scholarly journals Retinal Vibrations in Bacteriorhodopsin are Mechanically Harmonic but Electrically Anharmonic: Evidence From Overtone and Combination Bands

2021 ◽  
Vol 8 ◽  
Author(s):  
Victor A. Lorenz-Fonfria ◽  
Kiyoshi Yagi ◽  
Shota Ito ◽  
Hideki Kandori

Fundamental vibrations of the chromophore in the membrane protein bacteriorhodopsin (BR), a protonated Schiff base retinal, have been studied for decades, both by resonance Raman and by infrared (IR) difference spectroscopy. Such studies started comparing vibrational changes between the initial BR state (all-trans retinal) and the K intermediate (13-cis retinal), being later extended to the rest of intermediates. They contributed to our understanding of the proton-pumping mechanism of BR by exploiting the sensitivity of fundamental vibrational transitions of the retinal to its conformation. Here, we report on new bands in the 2,500 to 1,800 cm−1 region of the K-BR difference FT-IR spectrum. We show that the bands between 2,500 and 2,300 cm−1 originate from overtone and combination transitions from C-C stretches of the retinal. We assigned bands below 2,300 cm−1 to the combination of retinal C-C stretches with methyl rocks and with hydrogen-out-of-plane vibrations. Remarkably, experimental C-C overtone bands appeared at roughly twice the wavenumber of their fundamentals, with anharmonic mechanical constants ≤3.5 cm−1, and in some cases of ∼1 cm−1. Comparison of combination and fundamental bands indicates that most of the mechanical coupling constants are also very small. Despite the mechanical quasi-harmonicity of the C-C stretches, the area of their overtone bands was only ∼50 to ∼100 times smaller than of their fundamental bands. We concluded that electrical anharmonicity, the second mechanism giving intensity to overtone bands, must be particularly high for the retinal C-C stretches. We corroborated the assignments of negative bands in the K-BR difference FT-IR spectrum by ab initio anharmonic vibrational calculations of all-trans retinal in BR using a quantum-mechanics/molecular mechanics approach, reproducing reasonably well the small experimental anharmonic and coupling mechanical constants. Yet, and in spite accounting for both mechanical and electrical anharmonicities, the intensity of overtone C-C transitions was underestimated by a factor of 4–20, indicating room for improvement in state-of-the-art anharmonic vibrational calculations. The relatively intense overtone and combination bands of the retinal might open the possibility to detect retinal conformational changes too subtle to significantly affect fundamental transitions but leaving a footprint in overtone and combination transitions.

2021 ◽  
Author(s):  
Victor A. Lorenz-Fonfria ◽  
Kiyoshi Yagi ◽  
Shota Ito ◽  
Hideki Kandori

Vibrations of the chromophore in the membrane protein bacteriorhodopsin (BR), a protonated Schiff base retinal, have been studied for decades, both by resonance Raman and by infrared (IR) difference spectroscopy. In spite the light-induced IR difference spectrum between the K intermediate (13-cis retinal) and the initial BR state (all-trans retinal) being first published almost 40 years ago, we present here unreported bands in the 2500 to 1800 cm-1 region. We show that the bands between 2500 and 2300 cm-1 originate from overtone and combination transitions of retinal C-C stretches. We assigned some of the newly reported bands below 2300 cm-1 to the combination of retinal C-C stretches with methyl rocks and with hydrogen-out-of-plane vibrations. Remarkably, experimental C-C overtone bands appeared at roughly twice the wavenumber of their fundamentals, with anharmonic mechanical constants ≤ 3.5 cm-1, and in some cases of ≈ 1 cm-1. Comparison of combination and fundamental bands indicates that most of the mechanical coupling constants are also very small. Despite the mechanical quasi-harmonicity of the C-C stretches, the area of their overtone bands was only ≈50 to ≈100 times smaller than of their fundamental bands. We concluded that electronic anharmonicity, the second mechanism giving intensity to overtone bands, must be particularly high for the retinal C-C stretches. We corroborated the assignments of negative bands in the K-BR difference spectrum by ab initio anharmonic spectral calculations of all-trans retinal in BR, which also reproduced reasonably well the small experimental anharmonic and coupling mechanical constants. Yet, and in spite accounting for both mechanical and electronic anharmonicities, the intensity of overtone C-C transitions was underestimated by a factor of 4 to 20, indicating room for improvement in state-of-the-art anharmonic vibrational calculations.


2021 ◽  
Vol 11 (1) ◽  
Author(s):  
J. P. Vasco ◽  
V. Savona

AbstractWe optimize a silica-encapsulated silicon L3 photonic crystal cavity for ultra-high quality factor by means of a global optimization strategy, where the closest holes surrounding the cavity are varied to minimize out-of-plane losses. We find an optimal value of $$Q_c=4.33\times 10^7$$ Q c = 4.33 × 10 7 , which is predicted to be in the 2 million regime in presence of structural imperfections compatible with state-of-the-art silicon fabrication tolerances.


2021 ◽  
Vol 1883 (1) ◽  
pp. 012121
Author(s):  
Jing Li ◽  
Hongxiang Tian ◽  
Tingfeng Ming ◽  
Yunling Sun ◽  
Shuai Zhang

2001 ◽  
Vol 55 (9) ◽  
pp. 1161-1165 ◽  
Author(s):  
Steven S. Andrews ◽  
Steven G. Boxer

Heliyon ◽  
2021 ◽  
pp. e08204
Author(s):  
Mouna Medimagh ◽  
Noureddine Issaoui ◽  
Sofian Gatfaoui ◽  
Silvia Antonia Brandán ◽  
Omar Al-Dossary ◽  
...  

2020 ◽  
Vol 83 (1) ◽  
pp. 75-83
Author(s):  
Siti Aishah Mohd Ali ◽  
Jalifah Latip

Rapid methods based on untargeted analysis technique such as Fourier Transform Infrared (FT-IR) spectroscopy can provide much faster and easier solution for food authentication. However, studies on the metabolite content in UKMR-2 calyces using FT-IR spectroscopy has not been reported yet in any previous studies. Thus, the present study was performed to analyze the differences in metabolite content in UKMR-2 calyces under the influences of different [CO2] treatment by applying tri-step infrared based fingerprinting. The UKMR-2 plant cultivation was exposed to ambient [CO2] (400 µmol/mol) and elevated [CO2] (800 µmol/mol) treatment. The UKMR-2 calyx extracts were analysed by conventional infrared (1D-IR), second derivative infrared (SD-IR) and two-dimensional correlation infrared (2D-IR) spectroscopy. The 1D-IR spectrum results revealed a similar absorption spectrum in the range of 1900 - 650 cm-1, which suggest similar major metabolites content present in both extracts. For SD-IR spectrum, both treatments clearly showed have more peaks with different shape, position and intensity in the range of 1650 - 1450 cm-1 and 1200 - 950 cm-1, which is likely to have different flavonoid and carbohydrate content in UKMR-2 calyces. The 2D-IR synchronous correlation spectrum in the range of 1000 – 650 cm-1 clearly distinguished the metabolite content in the UKMR-2 calyx extract from different [CO2] treatment. Therefore, this tri-step infrared based fingerprinting has the potential as one of the effective methods to discriminate extract samples with similar infrared fingerprint features and indicate that the metabolite content in UKMR-2 calyces were influenced by different [CO2] treatments.


2009 ◽  
Vol 394 (8) ◽  
pp. 2277-2277
Author(s):  
Michael Schleeger ◽  
Christoph Wagner ◽  
Michiel J. Vellekoop ◽  
Bernhard Lendl ◽  
Joachim Heberle

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