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Dirk V Deubel - One of the best experts on this subject based on the ideXlab platform.
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mechanism and control of rare tautomer trapping at a metal metal bond adenine binding to dirhodium antitumor agents1
Journal of the American Chemical Society, 2008Co-Authors: Dirk V DeubelAbstract:The cause of mutations in the genome by the occurrence of nuclebases in their rare tautomeric forms was first proposed by Watson and Crick in 1953. Since this pioneering proposal, tremendous experimental and theoretical research efforts have aimed to elucidate the conditions under which nucleobase Tautomerizations can occur. Previous work raised the interesting question as to whether adenine binding to the anticancer drug cisplatin can induce Tautomerization of the nucleobase, but the results indicated such an event to be unlikely under physiological conditions. In this work, we have studied the reaction of three adenine (Ade) tautomers with metal−metal bonded dirhodium antitumor agents using high-level computations. The calculations reveal that the thermodynamically most stable compound in the reaction of Ade with dirhodium tetraformate in aqueous solution is a species in which a rare N6-imino tautomer spans the metal−metal bond via sites N7 and N6. However, comprehensive transition state predictions sug...
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Mechanism and Control of Rare Tautomer Trapping at a Metal−Metal Bond: Adenine Binding to Dirhodium Antitumor Agents1
Journal of the American Chemical Society, 2007Co-Authors: Dirk V DeubelAbstract:The cause of mutations in the genome by the occurrence of nuclebases in their rare tautomeric forms was first proposed by Watson and Crick in 1953. Since this pioneering proposal, tremendous experimental and theoretical research efforts have aimed to elucidate the conditions under which nucleobase Tautomerizations can occur. Previous work raised the interesting question as to whether adenine binding to the anticancer drug cisplatin can induce Tautomerization of the nucleobase, but the results indicated such an event to be unlikely under physiological conditions. In this work, we have studied the reaction of three adenine (Ade) tautomers with metal−metal bonded dirhodium antitumor agents using high-level computations. The calculations reveal that the thermodynamically most stable compound in the reaction of Ade with dirhodium tetraformate in aqueous solution is a species in which a rare N6-imino tautomer spans the metal−metal bond via sites N7 and N6. However, comprehensive transition state predictions sug...
Leonhard Grill - One of the best experts on this subject based on the ideXlab platform.
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Quantum tunneling in real space: Tautomerization of single porphycene molecules on the (111) surface of Cu, Ag, and Au
The Journal of chemical physics, 2018Co-Authors: Takashi Kumagai, Sylwester Gawinkowski, Jacek Waluk, Leonhard Grill, Janina N. Ladenthin, Yair Litman, Mariana Rossi, Mats PerssonAbstract:Tautomerization in single porphycene molecules is investigated on Cu(111), Ag(111), and Au(111) surfaces by a combination of low-temperature scanning tunneling microscopy (STM) experiments and density functional theory (DFT) calculations. It is revealed that the trans configuration is the thermodynamically stable form of porphycene on Cu(111) and Ag(111), whereas the cis configuration occurs as a meta-stable form. The trans → cis or cis → trans conversion on Cu(111) can be induced in an unidirectional fashion by injecting tunneling electrons from the STM tip or heating the surface, respectively. We find that the cis ↔ cis Tautomerization on Cu(111) occurs spontaneously via tunneling, verified by the negligible temperature dependence of the Tautomerization rate below ∼23 K. Van der Waals corrected DFT calculations are used to characterize the adsorption structures of porphycene and to map the potential energy surface of the Tautomerization on Cu(111). The calculated barriers are too high to be thermally overcome at cryogenic temperatures used in the experiment and zero-point energy corrections do not change this picture, leaving tunneling as the most likely mechanism. On Ag(111), the reversible trans ↔ cis conversion occurs spontaneously at 5 K and the cis ↔ cis Tautomerization rate is much higher than on Cu(111), indicating a significantly smaller Tautomerization barrier on Ag(111) due to the weaker interaction between porphycene and the surface compared to Cu(111). Additionally, the STM experiments and DFT calculations reveal that Tautomerization on Cu(111) and Ag(111) occurs with migration of porphycene along the surface; thus, the translational motion couples with the Tautomerization coordinate. On the other hand, the trans and cis configurations are not discernible in the STM image and no Tautomerization is observed for porphycene on Au(111). The weak interaction of porphycene with Au(111) is closest to the gas-phase limit and therefore the absence of trans and cis configurations in the STM images is explained either by the rapid Tautomerization rate or the similar character of the molecular frontier orbitals of the trans and cis configurations.
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Tautomerism - Direct Observation and Control of Single-Molecule Tautomerization by Low-Temperature Scanning Tunneling Microscopy
Tautomerism, 2016Co-Authors: Takashi Kumagai, Leonhard GrillAbstract:This chapter focuses on scanning tunneling microscopy (STM) studies of Tautomerization within a single molecule adsorbed on a surface. First, the operation principle and theory of STM is briefly described and then several examples from recent studies are discussed. STM can be used to manipulate single atoms and molecules, thereby enabling to build artificial structures on surfaces. The trans-trans Tautomerization of a single naphthalocyanine molecule, that is, the transfer of both H atoms in the cavity among the pyrrole rings can be induced if a voltage pulse larger than 1.4V is applied to the molecule. Tautomerization within porphyrin and phthalocyanine derivatives has been studied at cryogenic temperatures and induced by a voltage pulse of the STM. The Tautomerization mechanism has been attributed to inelastic electron tunneling. Time-resolved STM methods with the order of nanoseconds or picoseconds can be achieved by combining a short electric or optical pulse
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Hot Carrier-Induced Tautomerization within a Single Porphycene Molecule on Cu(111)
ACS nano, 2015Co-Authors: Janina N. Ladenthin, Sylwester Gawinkowski, Jacek Waluk, Leonhard Grill, Shuyi Liu, Takashi KumagaiAbstract:Here, we report the study of Tautomerization within a single porphycene molecule adsorbed on a Cu(111) surface using low-temperature scanning tunneling microscopy (STM) at 5 K. While molecules are adsorbed on the surface exclusively in the thermodynamically stable trans tautomer after deposition, a voltage pulse from the STM can induce the unidirectional trans → cis and reversible cis ↔ cis Tautomerization. From the voltage and current dependence of the Tautomerization yield (rate), it is revealed that the process is induced by vibrational excitation via inelastic electron tunneling. However, the metastable cis molecules are thermally switched back to the trans tautomer by heating the surface up to 30 K. Furthermore, we have found that the unidirectional Tautomerization can be remotely controlled at a distance from the STM tip. By analyzing the nonlocal process in dependence on various experimental parameters, a hot carrier-mediated mechanism is identified, in which hot electrons (holes) generated by the ...
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controlling intramolecular hydrogen transfer in a porphycene molecule with single atoms or molecules located nearby
Nature Chemistry, 2014Co-Authors: Takashi Kumagai, Felix Hanke, Sylwester Gawinkowski, John Sharp, Konstantinos Kotsis, Jacek Waluk, Mats Persson, Leonhard GrillAbstract:Although the local environment of a molecule can play an important role in its chemistry, rarely has it been examined experimentally at the level of individual molecules. Here we report the precise control of intramolecular hydrogen-transfer (Tautomerization) reactions in single molecules using scanning tunnelling microscopy. By placing, with atomic precision, a copper adatom close to a porphycene molecule, we found that the Tautomerization rates could be tuned up and down in a controlled fashion, surprisingly also at rather large separations. Furthermore, we extended our study to molecular assemblies in which even the arrangement of the pyrrolic hydrogen atoms in the neighbouring molecule influences the Tautomerization reaction in a given porphycene, with positive and negative cooperativity effects. Our results highlight the importance of controlling the environment of molecules with atomic precision and demonstrate the potential to regulate processes that occur in a single molecule.
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thermally and vibrationally induced Tautomerization of single porphycene molecules on a cu 110 surface
Physical Review Letters, 2013Co-Authors: Takashi Kumagai, Felix Hanke, Sylwester Gawinkowski, John Sharp, Konstantinos Kotsis, Jacek Waluk, Mats Persson, Leonhard GrillAbstract:We report the direct observation of intramolecular hydrogen atom transfer reactions (Tautomerization) within a single porphycene molecule on a Cu(110) surface by scanning tunneling microscopy. It is found that the Tautomerization can be induced via inelastic electron tunneling at 5 K. By measuring the bias-dependent Tautomerization rate of isotope-substituted molecules, we can assign the scanning tunneling microscopy-induced Tautomerization to the excitation of specific molecular vibrations. Furthermore, these vibrations appear as characteristic features in the dI/dV spectra measured over individual molecules. The vibrational modes that are associated with the Tautomerization are identified by density functional theory calculations. At higher temperatures above similar to 75 K, Tautomerization is induced thermally and an activation barrier of about 168 meV is determined from an Arrhenius plot.
Takashi Kumagai - One of the best experts on this subject based on the ideXlab platform.
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Quantum tunneling in real space: Tautomerization of single porphycene molecules on the (111) surface of Cu, Ag, and Au
The Journal of chemical physics, 2018Co-Authors: Takashi Kumagai, Sylwester Gawinkowski, Jacek Waluk, Leonhard Grill, Janina N. Ladenthin, Yair Litman, Mariana Rossi, Mats PerssonAbstract:Tautomerization in single porphycene molecules is investigated on Cu(111), Ag(111), and Au(111) surfaces by a combination of low-temperature scanning tunneling microscopy (STM) experiments and density functional theory (DFT) calculations. It is revealed that the trans configuration is the thermodynamically stable form of porphycene on Cu(111) and Ag(111), whereas the cis configuration occurs as a meta-stable form. The trans → cis or cis → trans conversion on Cu(111) can be induced in an unidirectional fashion by injecting tunneling electrons from the STM tip or heating the surface, respectively. We find that the cis ↔ cis Tautomerization on Cu(111) occurs spontaneously via tunneling, verified by the negligible temperature dependence of the Tautomerization rate below ∼23 K. Van der Waals corrected DFT calculations are used to characterize the adsorption structures of porphycene and to map the potential energy surface of the Tautomerization on Cu(111). The calculated barriers are too high to be thermally overcome at cryogenic temperatures used in the experiment and zero-point energy corrections do not change this picture, leaving tunneling as the most likely mechanism. On Ag(111), the reversible trans ↔ cis conversion occurs spontaneously at 5 K and the cis ↔ cis Tautomerization rate is much higher than on Cu(111), indicating a significantly smaller Tautomerization barrier on Ag(111) due to the weaker interaction between porphycene and the surface compared to Cu(111). Additionally, the STM experiments and DFT calculations reveal that Tautomerization on Cu(111) and Ag(111) occurs with migration of porphycene along the surface; thus, the translational motion couples with the Tautomerization coordinate. On the other hand, the trans and cis configurations are not discernible in the STM image and no Tautomerization is observed for porphycene on Au(111). The weak interaction of porphycene with Au(111) is closest to the gas-phase limit and therefore the absence of trans and cis configurations in the STM images is explained either by the rapid Tautomerization rate or the similar character of the molecular frontier orbitals of the trans and cis configurations.
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Force-induced Tautomerization in a single molecule
Nature chemistry, 2016Co-Authors: Janina N. Ladenthin, Sylwester Gawinkowski, Jacek Waluk, Mats Persson, Thomas Frederiksen, John C. Sharp, Takashi KumagaiAbstract:Heat transfer, electrical potential and light energy are common ways to activate chemical reactions. Applied force is another way, but dedicated studies for such a mechanical activation are limited, and this activation is poorly understood at the single-molecule level. Here, we report force-induced Tautomerization in a single porphycene molecule on a Cu(110) surface at 5 K, which is studied by scanning probe microscopy and density functional theory calculations. Force spectroscopy quantifies the force needed to trigger Tautomerization with submolecular spatial resolution. The calculations show how the reaction pathway and barrier of Tautomerization are modified in the presence of a copper tip and reveal the atomistic origin of the process. Moreover, we demonstrate that a chemically inert tip whose apex is terminated by a xenon atom cannot induce the reaction because of a weak interaction with porphycene and a strong relaxation of xenon on the tip as contact to the molecule is formed.
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Tautomerism - Direct Observation and Control of Single-Molecule Tautomerization by Low-Temperature Scanning Tunneling Microscopy
Tautomerism, 2016Co-Authors: Takashi Kumagai, Leonhard GrillAbstract:This chapter focuses on scanning tunneling microscopy (STM) studies of Tautomerization within a single molecule adsorbed on a surface. First, the operation principle and theory of STM is briefly described and then several examples from recent studies are discussed. STM can be used to manipulate single atoms and molecules, thereby enabling to build artificial structures on surfaces. The trans-trans Tautomerization of a single naphthalocyanine molecule, that is, the transfer of both H atoms in the cavity among the pyrrole rings can be induced if a voltage pulse larger than 1.4V is applied to the molecule. Tautomerization within porphyrin and phthalocyanine derivatives has been studied at cryogenic temperatures and induced by a voltage pulse of the STM. The Tautomerization mechanism has been attributed to inelastic electron tunneling. Time-resolved STM methods with the order of nanoseconds or picoseconds can be achieved by combining a short electric or optical pulse
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Hot Carrier-Induced Tautomerization within a Single Porphycene Molecule on Cu(111)
ACS nano, 2015Co-Authors: Janina N. Ladenthin, Sylwester Gawinkowski, Jacek Waluk, Leonhard Grill, Shuyi Liu, Takashi KumagaiAbstract:Here, we report the study of Tautomerization within a single porphycene molecule adsorbed on a Cu(111) surface using low-temperature scanning tunneling microscopy (STM) at 5 K. While molecules are adsorbed on the surface exclusively in the thermodynamically stable trans tautomer after deposition, a voltage pulse from the STM can induce the unidirectional trans → cis and reversible cis ↔ cis Tautomerization. From the voltage and current dependence of the Tautomerization yield (rate), it is revealed that the process is induced by vibrational excitation via inelastic electron tunneling. However, the metastable cis molecules are thermally switched back to the trans tautomer by heating the surface up to 30 K. Furthermore, we have found that the unidirectional Tautomerization can be remotely controlled at a distance from the STM tip. By analyzing the nonlocal process in dependence on various experimental parameters, a hot carrier-mediated mechanism is identified, in which hot electrons (holes) generated by the ...
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controlling intramolecular hydrogen transfer in a porphycene molecule with single atoms or molecules located nearby
Nature Chemistry, 2014Co-Authors: Takashi Kumagai, Felix Hanke, Sylwester Gawinkowski, John Sharp, Konstantinos Kotsis, Jacek Waluk, Mats Persson, Leonhard GrillAbstract:Although the local environment of a molecule can play an important role in its chemistry, rarely has it been examined experimentally at the level of individual molecules. Here we report the precise control of intramolecular hydrogen-transfer (Tautomerization) reactions in single molecules using scanning tunnelling microscopy. By placing, with atomic precision, a copper adatom close to a porphycene molecule, we found that the Tautomerization rates could be tuned up and down in a controlled fashion, surprisingly also at rather large separations. Furthermore, we extended our study to molecular assemblies in which even the arrangement of the pyrrolic hydrogen atoms in the neighbouring molecule influences the Tautomerization reaction in a given porphycene, with positive and negative cooperativity effects. Our results highlight the importance of controlling the environment of molecules with atomic precision and demonstrate the potential to regulate processes that occur in a single molecule.
Jacek Waluk - One of the best experts on this subject based on the ideXlab platform.
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Quantum tunneling in real space: Tautomerization of single porphycene molecules on the (111) surface of Cu, Ag, and Au
The Journal of chemical physics, 2018Co-Authors: Takashi Kumagai, Sylwester Gawinkowski, Jacek Waluk, Leonhard Grill, Janina N. Ladenthin, Yair Litman, Mariana Rossi, Mats PerssonAbstract:Tautomerization in single porphycene molecules is investigated on Cu(111), Ag(111), and Au(111) surfaces by a combination of low-temperature scanning tunneling microscopy (STM) experiments and density functional theory (DFT) calculations. It is revealed that the trans configuration is the thermodynamically stable form of porphycene on Cu(111) and Ag(111), whereas the cis configuration occurs as a meta-stable form. The trans → cis or cis → trans conversion on Cu(111) can be induced in an unidirectional fashion by injecting tunneling electrons from the STM tip or heating the surface, respectively. We find that the cis ↔ cis Tautomerization on Cu(111) occurs spontaneously via tunneling, verified by the negligible temperature dependence of the Tautomerization rate below ∼23 K. Van der Waals corrected DFT calculations are used to characterize the adsorption structures of porphycene and to map the potential energy surface of the Tautomerization on Cu(111). The calculated barriers are too high to be thermally overcome at cryogenic temperatures used in the experiment and zero-point energy corrections do not change this picture, leaving tunneling as the most likely mechanism. On Ag(111), the reversible trans ↔ cis conversion occurs spontaneously at 5 K and the cis ↔ cis Tautomerization rate is much higher than on Cu(111), indicating a significantly smaller Tautomerization barrier on Ag(111) due to the weaker interaction between porphycene and the surface compared to Cu(111). Additionally, the STM experiments and DFT calculations reveal that Tautomerization on Cu(111) and Ag(111) occurs with migration of porphycene along the surface; thus, the translational motion couples with the Tautomerization coordinate. On the other hand, the trans and cis configurations are not discernible in the STM image and no Tautomerization is observed for porphycene on Au(111). The weak interaction of porphycene with Au(111) is closest to the gas-phase limit and therefore the absence of trans and cis configurations in the STM images is explained either by the rapid Tautomerization rate or the similar character of the molecular frontier orbitals of the trans and cis configurations.
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Force-induced Tautomerization in a single molecule
Nature chemistry, 2016Co-Authors: Janina N. Ladenthin, Sylwester Gawinkowski, Jacek Waluk, Mats Persson, Thomas Frederiksen, John C. Sharp, Takashi KumagaiAbstract:Heat transfer, electrical potential and light energy are common ways to activate chemical reactions. Applied force is another way, but dedicated studies for such a mechanical activation are limited, and this activation is poorly understood at the single-molecule level. Here, we report force-induced Tautomerization in a single porphycene molecule on a Cu(110) surface at 5 K, which is studied by scanning probe microscopy and density functional theory calculations. Force spectroscopy quantifies the force needed to trigger Tautomerization with submolecular spatial resolution. The calculations show how the reaction pathway and barrier of Tautomerization are modified in the presence of a copper tip and reveal the atomistic origin of the process. Moreover, we demonstrate that a chemically inert tip whose apex is terminated by a xenon atom cannot induce the reaction because of a weak interaction with porphycene and a strong relaxation of xenon on the tip as contact to the molecule is formed.
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Hot Carrier-Induced Tautomerization within a Single Porphycene Molecule on Cu(111)
ACS nano, 2015Co-Authors: Janina N. Ladenthin, Sylwester Gawinkowski, Jacek Waluk, Leonhard Grill, Shuyi Liu, Takashi KumagaiAbstract:Here, we report the study of Tautomerization within a single porphycene molecule adsorbed on a Cu(111) surface using low-temperature scanning tunneling microscopy (STM) at 5 K. While molecules are adsorbed on the surface exclusively in the thermodynamically stable trans tautomer after deposition, a voltage pulse from the STM can induce the unidirectional trans → cis and reversible cis ↔ cis Tautomerization. From the voltage and current dependence of the Tautomerization yield (rate), it is revealed that the process is induced by vibrational excitation via inelastic electron tunneling. However, the metastable cis molecules are thermally switched back to the trans tautomer by heating the surface up to 30 K. Furthermore, we have found that the unidirectional Tautomerization can be remotely controlled at a distance from the STM tip. By analyzing the nonlocal process in dependence on various experimental parameters, a hot carrier-mediated mechanism is identified, in which hot electrons (holes) generated by the ...
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controlling intramolecular hydrogen transfer in a porphycene molecule with single atoms or molecules located nearby
Nature Chemistry, 2014Co-Authors: Takashi Kumagai, Felix Hanke, Sylwester Gawinkowski, John Sharp, Konstantinos Kotsis, Jacek Waluk, Mats Persson, Leonhard GrillAbstract:Although the local environment of a molecule can play an important role in its chemistry, rarely has it been examined experimentally at the level of individual molecules. Here we report the precise control of intramolecular hydrogen-transfer (Tautomerization) reactions in single molecules using scanning tunnelling microscopy. By placing, with atomic precision, a copper adatom close to a porphycene molecule, we found that the Tautomerization rates could be tuned up and down in a controlled fashion, surprisingly also at rather large separations. Furthermore, we extended our study to molecular assemblies in which even the arrangement of the pyrrolic hydrogen atoms in the neighbouring molecule influences the Tautomerization reaction in a given porphycene, with positive and negative cooperativity effects. Our results highlight the importance of controlling the environment of molecules with atomic precision and demonstrate the potential to regulate processes that occur in a single molecule.
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thermally and vibrationally induced Tautomerization of single porphycene molecules on a cu 110 surface
Physical Review Letters, 2013Co-Authors: Takashi Kumagai, Felix Hanke, Sylwester Gawinkowski, John Sharp, Konstantinos Kotsis, Jacek Waluk, Mats Persson, Leonhard GrillAbstract:We report the direct observation of intramolecular hydrogen atom transfer reactions (Tautomerization) within a single porphycene molecule on a Cu(110) surface by scanning tunneling microscopy. It is found that the Tautomerization can be induced via inelastic electron tunneling at 5 K. By measuring the bias-dependent Tautomerization rate of isotope-substituted molecules, we can assign the scanning tunneling microscopy-induced Tautomerization to the excitation of specific molecular vibrations. Furthermore, these vibrations appear as characteristic features in the dI/dV spectra measured over individual molecules. The vibrational modes that are associated with the Tautomerization are identified by density functional theory calculations. At higher temperatures above similar to 75 K, Tautomerization is induced thermally and an activation barrier of about 168 meV is determined from an Arrhenius plot.
Mats Persson - One of the best experts on this subject based on the ideXlab platform.
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Quantum tunneling in real space: Tautomerization of single porphycene molecules on the (111) surface of Cu, Ag, and Au
The Journal of chemical physics, 2018Co-Authors: Takashi Kumagai, Sylwester Gawinkowski, Jacek Waluk, Leonhard Grill, Janina N. Ladenthin, Yair Litman, Mariana Rossi, Mats PerssonAbstract:Tautomerization in single porphycene molecules is investigated on Cu(111), Ag(111), and Au(111) surfaces by a combination of low-temperature scanning tunneling microscopy (STM) experiments and density functional theory (DFT) calculations. It is revealed that the trans configuration is the thermodynamically stable form of porphycene on Cu(111) and Ag(111), whereas the cis configuration occurs as a meta-stable form. The trans → cis or cis → trans conversion on Cu(111) can be induced in an unidirectional fashion by injecting tunneling electrons from the STM tip or heating the surface, respectively. We find that the cis ↔ cis Tautomerization on Cu(111) occurs spontaneously via tunneling, verified by the negligible temperature dependence of the Tautomerization rate below ∼23 K. Van der Waals corrected DFT calculations are used to characterize the adsorption structures of porphycene and to map the potential energy surface of the Tautomerization on Cu(111). The calculated barriers are too high to be thermally overcome at cryogenic temperatures used in the experiment and zero-point energy corrections do not change this picture, leaving tunneling as the most likely mechanism. On Ag(111), the reversible trans ↔ cis conversion occurs spontaneously at 5 K and the cis ↔ cis Tautomerization rate is much higher than on Cu(111), indicating a significantly smaller Tautomerization barrier on Ag(111) due to the weaker interaction between porphycene and the surface compared to Cu(111). Additionally, the STM experiments and DFT calculations reveal that Tautomerization on Cu(111) and Ag(111) occurs with migration of porphycene along the surface; thus, the translational motion couples with the Tautomerization coordinate. On the other hand, the trans and cis configurations are not discernible in the STM image and no Tautomerization is observed for porphycene on Au(111). The weak interaction of porphycene with Au(111) is closest to the gas-phase limit and therefore the absence of trans and cis configurations in the STM images is explained either by the rapid Tautomerization rate or the similar character of the molecular frontier orbitals of the trans and cis configurations.
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Force-induced Tautomerization in a single molecule
Nature chemistry, 2016Co-Authors: Janina N. Ladenthin, Sylwester Gawinkowski, Jacek Waluk, Mats Persson, Thomas Frederiksen, John C. Sharp, Takashi KumagaiAbstract:Heat transfer, electrical potential and light energy are common ways to activate chemical reactions. Applied force is another way, but dedicated studies for such a mechanical activation are limited, and this activation is poorly understood at the single-molecule level. Here, we report force-induced Tautomerization in a single porphycene molecule on a Cu(110) surface at 5 K, which is studied by scanning probe microscopy and density functional theory calculations. Force spectroscopy quantifies the force needed to trigger Tautomerization with submolecular spatial resolution. The calculations show how the reaction pathway and barrier of Tautomerization are modified in the presence of a copper tip and reveal the atomistic origin of the process. Moreover, we demonstrate that a chemically inert tip whose apex is terminated by a xenon atom cannot induce the reaction because of a weak interaction with porphycene and a strong relaxation of xenon on the tip as contact to the molecule is formed.
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controlling intramolecular hydrogen transfer in a porphycene molecule with single atoms or molecules located nearby
Nature Chemistry, 2014Co-Authors: Takashi Kumagai, Felix Hanke, Sylwester Gawinkowski, John Sharp, Konstantinos Kotsis, Jacek Waluk, Mats Persson, Leonhard GrillAbstract:Although the local environment of a molecule can play an important role in its chemistry, rarely has it been examined experimentally at the level of individual molecules. Here we report the precise control of intramolecular hydrogen-transfer (Tautomerization) reactions in single molecules using scanning tunnelling microscopy. By placing, with atomic precision, a copper adatom close to a porphycene molecule, we found that the Tautomerization rates could be tuned up and down in a controlled fashion, surprisingly also at rather large separations. Furthermore, we extended our study to molecular assemblies in which even the arrangement of the pyrrolic hydrogen atoms in the neighbouring molecule influences the Tautomerization reaction in a given porphycene, with positive and negative cooperativity effects. Our results highlight the importance of controlling the environment of molecules with atomic precision and demonstrate the potential to regulate processes that occur in a single molecule.
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thermally and vibrationally induced Tautomerization of single porphycene molecules on a cu 110 surface
Physical Review Letters, 2013Co-Authors: Takashi Kumagai, Felix Hanke, Sylwester Gawinkowski, John Sharp, Konstantinos Kotsis, Jacek Waluk, Mats Persson, Leonhard GrillAbstract:We report the direct observation of intramolecular hydrogen atom transfer reactions (Tautomerization) within a single porphycene molecule on a Cu(110) surface by scanning tunneling microscopy. It is found that the Tautomerization can be induced via inelastic electron tunneling at 5 K. By measuring the bias-dependent Tautomerization rate of isotope-substituted molecules, we can assign the scanning tunneling microscopy-induced Tautomerization to the excitation of specific molecular vibrations. Furthermore, these vibrations appear as characteristic features in the dI/dV spectra measured over individual molecules. The vibrational modes that are associated with the Tautomerization are identified by density functional theory calculations. At higher temperatures above similar to 75 K, Tautomerization is induced thermally and an activation barrier of about 168 meV is determined from an Arrhenius plot.