@article {1237,
	title = {Time-resolved Fourier-transform infrared and visible luminescence spectroscopy of photoexcited porous silicon},
	journal = {Physical Review B},
	volume = {59},
	number = {7},
	year = {1999},
	note = {Wang, JP Song, L Zou, BS El-Sayed, MA},
	month = {Feb},
	pages = {5026-5031},
	abstract = {In order to identify the luminescent centers in aged porous silicon, both the time-resolved vibration spectra in the 750-2000-cm(-1) region and the visible luminescence spectra are studied for the same sample in the 0-440-mu s time domain. Laser excitation gives rise to emission characteristics of the porous silicon as well as strong bleach in the infrared spectrum in the region of the ground-stale silicon-oxygen stretching vibration frequencies at 1100 and 1235 cm(-1). In addition, new transient absorption bands appear in this region as a result of the laser excitation. Three characteristic Lifetimes in the decay of the bleach band at 1235 cm(-1) are observed on the 1-, 10-, and 100-mu s time scale. These are similar to the observed decay times of the photoluminescence from porous silicon. These results suggest that the emitting centers in aged porous silicon are trapped excitation sites in an inhomogeneously defected oxidized silicon surface. [S0163-1829(99)09207-3].},
	isbn = {0163-1829},
	doi = {10.1103/PhysRevB.59.5026},
	author = {Wang, Jianping and Song, Li and Zou, Bingsuo and El-Sayed, Mostafa A}
}
@article {1250,
	title = {Application of liquid waveguide to Raman spectroscopy in aqueous solution},
	journal = {Applied Spectroscopy},
	volume = {52},
	number = {10},
	year = {1998},
	note = {Song, L Liu, SY Zhelyaskov, V El-Sayed, MA},
	month = {Oct},
	pages = {1364-1367},
	isbn = {0003-7028},
	author = {Song, Li and Liu, S. Y. and Zhelyaskov, V. and El-Sayed, Mostafa A}
}
@article {1251,
	title = {Primary step in bacteriorhodopsin photosynthesis: Bond stretch rather than angle twist of its retinal excited-state structure},
	journal = {Journal of the American Chemical Society},
	volume = {120},
	number = {34},
	year = {1998},
	note = {Song, L El-Sayed, MA},
	month = {Sep},
	pages = {8889-8890},
	isbn = {0002-7863},
	doi = {10.1021/ja980390d},
	author = {Song, Li and El-Sayed, Mostafa A}
}
@article {1259,
	title = {A Comparison of the Photoelectric Current Responses Resulting from the Proton Pumping Process of Bacteriorhodopsin under Pulsed and CW Laser Excitations},
	journal = {The Journal of Physical Chemistry B},
	volume = {101},
	year = {1997},
	note = {doi: 10.1021/jp972475r},
	month = {1997},
	pages = {10599 - 10604},
	publisher = {American Chemical Society},
	abstract = {When excited with a pulsed laser, an electric field-oriented bacteriorhodopsin (bR) film on an indium-tin oxide (ITO) conductive electrode generates a photocurrent composed of at least three different components:  B1 (<100 ps), B2 (60 μs), and B3 (ms). When excited with an electronic shutter modulated CW light pulse (>200 ms in duration), a differential photocurrent (components D1 and D2 with decay times in milliseconds) is observed from the bR film. D1 is observed when the CW light is turned on, and D2 is observed when the CW light is turned off. In this paper, we compare the amplitudes and lifetimes of B2, B3, and D1 at various values of pH and ionic strength of the electrolyte solution in which the photocurrent is measured. It is found that changing the film orientation changes the polarity (sign) of B1 and B2, while it does not affect the polarity of B3 and D1. It is also found that B3 and D1 change their polarity upon changing the pH of electrolyte solution, whereas B1 and B2 do not. These results suggest that the origin of B3 and D1 is different from that of B1 and B2. Our results suggest that B3 and D1 are due to the formation of a transient proton capacitor between the two ITO electrodes resulting from the proton pumping in bR. The magnitude and sign of B3 and D1 are determined by the transient proton concentration change (accumulation or disappearance) occurring near the bR-modified ITO electrode interface on the millisecond time scale. The change of sign in B3 and D1 as a function of pH is due to the sequence of proton release/uptake in the bR photocycle:  It first releases protons into the aqueous solution at high pH, while it first takes up protons from the aqueous solution at low pH. The effects of buffer and ionic strength on B3 and D1 are discussed in terms of the kinetics of proton release/uptake and of the transportation of positive and negative ions in the electrolyte solution.},
	isbn = {1520-6106},
	url = {http://dx.doi.org/10.1021/jp972475r},
	author = {Wang, Jianping and Song, Li and Yoo, Seoung-Kyo and El-Sayed, Mostafa A}
}
@article {874,
	title = {Molecular Mechanism of the Differential Photoelectric Response of Bacteriorhodopsin},
	journal = {The Journal of Physical Chemistry B },
	volume = {101},
	year = {1997},
	note = {doi: 10.1021/jp962111j},
	month = {1997},
	pages = {3420 - 3423},
	publisher = {American Chemical Society},
	abstract = {In order to determine the molecular origin of the differential photocurrent from bacteriorhodopsin (bR), the photoelectric response of bR film deposited on an indium tin oxide (ITO) conductive glass electrode under CW excitation is compared with that under pulsed laser excitation at different pH and with opposite membrane orientation with respect to the ITO electrode surface. The characteristics (sign and magnitude) of the dominant component of the differential photocurrent (appearing on the millisecond time scale) are found to correlate with the process of proton release into, or uptake from, the aqueous solution during the photocycle under different experimental conditions. This suggests that the differential current results mainly from the change in the H+ concentration at the bR?ITO electrode interface.In order to determine the molecular origin of the differential photocurrent from bacteriorhodopsin (bR), the photoelectric response of bR film deposited on an indium tin oxide (ITO) conductive glass electrode under CW excitation is compared with that under pulsed laser excitation at different pH and with opposite membrane orientation with respect to the ITO electrode surface. The characteristics (sign and magnitude) of the dominant component of the differential photocurrent (appearing on the millisecond time scale) are found to correlate with the process of proton release into, or uptake from, the aqueous solution during the photocycle under different experimental conditions. This suggests that the differential current results mainly from the change in the H+ concentration at the bR?ITO electrode interface.},
	isbn = {1520-6106},
	url = {http://dx.doi.org/10.1021/jp962111j},
	author = {Wang, Jianping and Yoo, Seoung-Kyo and Song, Li and El-Sayed, Mostafa A}
}
@article {864,
	title = {Optical rotation of the second harmonic radiation from retinal in bacteriorhodopsin monomers in Langmuir-Blodgett film: evidence for nonplanar retinal structure.},
	journal = {Biophysical journal},
	volume = {73},
	year = {1997},
	month = {1997 Dec},
	pages = {3164-70},
	abstract = {We observed optical rotation of the plane of polarization of the second harmonic (SH) radiation at 532 nm (in resonance with the retinal absorption) generated in reflection geometry in Langmuir-Blodgett film of bacteriorhodopsin (bR). The analysis of the experimental data showed that this effect arises from the nonvanishing contribution of the antisymmetrical part of the hyperpolarizability tensor. This requires that the dipole moment of the resonant electronic transition, the change of the dipole moment upon electronic excitation, and the long axis of the retinal not be coplanar. Such conditions are satisfied only if the retinal has a nonplanar geometry, a conclusion that could lend support to the heterogeneity model of the origin of the biphasic band shape of the linear CD spectrum of the retinal in bR. On the basis of our theoretical analysis, we were able to estimate the angle between the induced dipole moment and the plan that contains the long axis of the chromophore and the transition dipole moment of the retinal absorption.},
	keywords = {Bacteriorhodopsins, Biophysical Phenomena, Biophysics, Circular Dichroism, Molecular Structure, Optics and Photonics, Retinaldehyde, Spectrophotometry},
	issn = {0006-3495},
	doi = {10.1016/S0006-3495(97)78342-5},
	author = {Volkov, V. V. and Svirko, Y P and Kamalov, Valey F. and Song, Li and El-Sayed, Mostafa A}
}
@article {1261,
	title = {Spectral diffusion within the porous silicon emission wavelength range on the nanosecond to millisecond time scale},
	journal = {J. Appl. Phys.Journal of Applied Physics},
	volume = {82},
	year = {1997},
	month = {1997},
	pages = {836},
	publisher = {AIP},
	abstract = {The emission spectrum from porous silicon (PS) at room temperature was recorded after different delay times ranging from 30 ns to 2.0 ms after pulsed laser excitation by using a gated charge-coupled device camera. In agreement with previous studies, the photoluminescence of porous silicon was found to redshift with delay time in the ns to 100 μs time scale. However, a study of the normalized band shape of the redshifted emission reveals that the emission spectrum retains its band shape rather than giving a distorted band shape that increases in intensity on the longer wavelength side. This behavior suggests that the redshift in the emission spectrum of porous silicon is a result of spectral diffusion resulting from energy transfer among emitters within the inhomogeneously broadened absorption spectrum. Furthermore, on the longer time scale (0.8{\textendash}2 ms), the much weaker, long wavelength emission spectrum is found to blueshift as the delay time is increased. Two peaks were resolved in the photoluminescence spectrum. One is centered around 650 nm and the other is centered around 750 nm. The photoluminescence at 600 and 800 nm have lifetimes of 0.35 and 0.19 ms, respectively. This observation suggests the existence of two distinct molecular species responsible for the observed photoluminescence in PS.},
	keywords = {elemental semiconductors, photoluminescence, porous materials, radiative lifetimes, red shift, silicon, spectral line breadth, spectral line shift, time resolved spectra},
	url = {http://dx.doi.org/10.1063/1.365781},
	author = {Song, Li},
	editor = {El-Sayed, Mostafa A and Chen, P.}
}
@article {865,
	title = {Studies of cation binding in ZnCl2-regenerated bacteriorhodopsin by x-ray absorption fine structures: effects of removing water molecules and adding Cl- ions.},
	journal = {Biophysical journal},
	volume = {73},
	year = {1997},
	month = {1997 Oct},
	pages = {2097-105},
	abstract = {The binding of Zn2+ in Zn2+-regenerated bacteriorhodopsin (bR) was studied under various conditions by x-ray absorption fine structures (XAFS). The 0.9:1 and 2:1 Zn2+:bR samples gave similar XAFS spectra, suggesting that Zn2+ might have only one strong binding site in bR. It was found that in aqueous bR solution, Zn2+ has an average of six oxygen or nitrogen ligands. Upon drying, two ligands are lost, suggesting the existence of two weakly bound water ligands near the cation-binding site in bacteriorhodopsin. When excess Cl- ions were present before drying in the Zn2+-regenerated bR samples, it was found that two of the ligands were replaced by Cl- ions in the dried film, whereas two remain unchanged. The above observations suggest that Zn2+ has three types of ligands in regenerated bR (referred to as types I, II, and III). Type I ligands are strongly bound. These ligands cannot be removed by drying or by exchanging with Cl- ions. Type II ligands cannot be removed by drying, but can be replaced by Cl- ligands. Type III ligands are weakly bound to the metal cation and are most likely water molecules that can be removed by evaporation under vacuum or by drying with anhydrous CaSO4. The results are discussed in terms of the possible structure of the strongly binding site of Zn2+ in bR.},
	keywords = {Bacteriorhodopsins, Binding Sites, Biophysical Phenomena, Biophysics, Cations, Chlorides, Kinetics, Ligands, Spectrum Analysis, Water, X-Rays, Zinc, Zinc Compounds},
	issn = {0006-3495},
	doi = {10.1016/S0006-3495(97)78240-7},
	author = {Zhang, K and Song, Li and Dong, J and El-Sayed, Mostafa A}
}
@article {1267,
	title = {Effect of Changing the Position and Orientation of Asp85 Relative to the Protonated Schiff Base within the Retinal Cavity on the Rate of Photoisomerization in Bacteriorhodopsin},
	journal = {The Journal of Physical Chemistry},
	volume = {100},
	year = {1996},
	note = {doi: 10.1021/jp960734r},
	month = {1996},
	pages = {10479 - 10481},
	publisher = {American Chemical Society},
	abstract = {Replacement of either Val49 with Ala or Ala53 with Val by site-specific mutagenesis is known to change the position and orientation of the protonated Schiff base relative to Asp85 within the retinal cavity of bacteriorhodopsin (bR) (Brown, L. S.; Gat, Y.; Sheves, M.; Yamazaki, Y.; Maeda, A.; Needleman, R.; Lanyi, J. K. Biochemistry 1994, 33, 12001). The effect of mutation on the rate of the subpicosecond photoisomerization of retinal in bR is examined by using a pump?probe technique. A decrease in the rate of photoisomerization of retinal in V49A and A53V is observed. This is discussed in terms of the previously proposed mechanism of the protein catalysis to the retinal photoisomerization process in bR.Replacement of either Val49 with Ala or Ala53 with Val by site-specific mutagenesis is known to change the position and orientation of the protonated Schiff base relative to Asp85 within the retinal cavity of bacteriorhodopsin (bR) (Brown, L. S.; Gat, Y.; Sheves, M.; Yamazaki, Y.; Maeda, A.; Needleman, R.; Lanyi, J. K. Biochemistry 1994, 33, 12001). The effect of mutation on the rate of the subpicosecond photoisomerization of retinal in bR is examined by using a pump?probe technique. A decrease in the rate of photoisomerization of retinal in V49A and A53V is observed. This is discussed in terms of the previously proposed mechanism of the protein catalysis to the retinal photoisomerization process in bR.},
	isbn = {0022-3654},
	doi = {doi: 10.1021/jp960734r},
	url = {http://dx.doi.org/10.1021/jp960734r},
	author = {Song, Li and El-Sayed, Mostafa A and Lanyi, Janos K.}
}
@article {869,
	title = {Excited-State Dynamics of a Protonated Retinal Schiff Base in Solution},
	journal = {The Journal of Physical Chemistry},
	volume = {100},
	year = {1996},
	note = {doi: 10.1021/jp962046d},
	month = {1996},
	pages = {18586 - 18591},
	publisher = {American Chemical Society},
	abstract = {The dynamics of all-trans and 13-cis retinal protonated Schiff base (RPSB) were studied in different solvents by means of picosecond transient spectroscopy. The decay time of the excited state absorption was found to be wavelength dependent due to the contribution of the faster decay of stimulated emission. The stimulated emission has a lifetime of a 2.5-4 ps while the excited state absorption decay is biexponential with lifetimes of 2.5-4 and 10-12 ps. The fluorescence quantum yield is strongly temperature dependent, but viscosity has a small effect on both excited-state lifetime and fluorescence quantum yield. This leads to the conclusion that there is a 600 cm-1 barrier in the excited-state which results from intramolecular electronic factors and not from the solvent viscosity. The comparison of these results with those for the retinal in rhodopsin and bacteriorhodopsin is discussed in terms of the protein catalysis for the retinal photoisomerization.},
	isbn = {0022-3654},
	url = {http://dx.doi.org/10.1021/jp962046d},
	author = {Logunov, Stephan L. and Song, Li and El-Sayed, Mostafa A}
}
@article {872,
	title = {Photoisomerization Quantum Yield and Apparent Energy Content of the K Intermediate in the Photocycles of Bacteriorhodopsin, Its Mutants D85N, R82Q, and D212N, and Deionized Blue Bacteriorhodopsin},
	journal = {The Journal of Physical Chemistry},
	volume = {100},
	year = {1996},
	note = {doi: 10.1021/jp9515242},
	month = {1996},
	pages = {2391 - 2398},
	publisher = {American Chemical Society},
	abstract = {The quantum yield of photoisomerization and the energy content of the K intermediate in the photocycle of bacteriorhodopsin and its mutants D85N, R82Q, and D212N and deionized blue bR were measured. Transient optical absorption and photoacoustic spectroscopy with excitation using 400 fs laser pulse were combined to obtain results. The spectroscopic characteristics of the excited state, the J and K intermediates in the photocycle of the mutants, and deionized blue bR were determined. The presence of both 13-cis and all-trans isomers in the ground state of light-adapted D85N, R82Q, and D212N and deionized blue bR makes extraction of the quantum yield for each isomer difficult. Thus, only average values of the quantum yield for these samples were determined. The replacement of charged groups in the vicinity of the retinal Schiff base was found to decrease the rate of the photoisomerization by up to 30 times, but with no signficant change in either the apparent quantum yield of the photoisomerization or the energy stored in the K intermediate. The results are discussed in terms of the different models for the excited and ground state potential surfaces of the retinal configuration in bacteriorhodopsin.The quantum yield of photoisomerization and the energy content of the K intermediate in the photocycle of bacteriorhodopsin and its mutants D85N, R82Q, and D212N and deionized blue bR were measured. Transient optical absorption and photoacoustic spectroscopy with excitation using 400 fs laser pulse were combined to obtain results. The spectroscopic characteristics of the excited state, the J and K intermediates in the photocycle of the mutants, and deionized blue bR were determined. The presence of both 13-cis and all-trans isomers in the ground state of light-adapted D85N, R82Q, and D212N and deionized blue bR makes extraction of the quantum yield for each isomer difficult. Thus, only average values of the quantum yield for these samples were determined. The replacement of charged groups in the vicinity of the retinal Schiff base was found to decrease the rate of the photoisomerization by up to 30 times, but with no signficant change in either the apparent quantum yield of the photoisomerization or the energy stored in the K intermediate. The results are discussed in terms of the different models for the excited and ground state potential surfaces of the retinal configuration in bacteriorhodopsin.},
	isbn = {0022-3654},
	url = {http://dx.doi.org/10.1021/jp9515242},
	author = {Logunov, Stephan L. and El-Sayed, Mostafa A and Song, Li and Lanyi, Janos K.}
}
@article {1283,
	title = {On the molecular mechanisms of the rapid and slow solar-to-electric energy storage processes by the other natural photosynthetic system, bacteriorhodopsin},
	journal = {Pure and applied chemistry},
	volume = {67},
	year = {1995},
	pages = {149-149},
	publisher = {BLACKWELL SCIENTIFIC PUBLICATIONS},
	abstract = {Upon the absorption of solar energy by retinal in bacterioi..>dopsin highly specific photoisomerization of the retinal around the C13 -C14 bond takes place. This is followed by the formation of a number of intermediates resulting from conformational changes of the protein around the retinal which leads to the deprotonation of the protonated Schiff base of the retinylidene system. Thisis the switch of the proton pump which leads to the last step in the storage of solar energy in the form of electric energy by this photosynthetic system. The removal of metal cations from bR is found to inhibit the deprotonation process.
In the present paper we summarize the results of our studies and the others regarding two important questions in the conversion process: 1) what is(are) the molecular mechanism(s) of the protein catalysis of the photoisomerizationprocess and 2) what is the role of metal cations in the deprotonation process of the protonated Schiff base (the switch of the proton pump)? In order to answer the first question, the results of the subpicosecondphotoisomerization rate of retinal in bR and in a number of its relevant mutants are discussed in terms of the steric and electronic factors. In an effort to answer the second question,we discussed the results of the binding studies of Ca*+to bR, to its mutants and to bR after its C- terminus is cleaved. From these results and the results of Roux et al. on the 31P NMR of Nd3+ regenerated bR, we concluded that one or two metal cations strongly bound to the protein but not on the surface, are functionally important. The model in which these metal cation@)control the pK values of Aspartic acids in the 85 and 212 positions and that of the protonated Schiff base (PSB) during the photocycle is discussed.},
	isbn = {0033-4545},
	author = {El-Sayed, Mostafa A and Griffiths, Jennifer A. and Song, Li and Zhang, N.}
}
@article {1268,
	title = {Retinal Isomer Composition in Some Bacteriorhodopsin Mutants under Light and Dark Adaptation Conditions},
	journal = {The Journal of Physical Chemistry},
	volume = {99},
	year = {1995},
	note = {doi: 10.1021/j100024a056},
	month = {1995},
	pages = {10052 - 10055},
	publisher = {American Chemical Society},
	abstract = {View http://dx.doi.org/10.1021/j100024a056 for the article{\textquoteright}s first page in lieu of an abstract},
	isbn = {0022-3654},
	doi = {doi: 10.1021/j100024a056},
	url = {http://dx.doi.org/10.1021/j100024a056},
	author = {Song, Li and Yang, Difei and El-Sayed, Mostafa A and Lanyi, Janos K.}
}
@article {1277,
	title = {pH Dependence of the Rate and Quantum Yield of the Retinal Photoisomerization in Bacteriorhodopsin},
	journal = {The Journal of Physical Chemistry},
	volume = {98},
	year = {1994},
	note = {doi: 10.1021/j100093a003},
	month = {1994},
	pages = {10674 - 10677},
	publisher = {American Chemical Society},
	abstract = {View http://dx.doi.org/10.1021/j100093a003 for article{\textquoteright}s front page in lieu of an abstract},
	isbn = {0022-3654},
	doi = {doi: 10.1021/j100093a003},
	url = {http://dx.doi.org/10.1021/j100093a003},
	author = {Logunov, Stephan L. and Song, Li and El-Sayed, Mostafa A}
}
@article {859,
	title = {The pH dependence of the subpicosecond retinal photoisomerization process in bacteriorhodopsin: evidence for parallel photocycles.},
	journal = {Biophysical journal},
	volume = {67},
	year = {1994},
	month = {1994 Nov},
	pages = {2008-12},
	abstract = {The pH dependence of the subpicosecond decay of the retinal photoexcited state in bacteriorhodopsin (bR) is determined in the pH range 6.8-11.3. A rapid change in the decay rate of the retinal photoexcited state is observed in the pH range 9-10, the same pH range in which a rapid change in the M412 formation kinetics was observed. This observation supports the previously proposed heterogeneity model in which parallel photocycles contribute to the observed pH dependence of the M412 formation kinetics in bR.},
	keywords = {Bacteriorhodopsins, Biophysical Phenomena, Biophysics, Hydrogen-Ion Concentration, Isomerism, Kinetics, Molecular Structure, Photochemistry, Retinaldehyde},
	issn = {0006-3495},
	doi = {10.1016/S0006-3495(94)80684-8},
	author = {Song, Li and Logunov, Stephan L. and Yang, Difei and El-Sayed, Mostafa A}
}
