R.; Tomasi, J. J. Phys. Chem. B 2007, 111, 6978-6982) is analyzed and compared to other commonly used screening factors. In addition, we show that implicit medium effects on the coupling, resulting from changes in the transition densities upon solvation, are strongly dependent on the particular system considered, thus preventing the possibility of defining a general empirical expression for such an effect.     

Rotationally resolved C2 symmetric conformers of bis-(4-hydroxyphenyl)methane: prototypical examples of excitonic coupling in the S1 and S2 electronic states

Rotationally resolved microwave and ultraviolet spectra of jet-cooled bis-(4-hydroxyphenyl)methane (b4HPM) have been obtained using Fourier-transform microwave and UV laser/molecular beam spectrometers. A recent vibronic level study of b4HPM [Rodrigo, C. P.; Mu?ller, C. W.; Pillsbury, N. R.; James, W. H., III; Plusquellic, D. F.; Zwier, T. S. J. Chem. Phys. 2011, 134, 164312] has assigned two conformers distinguished by the orientation of the in-plane OH groups and has identified two excitonic origins in each conformer. In the present study, the rotationally resolved bands of all four states have been well-fit to asymmetric rotor Hamiltonians. For the lower exciton (S(1)) levels, the transition dipole moment (TDM) orientations are perpendicular to the C(2) symmetry axes and consist of 41(2):59(2) and 34(2):66(2)% a:c hybrid-type character. The S(1) levels are therefore delocalized states of B symmetry and represent the antisymmetric combinations of the zero-order locally excited states of the p-cresol-like chromophores. The TDM polarizations of bands located at ≈132 cm(-1) above the S(1) origins are exclusively b-type and identify them as the upper exciton S(2) origin levels of A symmetry. The TDM orientations and the relative band strengths from the vibronic study have been analyzed within a dipole-dipole coupling model in terms of the localized TDM orientations, μ(loc), on the two chromophores. The out-of-the-ring plane angles of μ(loc) are both near 20° and are similar to results for diphenylmethane [Stearns, J. A.; Pillsbury, N. R.; Douglass, K. O.; Mu?ller, C. W.; Zwier, T. S.; Plusquellic, D. F. J. Chem. Phys. 2008, 129, 224305]. The in-plane angles are, however, rotated by 14 and 18° relative to DPM and, in part, explain the smaller than expected exciton splittings of these two conformers.     

Evaluation of data for atmospheric models: master equation/RRKM calculations on the combination reaction, BrO + NO2 --> BrONO2, a conundrum

Experimental data for the title reaction were modeled using master equation (ME)/RRKM methods based on the Multiwell suite of programs. The starting point for the exercise was the empirical fitting provided by the NASA (Sander, S. P.; Finlayson-Pitts, B. J.; Friedl, R. R.; Golden, D. M.; Huie, R. E.; Kolb, C. E.; Kurylo, M. J.; Molina, M. J.; Moortgat, G. K.; Orkin, V. L.; Ravishankara, A. R. Chemical Kinetics and Photochemical Data for Use in Atmospheric Studies, Evaluation Number 15; Jet Propulsion Laboratory: Pasadena, California, 2006)1 and IUPAC (Atkinson, R.; Baulch, D. L.; Cox, R. A.; R. F. Hampson, J.; Kerr, J. A.; Rossi, M. J.; Troe, J. J. Phys. Chem. Ref. Data 2000, 29, 167)2 data evaluation panels, which represents the data in the experimental pressure ranges rather well. Despite the availability of quite reliable parameters for these calculations (molecular vibrational frequencies (Parthiban, S.; Lee, T. J. J. Chem. Phys. 2000, 113, 145)3 and a value (Orlando, J. J.; Tyndall, G. S. J. Phys. Chem. 1996, 100, 19398)4 of the bond dissociation energy, D298(BrO-NO2) = 118 kJ mol-1, corresponding to DeltaH0o = 114.3 kJ mol-1 at 0 K) and the use of RRKM/ME methods, fitting calculations to the reported data or the empirical equations was anything but straightforward. Using these molecular parameters resulted in a discrepancy between the calculations and the database of rate constants of a factor of ca. 4 at, or close to, the low-pressure limit. Agreement between calculation and experiment could be achieved in two ways, either by increasing DeltaH0o to an unrealistically high value (149.3 kJ mol-1) or by increasing DeltaEd, the average energy transferred in a downward collision, to an unusually large value (>5000 cm-1). The discrepancy could also be reduced by making all overall rotations fully active. The system was relatively insensitive to changing the moments of inertia in the transition state to increase the centrifugal effect. The possibility of involvement of BrOONO was tested and cannot account for the difficulties of fitting the data.     

Photophysical properties of natural light-harvesting complexes studied by subsystem density functional theory

In this study, we investigate the excited states and absorption spectra of a natural light-harvesting system by means of subsystem density functional theory. In systems of this type, both specific interactions of the pigments with surrounding protein side chains as well as excitation energy transfer (EET) couplings resulting from the aggregation behavior of the chromophores modify the photophysical properties of the individual pigment molecules. It is shown that the recently proposed approximate scheme (J. Chem. Phys. 2007, 126, 134116) for coupled excitations within a subsystem approach to time-dependent DFT is capable of describing both effects in a consistent manner, and is efficient enough to study even the large assemblies of chromophores occurring in the light-harvesting complex 2 (LH2) of the purple bacterium Rhodopseudomonas acidophila. A way to extract phenomenological coupling constants as used in model calculations on EET rates is outlined. The resulting EET coupling constants and spectral properties are in reasonable agreement with the available reference data. Possible problems related to the effective exchange-correlation kernel are discussed.     

Luminescence and Raman spectra of acetylacetone at low temperatures

Raman spectra of acetylacetone were recorded for molecules isolated in an argon matrix at 10 K and for a polycrystalline sample. In the solid sample, broad bands appear superimposed on a much weaker Raman spectrum corresponding mainly to the stable enol form. The position of these bands depends on the excitation wavelength (514.5 and 488.8 nm argon ion laser lines were used), sample temperature, and cooling history. They are attributed to transitions from an excited electronic state to various isomer states in the ground electronic state. Laser photons have energies comparable to energies of a number of excited triplet states predicted for a free acetylacetone molecule (Chen, X.-B.; Fang, W.-H.; Phillips, D. L. J. Phys. Chem. A 2006, 110, 4434). Since singlet-to-triplet photon absorption transitions are forbidden, states existing in the solid have mixed singlet/triplet character. Their decay results in population of different isomer states, which except for the lowest isomers SYN enol, TS2 enol (described in Matanovi? I.; Dosli?, N. J. Phys. Chem. A 2005, 109, 4185), and the keto form, which can be detected in the Raman spectra of the solid, are not vibrationally resolved. Differential scanning calorimetry detected two signals upon cooling of acetylacetone, one at 229 K and one at 217 K, while upon heating, they appear at 254 and 225 K. The phase change at higher temperature is attributed to a freezing/melting transition, while the one at lower temperature seems to correspond to freezing/melting of keto domains, as suggested by Johnson et al. (Johnson, M. R.; Jones, N. H.; Geis, A; Horsewill. A. J.; Trommsdorff, H. P. J. Chem. Phys. 2002, 116, 5694). Using matrix isolation in argon, the vibrational spectrum of acetylacetone at 10 K was recorded. Strong bands at 1602 and 1629 cm(-1) are assigned as the SYN enol bands, while a weaker underlying band at 1687 cm(-1) and a medium shoulder at 1617 cm(-1) are assigned as TS2 enol bands.     

Bound state potential energy surface construction: ab initio zero-point energies and vibrationally averaged rotational constants

Collins' method of interpolating a potential energy surface (PES) from quantum chemical calculations for reactive systems (Jordan, M. J. T.; Thompson, K. C.; Collins, M. A. J. Chem. Phys. 1995, 102, 5647. Thompson, K. C.; Jordan, M. J. T.; Collins, M. A. J. Chem. Phys. 1998, 108, 8302. Bettens, R. P. A.; Collins, M. A. J. Chem. Phys. 1999, 111, 816) has been applied to a bound state problem. The interpolation method has been combined for the first time with quantum diffusion Monte Carlo calculations to obtain an accurate ground state zero-point energy, the vibrationally average rotational constants, and the vibrationally averaged internal coordinates. In particular, the system studied was fluoromethane using a composite method approximating the QCISD(T)/6-311++G(2df,2p) level of theory. The approach adopted in this work (a) is fully automated, (b) is fully ab initio, (c) includes all nine nuclear degrees of freedom, (d) requires no assumption of the functional form of the PES, (e) possesses the full symmetry of the system, (f) does not involve fitting any parameters of any kind, and (g) is generally applicable to any system amenable to quantum chemical calculations and Collins' interpolation method. The calculated zero-point energy agrees to within 0.2% of its current best estimate. A0 and B0 are within 0.9 and 0.3%, respectively, of experiment.     

Modeling study of non-line-narrowed hole-burned spectra in weakly coupled dimers and multi-chromophoric molecular assemblies

Several different models have been proposed to explain the origin of the complex anti-hole features observed in hole-burned (HB) spectra of excitonically coupled systems such as photosynthetic complexes. This lack of consensus presents a serious constraint on the interpretation of HB spectra and the underlying electronic structures of these systems. To resolve this problem we present results of modeling studies of non-resonant HB spectra taking uncorrelated excitation energy transfer and excitonic interactions into account. Simplified analytical results are compared with Monte Carlo simulations in which excitonic interactions are explicitly taken into account in order to disentangle a number of distinct effects. It is shown that these effects can accurately account for both hole shapes and the broad anti-hole structure observed in excitonically coupled systems. We argue that these models will provide a necessary framework for probing the electronic structure of these systems via HB spectroscopy.     

Internal electric field in cytochrome C explored by visible electronic circular dichroism spectroscopy

Electronic circular dichroism (ECD) is a valuable tool to explore the secondary and tertiary structure of proteins. With respect to heme proteins, the corresponding visible ECD spectra, which probe the chirality of the heme environment, have been used to explore functionally relevant structural changes in the heme vicinity. While the physical basis of the obtained ECD signal has been analyzed by Woody and co-workers in terms of multiple electronic coupling mechanism between the electronic transitions of the heme chromophore and of the protein (Hsu, M.C.; Woody, R.W. J. Am. Chem. Soc. 1971, 93, 3515), a theory for a detailed quantitative analysis of ECD profiles has only recently been developed (Schweitzer-Stenner, R.; Gorden, J. P.; Hagarman, A. J. Chem. Phys. 2007, 127, 135103). In the present study this theory is applied to analyze the visible ECD-spectra of both oxidation states of three cytochromes c from horse, cow and yeast. The results reveal that both B- and Q-bands are subject to band splitting, which is caused by a combination of electronic and vibronic perturbations. The B-band splittings are substantially larger than the corresponding Q-band splittings in both oxidation states. For the B-bands, the electronic contribution to the band splitting can be assigned to the internal electric field in the heme pocket, whereas the corresponding Q-band splitting is likely to reflect its gradient (Manas, E. S.; Vanderkooi, J. M.; Sharp, K. A. J. Phys. Chem. B 1999, 103, 6344). We found that the electronic and vibronic splitting is substantially larger in the oxidized than in the reduced state. Moreover, these states exhibit different signs of electronic splitting. These findings suggest that the oxidation process increases the internal electric field and changes its orientation with respect to the molecular coordinate system associated with the N-Fe-N lines of the heme group. For the reduced state, we used our data to calculate electric field strengths between 27 and 31 MV/cm for the investigated cytochrome c species. The field of the oxidized state is more difficult to estimate, owing to the lack of information about its orientation in the heme plane. Based on band splitting and the wavenumber of the band position we estimated a field-strength of ca. 40 MV/cm for oxidized horse heart cytochrome c. The thus derived difference between the field strengths of the oxidized and reduced state would contribute at least -55 kJ/mol to the enthalpic stabilization of the oxidized state. Our data indicate that the corresponding stabilization energy of yeast cytochrome c is smaller.     

Fluorescence studies of terrylene in a supersonic jet: indication of a dark electronic state below the allowed transition

Jet-cooled terrylene has been studied in helium buffer gas using a pulsed nozzle by means of laser-induced fluorescence. Fluorescence excitation and two-color depletion experiments (resulting in hole burning spectra) are presented. Analysis of the spectra leads to the conclusion that another excited electronic state is present in the vicinity of the allowed 1B1u state. Assuming (according to previous literature suggestions Karabunarliev, S.; Baumgarten, M.; Müllen, K. J. Phys. Chem. A 1998, 102, 7029) that this dark state is the 21Ag state, we discuss the vibrational structure of the fluorescence excitation spectrum in terms of two manifolds of vibronic states belonging to Sd(21Ag) and S1(1B1u) states. The anomalous shift between excitation and dispersed fluorescence spectra observed earlier for terrylene in a neon matrix is discussed as a consequence of terrylene electronic relaxation to the low-energy dark state.     

Mechanism and kinetics of the water-assisted formic acid + OH reaction under tropospheric conditions

In this work, we have revisited the mechanism of the formic acid + OH radical reaction assisted by a single water molecule. Density functional methods are employed in conjunction with large basis sets to explore the potential energy surface of this radical-molecule reaction. Computational kinetics calculations in a pseudo-second-order mechanism have been performed, taking into account average atmospheric water concentrations and temperatures. We have used this method recently to study the single water molecule assisted H-abstraction by OH radicals (Iuga, C.; Alvarez-Idaboy, J. R.; Reyes, L.; Vivier-Bunge, A. J. Phys. Chem. Lett. 2010, 1, 3112; Iuga, C.; Alvarez-Idaboy, J. R.; Vivier-Bunge, A. Chem. Phys. Lett. 2010, 501, 11; Iuga, C.; Alvarez-Idaboy, J. R.; Vivier-Bunge, A. Theor. Chem. Acc. 2011, 129, 209), and we showed that the initial water complexation step is essential in the rate constant calculation. In the formic acid reaction with OH radicals, we find that the water-acid complex concentration is small but relevant under atmospheric conditions, and it could in principle be large enough to produce a measurable increase in the overall rate constant. However, the water-assisted process occurs according to a formyl hydrogen abstraction, rather than abstraction of carboxylic hydrogen as in the water-free case. As a result, the overall reaction rate constant is considerably smaller. Products are different in the water-free and water-assisted processes.     

Ab initio potential energy surfaces, bound states, and electronic spectrum of the Ar-SH complex

New ab initio potential energy surfaces for the (2)Pi ground electronic state of the Ar-SH complex are presented, calculated at the RCCSD(T)/aug-cc-pV5Z level. Weakly bound rotation-vibration levels are calculated using coupled-channel methods that properly account for the coupling between the two electronic states. The resulting wave functions are analyzed and a new adiabatic approximation including spin-orbit coupling is proposed. The ground-state wave functions are combined with those obtained for the excited (2)Sigma(+) state [D. M. Hirst, R. J. Doyle, and S. R. Mackenzie, Phys. Chem. Chem. Phys. 6, 5463 (2004)] to produce transition dipole moments. Modeling the transition intensities as a combination of these dipole moments and calculated lifetime values [A. B. McCoy, J. Chem. Phys. 109, 170 (1998)] leads to a good representation of the experimental fluorescence excitation spectrum [M.-C. Yang, A. P. Salzberg, B.-C. Chang, C. C. Carter, and T. A. Miller, J. Chem. Phys. 98, 4301 (1993)].     

Solid-state 23Na NMR study of sodium lariat ether receptors exhibiting cation-pi interactions

Noncovalent cation-pi interactions are important in a variety of supramolecular and biochemical systems. We present a 23Na solid-state nuclear magnetic resonance (SSNMR) study of two sodium lariat ether complexes, 1 and 2, in which a sodium cation interacts with an indolyl group that models the side chain of tryptophan. Sodium-23 SSNMR spectra of magic-angle spinning (MAS) and stationary powdered samples have been acquired at three magnetic field strengths (9.4, 11.75, 21.1 T) and analyzed to provide key information on the sodium electric field gradient and chemical shift (CS) tensors which are representative of the cation-pi binding environment. Triple-quantum MAS NMR spectra acquired at 21.1 T clearly reveal two crystallographically distinct sites in both 1 and 2. The quadrupolar coupling constants, CQ(23Na), range from 2.92 +/- 0.05 MHz for site A of 1 to 3.33 +/- 0.05 MHz for site B of 2; these values are somewhat larger than those reported previously by Wong et al. (Wong, A.; Whitehead, R. D.; Gan, Z.; Wu, G. J. Phys. Chem. A 2004, 108, 10551) for NaBPh4, but very similar to the values obtained for sodium metallocenes by Willans and Schurko (Willans, M. J.; Schurko, R. W. J. Phys. Chem. B 2003, 107, 5144). We conclude from the 21.1 T data that the spans of the sodium CS tensors are less than 20 ppm for 1 and 2 and that the largest components of the EFG and CS tensors are non-coincident. Quantum chemical calculations of the NMR parameters substantiate the experimental findings and provide additional insight into the dependence of CQ(23Na) on the proximity of the indole ring to Na+. Taken together, this work has provided novel information on the NMR interaction tensors characteristic of a sodium cation interacting with a biologically important arene.     

Interpreting DNA vibrational circular dichroism spectra using a coupling model from two-dimensional infrared spectroscopy

Two-dimensional infrared spectroscopy was recently used to measure the vibrational couplings between carbonyl bonds located on DNA nucleobases (Krummel, A. T.; Mukherjee, P.; Zanni, M. T. J. Phys. Chem. B 2003, 107, 9165 and Krummel, A. T.; Zanni, M. T. J. Phys. Chem. B 2006, 110, 13991). Here, we extend the coupling model derived from these 2D IR experiments to simulate the vibrational absorption and vibrational circular dichroism (VCD) spectra of three double-stranded DNA oligomers: poly(dG)-poly(dC), poly(dG-dC), and dGGCC. Using this model, we determine that the VCD spectrum of A-form poly(dG)-poly(dC) is dominated by interactions between stacked bases, whereas the coupling between base pairs and stacked bases carries equal importance in the VCD spectrum of B-form poly(dG-dC). We also simulate the absorption and VCD spectra of dGGCC, which is a combination of A- and B-form configurations. These simulations give insight into the structural interpretation of VCD and absorption spectroscopies that have long been used to monitor DNA secondary structure and kinetics.     

Effect of polymer microenvironment on excitation energy migration and transfer

Excitation energy transfer between the dye pair acriflavine (donor) to rhodamine-6G (acceptor) in various polymers [polyvinyl alcohol (PVA), cellulose acetate, and polymethyl methacrylate (PMMA)] was studied using steady-state and time-resolved fluorescence spectroscopy at room temperature. In all these polymers, at higher acceptor concentrations, direct energy transfer from acriflavine to rhodamine-6G followed the F?rster theory, which is indicated by the agreement in the values of the observed critical transfer distance with that calculated from spectral overlap. On the other hand, at low acceptor concentrations, the excitation energy migration influences the kinetics, resulting in a significantly higher value of the observed critical transfer distance, which is explained on the basis of Loring et al. (Loring, R. F.; Anderson, H. C.; Fayer, M. D. J. Chem. Phys. 1984, 80, 5731-5744) and Huber (Huber, D. L. Phys. Rev. B: Condens. Matter Mater. Phys. 1979, 20 2307-2314) theories. It was observed that the spectral overlap for donor-donor transport (excitation migration) and donor-acceptor transfer (energy transfer) and thereby other energy transfer parameters were influenced by the microenvironment of the polymers. The efficiency of energy transfer (eta) was the highest in PMMA and the lowest in PVA. Further, the study of acceptor dynamics under energy transfer showed that the rise time of the acceptor also depends on the nature of the polymer microenvironment.