Rhodopsins contain a retinal molecule, and convert light into chemical energy or signal. The chromophore of visual or microbial rhodopsins is a retinal Schiff base of the 11-cis or all-trans form, respectively, where specific chromophore-protein interaction determines their colors. Upon light absorption, ultrafast photoisomerization initiates protein structural changes, leading to each functional expression. By use of spectroscopic methods, we have been studying how rhodopsins respond to light. Ultrafast spectroscopy of visual rhodopsin revealed that cis-trans isomerization is the primary event in our vision, which is optimized in protein environment. Fourier-transform infrared (FTIR) spectroscopy of visual and microbial rhodopsins provides various important vibrational bands related to structural changes of these proteins. Detection of protein-bound water molecules is one of the research highlights, and the comprehensive FTIR study has shown that a strongly hydrogen-bonded water molecule is the functional determinant of light-driven proton pump proteins. Here I review our spectroscopic challenge for > 25 years, particularly focusing our recent findings.
{"title":"Molecular Science of Rhodopsins","authors":"H. Kandori","doi":"10.3175/MOLSCI.5.A0043","DOIUrl":"https://doi.org/10.3175/MOLSCI.5.A0043","url":null,"abstract":"Rhodopsins contain a retinal molecule, and convert light into chemical energy or signal. The chromophore of visual or microbial rhodopsins is a retinal Schiff base of the 11-cis or all-trans form, respectively, where specific chromophore-protein interaction determines their colors. Upon light absorption, ultrafast photoisomerization initiates protein structural changes, leading to each functional expression. By use of spectroscopic methods, we have been studying how rhodopsins respond to light. Ultrafast spectroscopy of visual rhodopsin revealed that cis-trans isomerization is the primary event in our vision, which is optimized in protein environment. Fourier-transform infrared (FTIR) spectroscopy of visual and microbial rhodopsins provides various important vibrational bands related to structural changes of these proteins. Detection of protein-bound water molecules is one of the research highlights, and the comprehensive FTIR study has shown that a strongly hydrogen-bonded water molecule is the functional determinant of light-driven proton pump proteins. Here I review our spectroscopic challenge for > 25 years, particularly focusing our recent findings.","PeriodicalId":19105,"journal":{"name":"Molecular Science","volume":"51 1","pages":""},"PeriodicalIF":0.0,"publicationDate":"2011-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"83216584","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Two novel electronics based on molecular conductors are discussed. One is a crystalline supramolecular nanowire comprising conducting cation-radical molecules and halogen-bonded insulating networks. The way to utilize this nanowire for nano-size wiring in high-density memory is proposed. The other is a field effect transistor with highly correlated electrons on the conducting molecules. The Mott insulating state of organic interface is transformed into a metallic-like state by electrostatic doping, or band-filling control due to the capacitive effect of the transistor configuration. The Mott-transition transistor can be a new type of transistor driven by a phase transition.
{"title":"Development of Organic Electronics and Mott-FETs Based on Molecular Conductors","authors":"H. Yamamoto","doi":"10.3175/MOLSCI.4.A0032","DOIUrl":"https://doi.org/10.3175/MOLSCI.4.A0032","url":null,"abstract":"Two novel electronics based on molecular conductors are discussed. One is a crystalline supramolecular nanowire comprising conducting cation-radical molecules and halogen-bonded insulating networks. The way to utilize this nanowire for nano-size wiring in high-density memory is proposed. The other is a field effect transistor with highly correlated electrons on the conducting molecules. The Mott insulating state of organic interface is transformed into a metallic-like state by electrostatic doping, or band-filling control due to the capacitive effect of the transistor configuration. The Mott-transition transistor can be a new type of transistor driven by a phase transition.","PeriodicalId":19105,"journal":{"name":"Molecular Science","volume":"8 1","pages":""},"PeriodicalIF":0.0,"publicationDate":"2010-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"77629691","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Flagellar motor is a nano-sized rotary machine. Despite of 40-year research on the flagella, the physic-chemical principle of torque generation in the motor is not clear. Even the conventional technique for measuring torque has a flaw as an experimental method. Image of the flagellar motor is extensively changing at the moment. Updated information on the flagellar motor is presented.
{"title":"Turning Point of Flagella Research","authors":"S. Aizawa","doi":"10.3175/MOLSCI.4.A0034","DOIUrl":"https://doi.org/10.3175/MOLSCI.4.A0034","url":null,"abstract":"Flagellar motor is a nano-sized rotary machine. Despite of 40-year research on the flagella, the physic-chemical principle of torque generation in the motor is not clear. Even the conventional technique for measuring torque has a flaw as an experimental method. Image of the flagellar motor is extensively changing at the moment. Updated information on the flagellar motor is presented.","PeriodicalId":19105,"journal":{"name":"Molecular Science","volume":"13 1","pages":""},"PeriodicalIF":0.0,"publicationDate":"2010-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"84202263","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
In visual systems and fluorescent proteins, controlling the photo-absorption/emission energy (color tuning) of the chromophore is the essentials to furnish a protein with the photo-functionality. Depending on the protein environment, the chromophores show a variety of colors, which are relevant to the character of the excited states and to the interactions between the chromophore and the environment. Here we summarize our recent studies on the spectral tuning mechanism of the human visual cone pigments and the fluorescent proteins. These studies elucidated a common feature in the color tuning, which also suggests a strategy to artificially control the color of proteins. We also explain our recent progress in developing the symmetry-adapted cluster-configuration interaction (SAC-CI) method and hybrid quantum mechanical/molecular mechanical (QM/MM) method particularly for studying the photo-functional proteins.
{"title":"Quantum Chemistry of the Color Tuning Mechanism in the Photobiological System","authors":"J. Hasegawa","doi":"10.3175/MOLSCI.4.A0031","DOIUrl":"https://doi.org/10.3175/MOLSCI.4.A0031","url":null,"abstract":"In visual systems and fluorescent proteins, controlling the photo-absorption/emission energy (color tuning) of the chromophore is the essentials to furnish a protein with the photo-functionality. Depending on the protein environment, the chromophores show a variety of colors, which are relevant to the character of the excited states and to the interactions between the chromophore and the environment. Here we summarize our recent studies on the spectral tuning mechanism of the human visual cone pigments and the fluorescent proteins. These studies elucidated a common feature in the color tuning, which also suggests a strategy to artificially control the color of proteins. We also explain our recent progress in developing the symmetry-adapted cluster-configuration interaction (SAC-CI) method and hybrid quantum mechanical/molecular mechanical (QM/MM) method particularly for studying the photo-functional proteins.","PeriodicalId":19105,"journal":{"name":"Molecular Science","volume":"6 1","pages":""},"PeriodicalIF":0.0,"publicationDate":"2010-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"84290969","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Recombinative desorption of molecules from a metal surface is a fundamental step in heterogeneous catalytic reactions. Understanding this elementary mechanism can bring precious information on both the dynamics and the kinetics of gas-surface reactions.The aim of this work was to combine classical trajectory calculations and transition state theory (TST) based approaches to study the dynamics of molecular associative desorption. We were particularly interested in the description of state distributions in the products of associative molecular desorption. For late barrier processes such as H2/Pt(111), energy transfers between vibrational, rotational and translational motions of the departing molecule are too weak to alter its state distributions estimated at the transition state (TS). Accordingly, TST gives a straightforward description of final state distributions. On the opposite, for early barrier processes, such as H2/Cu(111), strong energy transfers occur along the exit channel. Therefore, we must apply the so-called "Statistico-Dynamical Approach" (SDA). This method is partly based upon TST and takes into account energy transfers which occur between rotational and translational motions en route to the gas phase. Therefore, SDA gives a description of rotational state distributions of desorbed molecules. For both processes under investigation, statistical methods were found to be in good agreement with both classical trajectory calculations and experimental results.
{"title":"Transition State Theory: A Reaction Dynamics Tool Applied to Gas-Surface Reactions","authors":"J. Rayez, L. Bonnet, P. Larrégaray, A. Perrier","doi":"10.3175/MOLSCI.3.A0029","DOIUrl":"https://doi.org/10.3175/MOLSCI.3.A0029","url":null,"abstract":"Recombinative desorption of molecules from a metal surface is a fundamental step in heterogeneous catalytic reactions. Understanding this elementary mechanism can bring precious information on both the dynamics and the kinetics of gas-surface reactions.The aim of this work was to combine classical trajectory calculations and transition state theory (TST) based approaches to study the dynamics of molecular associative desorption. We were particularly interested in the description of state distributions in the products of associative molecular desorption. For late barrier processes such as H2/Pt(111), energy transfers between vibrational, rotational and translational motions of the departing molecule are too weak to alter its state distributions estimated at the transition state (TS). Accordingly, TST gives a straightforward description of final state distributions. On the opposite, for early barrier processes, such as H2/Cu(111), strong energy transfers occur along the exit channel. Therefore, we must apply the so-called \"Statistico-Dynamical Approach\" (SDA). This method is partly based upon TST and takes into account energy transfers which occur between rotational and translational motions en route to the gas phase. Therefore, SDA gives a description of rotational state distributions of desorbed molecules. For both processes under investigation, statistical methods were found to be in good agreement with both classical trajectory calculations and experimental results.","PeriodicalId":19105,"journal":{"name":"Molecular Science","volume":"2 1","pages":""},"PeriodicalIF":0.0,"publicationDate":"2009-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"78782522","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Peptide aptamers are artificially created short peptide sequences that have specific recognition abilities. The technique to create peptide aptamers has been developed in biology field and many peptides that bind to various biomolecules including enzymes, receptors etc. have been isolated since 1990. Recently, this methodology has been applied to create artificial peptides that specifically bind to the surfaces of inorganic materials. Here I introduce our studies on peptide aptamers against titanium and carbon nanohorns, and discuss on the "specificity" that is required for bionanotechnology.
{"title":"Specific Recognition of the Surfaces of Inorganic Materials by Peptide Aptamers","authors":"K. Shiba","doi":"10.3175/MOLSCI.2.A0023","DOIUrl":"https://doi.org/10.3175/MOLSCI.2.A0023","url":null,"abstract":"Peptide aptamers are artificially created short peptide sequences that have specific recognition abilities. The technique to create peptide aptamers has been developed in biology field and many peptides that bind to various biomolecules including enzymes, receptors etc. have been isolated since 1990. Recently, this methodology has been applied to create artificial peptides that specifically bind to the surfaces of inorganic materials. Here I introduce our studies on peptide aptamers against titanium and carbon nanohorns, and discuss on the \"specificity\" that is required for bionanotechnology.","PeriodicalId":19105,"journal":{"name":"Molecular Science","volume":"48 1","pages":""},"PeriodicalIF":0.0,"publicationDate":"2008-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"75715557","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
{"title":"Department of Chemistry, Seoul National University","authors":"S. K. Kim","doi":"10.3175/MOLSCI.2.A0028","DOIUrl":"https://doi.org/10.3175/MOLSCI.2.A0028","url":null,"abstract":"","PeriodicalId":19105,"journal":{"name":"Molecular Science","volume":"9 1","pages":""},"PeriodicalIF":0.0,"publicationDate":"2008-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"82579696","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
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