Kinetic effects on the morphology and stability of the pressure-induced extended-solid of carbon monoxide.

In this work, the dependence of the morphology and stability of the extended solid of carbon monoxide (CO) is correlated to the rate of transformation from the molecular CO to extended solid of CO using optical imaging, photoluminescence, Raman spectroscopy, and X-ray diffraction. The analyses show the rate and pressure of the transformation to be strongly controlled by catalytic effects, both chemical and optical. In a larger volume per reaction area, the transformation was found to require either a longer time at an elevated pressure or a higher pressure compared to a sample synthesized in a smaller volume per reaction area, leading to the conclusion that the transformation rate is slower for a sample in a larger volume per reaction area. A faster rate of transformation was also noted when the reaction area of a CO sample was catalyzed with H2SO4. Through variation of the volume per reaction area, pressure or the addition of catalysts, it was possible to control the rate of the phase transition and therefore the morphology. In general, the extended solid of CO synthesized with a faster rate showed a more ordered structure and increased metastability relative to the material formed with a slower compression rate.

Diffusion of squalene in n-alkanes and squalane.

Squalene, an intermediate in the biosynthesis of cholesterol, has a 24-carbon backbone with six methyl groups and six isolated double bonds. Capillary flow techniques have been used to determine its translational diffusion constant, D, at room temperature in squalane, n-C16, and three n-C8-squalane mixtures. The D values have a weaker dependence on viscosity, η, than predicted by the Stokes-Einstein relation, D = kBT/(6πηr). A fit to the modified relation, D/T = ASE/η(p), gives p = 0.820 ± 0.028; p = 1 for the Stokes-Einstein limit. The translational motion of squalene appears to be much like that of n-alkane solutes with comparable chain lengths; their D values show similar deviations from the Stokes-Einstein model. The n-alkane with the same carbon chain length as squalene, n-C24, has a near-equal p value of 0.844 ± 0.018 in n-alkane solvents. The values of the hydrodynamic radius, r, for n-C24, squalene, and other n-alkane solutes decrease as the viscosity increases and have a common dependence on the van der Waals volumes of the solute and solvent. The possibility of studying squalene in lipid droplets and membranes is discussed.

Shock Hugoniot equations of state for binary ideal (toluene/fluorobenzene) and nonideal (ethanol/water) liquid mixtures.

Laser shock Hugoniot data were obtained using ultrafast dynamic ellipsometry (UDE) for both nonideal (ethanol/water solutions with mole percent χ(ethanol) = 0%, 3.4%, 5.4%, 7.5%, 9.7%, 11%, 18%, 33%, 56%, 100%) and ideal liquid mixtures (toluene/fluorobenzene solutions with mole percent χ(toluene) = 0%, 26.0%, 49.1%, 74.9%, 100%). The shock and particle velocities obtained from the UDE data were compared to the universal liquid Hugoniot (ULH) and to literature shock (plate impact) data where available. It was found that the water UDE data fit to a ULH-form equation suggests an intercept of 1.32 km/s, lower than the literature ambient sound speed in water of 1.495 km/s (Mijakovic et al. J. Mol. Liq. 2011, 164, 66-73). Similarly, the ethanol UDE data fit to a ULH-form equation suggests an intercept of 1.45 km/s, which lies above the literature ambient sound speed in ethanol of 1.14 km/s. Both the literature plate impact and UDE Hugoniot data lie below the ULH for water. Likewise, the literature plate impact and UDE Hugoniot data lie above the ULH for ethanol. The UDE Hugoniot data for the mixtures of water and ethanol cross the predictions of the ULH near the same concentration where the sound speed reaches a maximum. In contrast, the UDE data from the ideal liquids and their mixtures are well behaved and agree with ULH predictions across the concentration range. The deviations of the nonideal ethanol/water data from the ULH suggest that complex hydrogen bonding networks in ethanol/water mixtures alter the compressibility of the mixture.

Low-temperature frequency domain study of excitation energy transfer in ethynyl-linked chlorophyll trefoils and aggregates.

Using hole-burning spectroscopy, we show that excitation energy transfer (EET) time in ethynyl-linked chlorophyll trefoil (ChlT1) monomer is very fast (∼2.5 ps) at liquid helium temperature. This is consistent with data obtained by femtosecond transient spectroscopy experiments performed at room temperature, in which an EET time of 1.8 ps was observed (Kelley, R. F. et al. Angew. Chem. Int. Ed. 2006, 45, 7979). This finding further supports the importance of through-bond electronic coupling at low temperature. In addition, we show that ChlT1 (even at very low concentrations) in methyl tetrahydrofuran-ethanol glass (1:200 v/v; T ∼ 5 K) forms different types of aggregates. It is demonstrated that the relative distribution of various types of aggregates (whose possible structures are briefly discussed) depends on the cooling rate and matrix composition. For example, the EET time in two types of ChlT1-based aggregates is slower by a factor of ∼5-7 with respect to that observed for ChlT1 monomer. This indicates that ChlT1 aggregates can retain ultrafast energy transfer properties similar to those observed in natural photosynthetic antennas. It is anticipated that such building blocks could be utilized in future photovoltaic devices.

Time-resolved spectroscopic measurements of shock-wave induced decomposition in cyclotrimethylene trinitramine (RDX) crystals: anisotropic response.

Plate impact experiments on the (210), (100), and (111) planes were performed to examine the role of crystalline anisotropy on the shock-induced decomposition of cyclotrimethylenetrinitramine (RDX) crystals. Time-resolved emission spectroscopy was used to probe the decomposition of single crystals shocked to peak stresses ranging between 7 and 20 GPa. Emission produced by decomposition intermediates was analyzed in terms of induction time to emission, emission intensity, and the emission spectra shapes as a function of stress and time. Utilizing these features, we found that the shock-induced decomposition of RDX crystals exhibits considerable anisotropy. Crystals shocked on the (210) and (100) planes were more sensitive to decomposition than crystals shocked on the (111) plane. The possible sources of the observed anisotropy are discussed with regard to the inelastic deformation mechanisms of shocked RDX. Our results suggest that, despite the anisotropy observed for shock initiation, decomposition pathways for all three orientations are similar.

Insight into the electronic structure of the CP47 antenna protein complex of photosystem II: hole burning and fluorescence study.

We report low temperature (T) optical spectra of the isolated CP47 antenna complex from Photosystem II (PSII) with a low-T fluorescence emission maximum near 695 nm and not, as previously reported, at 690-693 nm. The latter emission is suggested to result from three distinct bands: a lowest-state emission band near 695 nm (labeled F1) originating from the lowest-energy excitonic state A1 of intact complexes (located near 693 nm and characterized by very weak oscillator strength) as well as emission peaks near 691 nm (FT1) and 685 nm (FT2) originating from subpopulations of partly destabilized complexes. The observation of the F1 emission is in excellent agreement with the 695 nm emission observed in intact PSII cores and thylakoid membranes. We argue that the band near 684 nm previously observed in singlet-minus-triplet spectra originates from a subpopulation of partially destabilized complexes with lowest-energy traps located near 684 nm in absorption (referred to as AT2) giving rise to FT2 emission. It is demonstrated that varying contributions from the F1, FT1, and FT2 emission bands led to different maxima of fluorescence spectra reported in the literature. The fluorescence spectra are consistent with the zero-phonon hole action spectra obtained in absorption mode, the profiles of the nonresonantly burned holes as a function of fluence, as well as the fluorescence line-narrowed spectra obtained for the Q(y) band. The lowest Q(y) state in absorption band (A1) is characterized by an electron-phonon coupling with the Huang-Rhys factor S of approximately 1 and an inhomogeneous width of approximately 180 cm(-1). The mean phonon frequency of the A1 band is 20 cm(-1). In contrast to previous observations, intact isolated CP47 reveals negligible contribution from the triplet-bottleneck hole, i.e., the AT2 trap. It has been shown that Chls in intact CP47 are connected via efficient excitation energy transfer to the A1 trap near 693 nm and that the position of the fluorescence maximum depends on the burn fluence. That is, the 695 nm fluorescence maximum shifts blue with increasing fluence, in agreement with nonresonant hole burned spectra. The above findings provide important constraints and parameters for future excitonic calculations, which in turn should offer new insight into the excitonic structure and composition of low-energy absorption traps.

Hyperquenched glassy water and hyperquenched glassy ethanol probed by single molecule spectroscopy.

It is still unclear whether hyperquenched water (i.e., amorphous glassy water) heated to about 140-150 K remains glassy until it crystallizes near 154 K or whether instead it turns into a supercooled and very viscous liquid. It has been proposed that the glass transition temperature (T(g)) for water is 165 K and not, as previously thought, 136 K [V. Velikov et al., Science, 294, 2335 (2001)]. Support for both interpretations exists in the literature, since the T(g) of water is difficult to measure due to the formation of metastable cubic ice (I(c)) near 154 K. To address the nature of water in the 110-160 K temperature range, a confocal microscopy approach is used to study whether single-probe molecules (i.e., Rhodamine 700, Rh-700) embedded in hyperquenched glassy water (HGW) rotate in the temperature range of 110-160 K. If T(g) is 136 K and the liquid above this temperature is fragile (or strong with the fragility index m > 7), then rotation of the Rh-700 molecules should be observed several degrees above T(g). It is shown that no anticorrelated fluorescence intensity changes of single molecules in HGW (when excited at orthogonal polarizations) were observed up to temperatures of 160 K, although such changes were detected in control experiments performed for hyperquenched glassy ethanol (fragile liquid) at 99 K, that is, at T(g) + 2 K. The viscosity at which single Rh-700 molecules rotate in ethanol at 99 K is estimated to be about 10(12) poise. Since single-molecule spectroscopy did not reveal any rotation of probe molecules in HGW above 136 K, we conclude that water above 136 K is most likely a solid (i.e., glass), supporting the assignment that water remains glassy until it crystallizes near T = 154 K. It cannot be excluded, of course, that the value of m for water is smaller than 7 (i.e., water above 136 K could be an extremely strong liquid), but this possibility is considered unlikely as this would make water the strongest liquid ever known.

The CP43 proximal antenna complex of higher plant photosystem II revisited: modeling and hole burning study. I.

The CP43 core antenna complex of photosystem II is known to possess two quasi-degenerate "red"-trap states (Jankowiak, R. et al. J. Phys. Chem. B 2000, 104, 11805). It has been suggested recently (Zazubovich, V.; Jankowiak, R. J. Lumin. 2007, 127, 245) that the site distribution functions of the red states (A and B) are uncorrelated and that narrow holes are burned in the subpopulations of chlorophylls (Chls) from states A and B that are the lowest-energy Chl in their complex and previously thought not to transfer energy. This model of uncorrelated excitation energy transfer (EET) between the quasidegenerate bands is expanded by taking into account both electron-phonon and vibrational coupling. The model is applied to fit simultaneously absorption, emission, zero-phonon action, and transient hole burned (HB) spectra obtained for the CP43 complex with minimized contribution from aggregation. It is demonstrated that the above listed spectra can be well-fitted using the uncorrelated EET model, providing strong evidence for the existence of efficient energy transfer between the two lowest energy states, A and B (either from A to B or from B to A), in CP43. Possible candidate Chls for the low-energy A and B states are discussed, providing a link between CP43 structure and spectroscopy. Finally, we propose that persistent holes originate from regular NPHB accompanied by the redistribution of oscillator strength due to excitonic interactions, rather than photoconversion involving Chl-protein hydrogen bonding, as suggested before ( Hughes J. L. et al. Biochemistry 2006, 45, 12345 ). In the accompanying paper (Reppert, M.; Zazubovich, V.; Dang, N. C.; Seibert, M.; Jankowiak, R. J. Phys. Chem. B 2008, 9934), it is demonstrated that the model discussed in this manuscript is consistent with excitonic calculations, which also provide very good fits to both transient and persistent HB spectra obtained under non-line-narrowing conditions.

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.

Spectral differentiation and immunoaffinity capillary electrophoresis separation of enantiomeric benzo(a)pyrene diol epoxide-derived DNA adducts.

Antibody cross-reactivity makes separation and differentiation of enantiomeric analytes one of the most challenging problems in immunoanalytical research, particularly for the analysis of structurally related biological molecules [such as benzo( a)pyrene (BP) metabolites and BP-derived DNA adducts]. It has recently been shown that the interaction of enantiomers of BP tetrols (BPT) with a promiscuous anti-polycyclic aromatic hydrocarbon ( anti-PAH) monoclonal antibody (mAb) allowed for separation of all four enantiomeric isomers using immunoaffinity capillary electrophoresis [ Grubor, N. M. , Armstrong, D. W. , and Jankowiak, R. ( 2006) Electrophoresis 27, 1078 ] and unambiguous spectral resolution using fluorescence line narrowing spectroscopy (FLNS) [ Grubor, N. M. , Liu, Y. , Han, X. , Armstrong, D.W. , and Jankowiak, R. ( 2006) J. Am.Chem. Soc. 128, 6409 ]. Here, we expand the use of the above two methodologies to the group of biologically important molecules that are products of BP diol epoxide (BPDE)-induced DNA damage. Four diastereomeric anti-BPDE-derived deoxyguanosine (dG) adducts, that is, (+)- and (-)- anti-trans-BPDE- N (2)-dG and (+)- and (-)- anti-cis-BPDE- N (2)-dG, were electrophoretically separated and spectroscopically differentiated using 8E11 mAb raised against BP-DNA conjugates. In fluorescence line narrowing spectroscopy (FLNS) experiments, complexes of BPDE-dG adducts with mAb revealed differences in fluorescence origin band positions, bandwidths, and vibrational patterns for all four BPDE- N (2)-dG adducts. Narrow fluorescence origin bands observed for (-)- trans-BPDE-dG (70 cm (-1)) and (+)- trans-BPDE- N (2)-dG (80 cm (-1)) suggest spatial constraint within the mAb binding pocket. Broader origin bands observed for cis type adducts ( approximately 120 cm (-1)) in 8E11 mAb suggest different binding geometries and/or conformational changes, as also indicated by changes in vibrational frequencies observed for the (+)- anti-cis and (-)- anti-cis adducts complexed with mAb. FLNS revealed that binding conformations and interactions within the mAb binding pocket are different for each adduct, enabling unambiguous positive identification. The methodologies described in this manuscript could also be used for analysis of DNA adducts following enzymatic hydrolysis of BPDE-adducted DNA to free nucleosides.