45 results on '"Hamm, Peter"'
Search Results
2. Flexible to rigid: IR spectroscopic investigation of a rhenium-tricarbonyl-complex at a buried interface
- Author
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Oppelt, Kerstin T, Sevéry, Laurent, Utters, Mirjam, Tilley, S David, Hamm, Peter, University of Zurich, and Oppelt, Kerstin T
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10120 Department of Chemistry ,Materials science ,UFSP13-6 Solar Light to Chemical Energy Conversion ,General Physics and Astronomy ,Infrared spectroscopy ,chemistry.chemical_element ,02 engineering and technology ,010402 general chemistry ,01 natural sciences ,Atomic layer deposition ,540 Chemistry ,Molecule ,Physics::Chemical Physics ,Physical and Theoretical Chemistry ,Quenching (fluorescence) ,Rhenium ,021001 nanoscience & nanotechnology ,3100 General Physics and Astronomy ,0104 chemical sciences ,chemistry ,Excited state ,Physical chemistry ,Steady state (chemistry) ,1606 Physical and Theoretical Chemistry ,0210 nano-technology ,Layer (electronics) - Abstract
This work explores the solid-liquid interface of a rhenium-tricarbonyl complex embedded in a layer of zirconium oxide deposited by atomic layer deposition (ALD). Time-resolved and steady state infrared spectroscopy were applied to reveal the correlations between the thickness of the ALD layer and the spectroscopic response of the system. We observed a transition of the molecular environment from flexible to rigid, as well as limitations to ligand exchange and excited state quenching on the embedded complexes, when the ALD layer is roughly of the same height as the molecules.
- Published
- 2021
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3. A highly stable rhenium-cobalt system for photocatalytic [H.sub.2] production: unraveling the performance-limiting steps
- Author
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Rodenberg, Alexander, Probst, Benjamin, Guttentag, Miguel, Hamm, Peter, and Alberto,Roger
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Amines -- Chemical properties ,Cobalt -- Chemical properties ,Cobalt -- Optical properties ,Organometallic compounds -- Structure ,Organometallic compounds -- Chemical properties ,Organometallic compounds -- Electric properties ,Pyrimidines -- Chemical properties ,Pyrimidines -- Structure ,Rhenium -- Chemical properties ,Rhenium -- Optical properties ,Chemistry - Published
- 2010
4. Markov state model of the two-state behaviour of water
- Author
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Hamm, Peter, University of Zurich, and Hamm, Peter
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10120 Department of Chemistry ,Phase transition ,Population ,Analytical chemistry ,General Physics and Astronomy ,Markov process ,010402 general chemistry ,Radial distribution function ,01 natural sciences ,Critical point (mathematics) ,symbols.namesake ,540 Chemistry ,0103 physical sciences ,Statistical physics ,Physical and Theoretical Chemistry ,education ,Molecular diffusion ,education.field_of_study ,010304 chemical physics ,Markov chain ,Chemistry ,Atmospheric temperature range ,3100 General Physics and Astronomy ,0104 chemical sciences ,symbols ,1606 Physical and Theoretical Chemistry - Abstract
With the help of a Markov State Model (MSM), two-state behaviour is resolved for two computer models of water in a temperature range from 255 K to room temperature (295 K). The method is first validated for ST2 water, for which the so far strongest evidence for a liquid-liquid phase transition exists. In that case, the results from the MSM can be cross-checked against the radial distribution function g5(r) of the 5th-closest water molecule around a given reference water molecule. The latter is a commonly used local order parameter, which exhibits a bimodal distribution just above the liquid-liquid critical point that represents the low-density form of the liquid (LDL) and the high density liquid. The correlation times and correlation lengths of the corresponding spatial domains are calculated and it is shown that they are connected via a simple diffusion model. Once the approach is established, TIP4P/2005 will be considered, which is the much more realistic representation of real water. The MSM can resolve two-state behavior also in that case, albeit with significantly smaller correlation times and lengths. The population of LDL-like water increases with decreasing temperature, thereby explaining the density maximum at 4 °C along the lines of the two-state model of water.
- Published
- 2016
5. What can we learn from three-dimensional infrared spectroscopy?
- Author
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Garrett-Roe, Sean and Hamm, Peter
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Hydrogen bonding -- Structure ,Infrared spectroscopy -- Usage ,Raman spectroscopy -- Usage ,Solvents -- Atomic properties ,Solvents -- Chemical properties ,Vibrational spectra -- Evaluation ,Chemistry ,Science and technology - Published
- 2009
6. An efficient homogeneous intermolecular rhenium-based photocatalytic system for the production of H[sub.2]
- Author
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Probst, Benjamin, Kolano, Christoph, Hamm, Peter, and Alberto, Roger
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Hydrogen -- Research ,Photocatalysis -- Research ,Rhenium -- Research ,Chemistry - Published
- 2009
7. Two-dimensional infrared spectroscopy of photoswitchable peptides
- Author
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Hamm, Peter, Helbing, Jan, and Bredenbeck, Jens
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Infrared spectroscopy -- Analysis ,Polypeptides -- Structure ,Polypeptides -- Chemical properties ,Polypeptides -- Spectra ,Dipole moments -- Analysis ,Chemistry - Abstract
The two-dimensional infrared (2D-IR) spectroscopy technique is employed to study the ultrafast structural dynamics of the photoswitchable peptides. The mechanism involved in the unfolding of the peptide secondary structure motifs is also discussed.
- Published
- 2008
8. A fast photoswitch for minimally perturbed peptides: investigation of the trans (rarr) cis photoisomerization of N-methylthioacetamide
- Author
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Helbing, Jan, Bregy, Harald, Bredenbeck, Jens, Pfister, Rolf, Hamm, Peter, Huber, Rober, Loivucci, Massimo, De Vico, Luca, and Wachtveitl, Josef
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Amino acids -- Chemical properties ,Nitrogen -- Chemical properties ,Isomerization -- Research ,Chemistry - Abstract
Thio amino acids can be infused into the essence of peptides without excessively disturbing their structure. The photoisomerization of the trans form of N-methylthioacetamide as a model conformational photoswtich is examined.
- Published
- 2004
9. Labeling vibrations by light: ultrafast transient 2D-IR spectroscopy tracks vibrational modes during photoinduced charge transfer
- Author
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Bredenbeck, Jens, Helbing, Jan, and Hamm, Peter
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Peptides -- Research ,Molecular structure -- Research ,Infrared spectroscopy -- Usage ,Chemistry - Abstract
Ultrafast two-dimensional infrared spectroscopy (2D-IR) is a promising tool to investigate molecular structure. The investigation of this conformational transition of a photoswitchable cyclic peptide by transient 2D-IR spectroscopy (T2D-IR) is done.
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- 2004
10. 2D-Raman-THz spectroscopy: A sensitive test of polarizable water models
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Hamm, Peter, University of Zurich, and Hamm, Peter
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10120 Department of Chemistry ,Chemistry ,Isotropy ,General Physics and Astronomy ,Molecular physics ,3100 General Physics and Astronomy ,Force field (chemistry) ,Molecular dynamics ,symbols.namesake ,Polarizability ,Molecular Response ,540 Chemistry ,Water model ,symbols ,Physical and Theoretical Chemistry ,Atomic physics ,1606 Physical and Theoretical Chemistry ,Anisotropy ,Raman spectroscopy - Abstract
In a recent paper, the experimental 2D-Raman-THz response of liquid water at ambient conditions has been presented [J. Savolainen, S. Ahmed, and P. Hamm, Proc. Natl. Acad. Sci. U. S. A. 110, 20402 (2013)]. Here, all-atom molecular dynamics simulations are performed with the goal to reproduce the experimental results. To that end, the molecular response functions are calculated in a first step, and are then convoluted with the laser pulses in order to enable a direct comparison with the experimental results. The molecular dynamics simulation are performed with several different water models: TIP4P/2005, SWM4-NDP, and TL4P. As polarizability is essential to describe the 2D-Raman-THz response, the TIP4P/2005 water molecules are amended with either an isotropic or a anisotropic polarizability a posteriori after the molecular dynamics simulation. In contrast, SWM4-NDP and TL4P are intrinsically polarizable, and hence the 2D-Raman-THz response can be calculated in a self-consistent way, using the same force field as during the molecular dynamics simulation. It is found that the 2D-Raman-THz response depends extremely sensitively on details of the water model, and in particular on details of the description of polarizability. Despite the limited time resolution of the experiment, it could easily distinguish between various water models. Albeit not perfect, the overall best agreement with the experimental data is obtained for the TL4P water model.
- Published
- 2014
11. Vibrational dynamics of hydrogen bonds.
- Author
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Castleman, A.W., Toennies, J.P., Yamanouchi, K., Zinth, W., Kühn, Oliver, Wöste, Ludger, Nibbering, Erik T.J., Dreyer, Jens, Bredenbeck, Jens, Hamm, Peter, and Elsaesser, Thomas
- Abstract
Hydrogen bonds are ubiquitous and of fundamental relevance in nature. Representing a local attractive interaction between a hydrogen donor and an adjacent acceptor group, they result in the formation of single or multiple local bonds with binding energies in the range from 4 to 50 kJ mol-1, much weaker than a covalent bond, but stronger than most other intermolecular forces and thus decisive for structural and dynamical properties of a variety of molecular systems [1-4]. [ABSTRACT FROM AUTHOR]
- Published
- 2007
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12. Coherence and control of molecular dynamics in rare gas matrices.
- Author
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Castleman, A.W., Toennies, J.P., Yamanouchi, K., Zinth, W., Kühn, Oliver, Wöste, Ludger, Bargheer, Matias, Borowski, Alexander, Cohen, Arik, Fushitani, Mizuho, Gerber, R. Benny, Gühr, Markus, Hamm, Peter, Ibrahim, Heide, Kiljunen, Toni, Korolkov, Mikhail V., Manz, Jörn, Schmidt, Burkhard, Schröder, Maike, and Schwentner, Nikolaus
- Abstract
A bridge is established in this chapter connecting the subject of isolated molecules from Chaps. 2 and 3 with the multidimensional and more complex systems treated in the following chapters. Explicitly this chapter considers the dynamics of a chromophore coupled to a conceptionally infinite crystalline environment of rare gas matrices. [ABSTRACT FROM AUTHOR]
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- 2007
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13. Sequence of Events during Peptide Unbinding from RNase S: A Complete Experimental Description
- Author
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Jeannette Ruf, Claudio Zanobini, Brankica Jankovic, David Buhrke, Peter Hamm, Olga Bozovic, University of Zurich, and Hamm, Peter
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Protein Conformation, alpha-Helical ,10120 Department of Chemistry ,0301 basic medicine ,Light ,RNase P ,Binding pocket ,FOS: Physical sciences ,Sequence (biology) ,Peptide ,010402 general chemistry ,01 natural sciences ,03 medical and health sciences ,chemistry.chemical_compound ,Ribonucleases ,540 Chemistry ,Moiety ,General Materials Science ,Physics - Biological Physics ,Amino Acid Sequence ,Physical and Theoretical Chemistry ,Protein Unfolding ,chemistry.chemical_classification ,030102 biochemistry & molecular biology ,Chemistry ,Biomolecules (q-bio.BM) ,Helicity ,2500 General Materials Science ,0104 chemical sciences ,Intrinsically Disordered Proteins ,Kinetics ,Quantitative Biology - Biomolecules ,Azobenzene ,Biological Physics (physics.bio-ph) ,FOS: Biological sciences ,Biophysics ,Peptides ,1606 Physical and Theoretical Chemistry ,Azo Compounds ,Protein Binding - Abstract
The photo-triggered unbinding of the intrinsically disordered S-peptide from the RNase S complex is studied with the help of transient IR spectroscopy, covering a wide range of time scales from 100 ps to 10 ms. To that end, an azobenzene moiety has been linked to the S-peptide in a way that its helicity is disrupted by light, thereby initiating its complete unbinding. The full sequence of events is observed, starting from unfolding of the helical structure of the S-peptide on a 20 ns timescale while still being in the binding pocket of the S-protein, S-peptide unbinding after 300 microseconds, and the structural response of the S-protein after 3 ms. With regard to the S-peptide dynamics, the binding mechanism can be classified as an induced fit, while the structural response of the S-protein is better described as conformational selection.
- Published
- 2021
14. Intrinsic Dynamics of Protein–Peptide Unbinding
- Author
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Brankica Jankovic, Peter Hamm, Olga Bozovic, University of Zurich, and Hamm, Peter
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chemistry.chemical_classification ,10120 Department of Chemistry ,0303 health sciences ,1303 Biochemistry ,Photoswitch ,RNase P ,030302 biochemistry & molecular biology ,Proteins ,Peptide ,Biochemistry ,03 medical and health sciences ,chemistry.chemical_compound ,Microsecond ,Kinetics ,Ribonucleases ,Spectrometry, Fluorescence ,Azobenzene ,chemistry ,Orders of magnitude (time) ,Covalent bond ,540 Chemistry ,Biophysics ,Moiety ,Peptides ,Protein Binding - Abstract
The dynamics of peptide–protein binding and unbinding of a variant of the RNase S system has been investigated. To initiate the process, a photoswitchable azobenzene moiety has been covalently linked to the S-peptide, thereby switching its binding affinity to the S-protein. Transient fluorescence quenching was measured with the help of a time-resolved fluorometer, which has been specifically designed for these experiments and is based on inexpensive light-emitting diodes and laser diodes only. One mutant shows on–off behavior with no specific binding detectable in one of the states of the photoswitch. Unbinding is faster by at least 2 orders of magnitude, compared to that of other variants of the RNase S system. We conclude that unbinding is essentially barrier-less in that case, revealing the intrinsic dynamics of the unbinding event, which occurs on a time scale of a few hundred microseconds in a strongly stretched-exponential manner.
- Published
- 2021
15. The Speed of Allosteric Signaling Within a Single-Domain Protein
- Author
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Brankica Jankovic, Jeannette Ruf, Peter Hamm, David Buhrke, Philip J. M. Johnson, Olga Bozovic, Claudio Zanobini, University of Zurich, and Hamm, Peter
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0301 basic medicine ,10120 Department of Chemistry ,Time Factors ,Spectrophotometry, Infrared ,Protein domain ,Allosteric regulation ,FOS: Physical sciences ,Peptide ,Plasma protein binding ,010402 general chemistry ,01 natural sciences ,03 medical and health sciences ,Allosteric Regulation ,Protein Domains ,Postsynaptic potential ,540 Chemistry ,Moiety ,General Materials Science ,Physics - Biological Physics ,Physical and Theoretical Chemistry ,chemistry.chemical_classification ,Stereoisomerism ,2500 General Materials Science ,3. Good health ,0104 chemical sciences ,030104 developmental biology ,chemistry ,Biological Physics (physics.bio-ph) ,Helix ,Biophysics ,Spectrophotometry, Ultraviolet ,Signal transduction ,Peptides ,1606 Physical and Theoretical Chemistry ,Azo Compounds ,Disks Large Homolog 4 Protein ,Allosteric Site ,Protein Binding - Abstract
While much is known about different allosteric regulation mechanisms, the nature of the "allosteric signal", and the timescale on which it propagates, remains elusive. The PDZ3 domain from postsynaptic density-95 protein is a small protein domain with a terminal third alpha helix -- the $\alpha$3-helix, which is known to be allosterically active. By cross-linking the allosteric helix with an azobenzene moiety, we obtained a photocontrollable PDZ3 variant. Photoswitching triggers its allosteric transition, resulting in a change in binding affnity of a peptide to the remote binding pocket. Using time-resolved infrared and UV/Vis spectroscopy, we follow the allosteric signal transduction and reconstruct the timeline in which the allosteric signal propagates through the protein within 200 ns.
- Published
- 2021
16. Vibrational energy transport in the presence of intrasite vibrational energy redistribution
- Author
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Hamm, Peter [Physikalisch-Chemisches Institut, Universitaet Zuerich, Winterthurerstr. 190, CH-8057 Zuerich (Switzerland)]
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- 2009
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17. Real-time observation of ligand-induced allosteric transitions in a PDZ domain
- Author
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Adnan Gulzar, Peter Hamm, Gerhard Stock, David Buhrke, Brankica Jankovic, Olga Bozovic, Steffen Wolf, Claudio Zanobini, Matthias Post, University of Zurich, Stock, Gerhard, and Hamm, Peter
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10120 Department of Chemistry ,Spectrophotometry, Infrared ,Protein Conformation ,Entropy ,PDZ domain ,Allosteric regulation ,Protein domain ,PDZ Domains ,FOS: Physical sciences ,Molecular Dynamics Simulation ,010402 general chemistry ,Ligands ,01 natural sciences ,Domain (software engineering) ,03 medical and health sciences ,Molecular dynamics ,Protein structure ,Allosteric Regulation ,540 Chemistry ,Humans ,Physics - Biological Physics ,030304 developmental biology ,0303 health sciences ,1000 Multidisciplinary ,Multidisciplinary ,Binding Sites ,Photoswitch ,Chemistry ,Biomolecules (q-bio.BM) ,Ligand (biochemistry) ,0104 chemical sciences ,Quantitative Biology - Biomolecules ,Biological Physics (physics.bio-ph) ,FOS: Biological sciences ,Physical Sciences ,Mutation ,Biophysics ,Protein Tyrosine Phosphatases ,Protein Binding - Abstract
While allostery is of paramount importance for protein regulation, the underlying dynamical process of ligand (un)binding at one site, resulting time evolution of the protein structure, and change of the binding affinity at a remote site is not well understood. Here the ligand-induced conformational transition in a widely studied model system of allostery, the PDZ2 domain, is investigated by transient infrared spectroscopy accompanied by molecular dynamics simulations. To this end, an azobenzene derived photoswitch is linked to a peptide ligand in a way that its binding affinity to the PDZ2 domain changes upon switching, thus initiating an allosteric transition in the PDZ2 domain protein. The subsequent response of the protein, covering four decades of time ranging from $\sim$1~ns to $\sim$10~$\mu$s, can be rationalize by a remodelling of its rugged free energy landscape, with ver subtle shifts in the populations of a small number of structurally well defined states. It is proposed that structurally and dynamically driven allostery, often discussed as limiting scenarios of allosteric communication, actually go hand-in-hand, allowing the protein to adapt its free energy landscape to incoming signals., Comment: This unedited earlier version of the manuscript may be downloaded for personal use only. Any other use requires prior permission of the author and the National Academy of Sciences USA. The final manuscript was published in Proceedings of the National Academy of Sciences USA 117, 26031-26039 (2020) and can be found under https://www.pnas.org/content/117/42/26031.short
- Published
- 2020
- Full Text
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18. Quantifying Biomolecular Recognition with Site-Specific 2D Infrared Probes
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Peter Hamm, Klemens L. Koziol, Philip J. M. Johnson, University of Zurich, and Hamm, Peter
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10120 Department of Chemistry ,0301 basic medicine ,chemistry.chemical_classification ,Infrared ,Chemistry ,Analytical chemistry ,Infrared spectroscopy ,010402 general chemistry ,01 natural sciences ,Local structure ,2500 General Materials Science ,0104 chemical sciences ,Amino acid ,03 medical and health sciences ,030104 developmental biology ,540 Chemistry ,Biophysics ,Side chain ,General Materials Science ,Sensitivity limit ,Physical and Theoretical Chemistry ,1606 Physical and Theoretical Chemistry - Abstract
Azidohomoalanine (Aha) is an unnatural amino acid containing an infrared active azido side chain group that can, through frequency shifts of the azido stretch vibration, act as a probe of local structure. To realize the potential of such structural probes for protein science, we have developed a two-dimensional infrared spectrometer employing fast mechanical scanning and intrinsic phasing of the resulting spectra, leading to a lower sensitivity limit of ∼100 μOD level samples. Using this approach, we quantify the biomolecular recognition between a PDZ2 domain and two Aha-mutated peptides. It is shown that this method can distinguish different binding modes and that the energetics of binding can be determined.
- Published
- 2017
19. Azidohomoalanine: A Minimally Invasive, Versatile, and Sensitive Infrared Label in Proteins To Study Ligand Binding
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Klemens L. Koziol, Olga Bozovic, Adnan Gulzar, Claudio Zanobini, Gerhard Stock, Peter Hamm, Philip J. M. Johnson, Brankica Jankovic, Steffen Wolf, University of Zurich, and Hamm, Peter
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chemistry.chemical_classification ,10120 Department of Chemistry ,Circular dichroism ,010405 organic chemistry ,2508 Surfaces, Coatings and Films ,Infrared spectroscopy ,Isothermal titration calorimetry ,010402 general chemistry ,01 natural sciences ,0104 chemical sciences ,Surfaces, Coatings and Films ,Amino acid ,Surfaces ,Coatings and Films ,Molecular dynamics ,Protein structure ,chemistry ,540 Chemistry ,Side chain ,Biophysics ,Materials Chemistry ,Protein folding ,Physical and Theoretical Chemistry ,1606 Physical and Theoretical Chemistry ,2505 Materials Chemistry - Abstract
The noncanonical amino acid azidohomoalanine (Aha) is known to be an environment-sensitive infrared probe for the site-specific investigation of protein structure and dynamics. Here, the capability of that label is explored to detect protein-ligand interactions by incorporating it in the vicinity of the binding groove of a PDZ2 domain. Circular dichroism and isothermal titration calorimetry measurements reveal that the perturbation of the protein system by mutation is negligible, with minimal influence on protein stability and binding affinity. Two-dimensional infrared spectra exhibit small (1-3 cm-1) but clearly measurable red shifts of the Aha vibrational frequency upon binding of two different peptide ligands, while accompanying molecular dynamics simulations suggest that these red shifts are induced by polar contacts with side chains of the peptide ligands. Hence, Aha is a versatile and minimally invasive vibrational label that is not only able to report on large structural changes during, e.g., protein folding, but also on very subtle changes of the electrostatic environment upon ligand binding.
- Published
- 2018
20. Quinones as Reversible Electron Relays in Artificial Photosynthesis
- Author
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Mathias Mosberger, Peter Hamm, Alexander Rodenberg, Margherita Orazietti, Cyril Bachmann, Roger Alberto, Benjamin Probst, University of Zurich, and Hamm, Peter
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10120 Department of Chemistry ,Spectrophotometry, Infrared ,Semiquinone ,Inorganic chemistry ,Quantum yield ,Electrons ,Electron donor ,02 engineering and technology ,3107 Atomic and Molecular Physics, and Optics ,010402 general chemistry ,Photochemistry ,7. Clean energy ,01 natural sciences ,Redox ,Artificial photosynthesis ,chemistry.chemical_compound ,540 Chemistry ,Photosynthesis ,Physical and Theoretical Chemistry ,Quinones ,021001 nanoscience & nanotechnology ,Atomic and Molecular Physics, and Optics ,0104 chemical sciences ,chemistry ,TCEP ,Flash photolysis ,Water splitting ,Spectrophotometry, Ultraviolet ,1606 Physical and Theoretical Chemistry ,0210 nano-technology - Abstract
We explore the potential of various hydroquinone/quinone redox couples as electron relays in a homogenous water reduction system between a Re-based photosensitizer and a sacrificial electron donor [tris-(2-carboxyethyl)-phosphine, TCEP]. By using transient IR spectroscopy, flash photolysis as well as stopped-flow techniques covering timescales from picoseconds to 100 ms, we determine quenching rates and cage escape yields, the kinetics of the follow-up chemistry of the semiquinone, the recombination rates, as well as the re-reduction rates by TCEP. The overall quantum yield of hydrogen production is low, and we show that the limiting factors are the small cage escape yields and, more importantly, the slow regeneration rate by TCEP in comparison to the undesired charge recombination with the reduced water reduction catalyst.
- Published
- 2016
21. Solvation Layer of Antifreeze Proteins Analyzed with a Markov State Model
- Author
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Peter Hamm, Sebastian Wellig, University of Zurich, and Hamm, Peter
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10120 Department of Chemistry ,Protein Conformation ,Molecular Dynamics Simulation ,010402 general chemistry ,01 natural sciences ,Vibration ,Coatings and Films ,Antifreeze protein ,Antifreeze Proteins ,540 Chemistry ,0103 physical sciences ,Materials Chemistry ,Physical and Theoretical Chemistry ,Layer (object-oriented design) ,2505 Materials Chemistry ,State model ,Binding Sites ,010304 chemical physics ,Markov chain ,Chemistry ,2508 Surfaces, Coatings and Films ,Solvation ,Hydrogen Bonding ,Markov Chains ,0104 chemical sciences ,Surfaces, Coatings and Films ,Surfaces ,Solubility ,Chemical physics ,1606 Physical and Theoretical Chemistry ,Mechanism (sociology) - Abstract
Three structurally very different antifreeze proteins (AFPs) are studied, addressing the question as to what extent the hypothesized preordering-binding mechanism is still relevant in the second solvation layer of the protein and beyond. Assuming a two-state model of water, the solvation layers are analyzed with the help of molecular dynamics simulations together with a Markov state model, which investigates the local tedrahedrality of the water hydrogen-bond network around a given water molecule. It has been shown previously that this analysis can discriminate the high-entropy, high-density state of the liquid (HDL) from its more structured low-density state (LDL). All investigated proteins, regardless of whether they are an AFP or not, have a tendency to increase the amount of HDL in their second solvation layer. The ice binding site (IBS) of the antifreeze proteins counteracts that trend, with either a hole in the HDL layer or a true excess of LDL. The results correlate to a certain extent with recent experiments, which have observed ice-like vibrational (VSFG) spectra for the water atop the IBS of only a subset of antifreeze proteins. It is concluded that the preordering-binding mechanism indeed seems to play a role but is only part of the overall picture.
- Published
- 2018
22. Characterization of the Platinum-Hydrogen Bond by Surface-Sensitive Time-Resolved Infrared Spectroscopy
- Author
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Jinggang Lan, David Paleček, Gökçen Tek, Peter Hamm, Marcella Iannuzzi, University of Zurich, and Hamm, Peter
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10120 Department of Chemistry ,Materials science ,Hydrogen bond ,Anharmonicity ,Absorption cross section ,Infrared spectroscopy ,chemistry.chemical_element ,02 engineering and technology ,010402 general chemistry ,021001 nanoscience & nanotechnology ,01 natural sciences ,2500 General Materials Science ,0104 chemical sciences ,chemistry ,Attenuated total reflection ,540 Chemistry ,Physical chemistry ,Water splitting ,General Materials Science ,Density functional theory ,Physical and Theoretical Chemistry ,0210 nano-technology ,Platinum ,1606 Physical and Theoretical Chemistry - Abstract
The vibrational dynamics of Pt–H on a nanostructured platinum surface has been examined by ultrafast infrared spectroscopy. Three bands are observed at 1800, 2000, and 2090 cm–1, which are assigned to Pt–CO in a bridged and linear configuration and Pt–H, respectively. Lifetime analysis revealed a time constant of (0.8 ± 0.1) ps for the Pt–H mode, considerably shorter than that of Pt–CO because of its stronger coupling to the metal substrate. Two-dimensional attenuated total reflection infrared spectroscopy provided additional evidence for the assignment based on the anharmonic shift, which is large in the case of Pt–H (90 cm–1), in agreement with the density functional theory calculations. The absorption cross section of Pt–H is smaller than that of the very strong Pt–CO vibration by only a modest factor of ∼1.5–3. Because Pt–H is transiently involved in catalytic water splitting on Pt, the present spectroscopic characterization paves the way for in-operando kinetic studies of such reactions.
- Published
- 2018
23. 2D IR spectroscopy of high-pressure phases of ice
- Author
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Ana V. Cunha, Jacob J. Shephard, Andrey Shalit, Halina Tran, Peter Hamm, Thomas L. C. Jansen, Christoph G. Salzmann, Theory of Condensed Matter, University of Zurich, and Hamm, Peter
- Subjects
10120 Department of Chemistry ,LIQUID WATER ,Ice V ,2-DIMENSIONAL INFRARED-SPECTROSCOPY ,CRYSTAL NEUTRON-DIFFRACTION ,General Physics and Astronomy ,Infrared spectroscopy ,Ice Ih ,010402 general chemistry ,01 natural sciences ,Molecular physics ,Physics::Geophysics ,symbols.namesake ,Molecular dynamics ,540 Chemistry ,0103 physical sciences ,H2O ,RAMAN-SPECTRA ,Physical and Theoretical Chemistry ,Physics::Atmospheric and Oceanic Physics ,010304 chemical physics ,Chemistry ,Hydrogen bond ,Ice II ,IH ,3100 General Physics and Astronomy ,0104 chemical sciences ,STRETCHING VIBRATIONS ,Crystallography ,HYDROGEN-BONDS ,MOLECULAR-DYNAMICS ,Molecular vibration ,symbols ,Astrophysics::Earth and Planetary Astrophysics ,1606 Physical and Theoretical Chemistry ,Raman spectroscopy ,HEAVY-WATER - Abstract
We present experimental and simulated 2D IR spectra of some high-pressure forms of isotope-pure D2O ice and compare the results to those of ice Ih published previously [F. Perakis and P. Hamm, Phys. Chem. Chem. Phys. 14, 6250 (2012); L. Shi et al., ibid. 18, 3772 (2016)]. Ice II, ice V, and ice XIII have been chosen for this study, since this selection covers many aspects of the polymorphism of ice. That is, ice II is a hydrogen-ordered phase of ice, in contrast to ice Ih, while ice V and ice XIII are a hydrogen-disordered/ordered couple that shares essentially the same oxygen structure and hydrogen-bonded network. For the transmission 2D IR spectroscopy, a novel method had to be developed for the preparation of ultrathin films (1-2 mu m) of high-pressure ices with good optical quality. We also simulated 2D IR spectra based on molecular dynamics simulations connected to a vibrational exciton picture. These simulations agree with the experimental results in a semi-quantitative manner for ice II, while the same approach failed for ice V and ice XIII. From the perspective of 2D IR spectroscopy, ice II appears to be more inhomogeneously broadened than ice Ih, despite its hydrogen-order, which we attribute to the fact that ice II is structurally more complex with four distinguishable hydrogen bonds that mix due to exciton coupling. Ice V and ice XIII, on the other hand, behave as expected with the hydrogen-disordered case (ice V) being more inhomogenously broadened. Furthermore, in all hydrogen-ordered forms (ice II and ice XIII), cross peaks could be identified in the anisotropic 2D IR spectrum, whose signs reveal the relative direction of the corresponding excitonic states. Published by AIP Publishing.
- Published
- 2017
24. A surprisingly simple correlation between the classical and quantum structural networks in liquid water
- Author
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Sotiris S. Xantheas, Peter Hamm, George S. Fanourgakis, University of Zurich, and Hamm, Peter
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10120 Department of Chemistry ,Range (particle radiation) ,010304 chemical physics ,Chemistry ,Diagram ,General Physics and Astronomy ,Thermodynamics ,Atmospheric temperature range ,010402 general chemistry ,01 natural sciences ,3100 General Physics and Astronomy ,0104 chemical sciences ,Polarizability ,Quantum mechanics ,0103 physical sciences ,540 Chemistry ,Linear scale ,Physical and Theoretical Chemistry ,Spectroscopy ,1606 Physical and Theoretical Chemistry ,Quantum ,Phase diagram - Abstract
Nuclear quantum effects in liquid water have profound implications for several of its macroscopic properties related to the structure, dynamics, spectroscopy, and transport. Although several of water's macroscopic properties can be reproduced by classical descriptions of the nuclei using interaction potentials effectively parameterized for a narrow range of its phase diagram, a proper account of the nuclear quantum effects is required to ensure that the underlying molecular interactions are transferable across a wide temperature range covering different regions of that diagram. When performing an analysis of the hydrogen-bonded structural networks in liquid water resulting from the classical (class) and quantum (qm) descriptions of the nuclei with two interaction potentials that are at the two opposite ends of the range in describing quantum effects, namely the flexible, pair-wise additive q-TIP4P/F, and the flexible, polarizable TTM3-F, we found that the (class) and (qm) results can be superimposed over the temperature range T = 250-350 K using a surprisingly simple, linear scaling of the two temperatures according to T(qm) = α T(class) + ΔT, where α = 0.99 and ΔT = -6 K for q-TIP4P/F and α = 1.24 and ΔT = -64 K for TTM3-F. This simple relationship suggests that the structural networks resulting from the quantum and classical treatment of the nuclei with those two very different interaction potentials are essentially similar to each other over this extended temperature range once a model-dependent linear temperature scaling law is applied.
- Published
- 2017
25. Intramolecular Light-Driven Accumulation of Reduction Equivalents by Proton-Coupled Electron Transfer
- Author
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Oliver S. Wenger, Margherita Orazietti, Martin Kuss-Petermann, Markus Neuburger, Peter Hamm, University of Zurich, and Hamm, Peter
- Subjects
10120 Department of Chemistry ,1303 Biochemistry ,Proton ,1503 Catalysis ,010405 organic chemistry ,Chemistry ,1600 General Chemistry ,1505 Colloid and Surface Chemistry ,General Chemistry ,010402 general chemistry ,Photochemistry ,01 natural sciences ,Biochemistry ,Acceptor ,Catalysis ,0104 chemical sciences ,chemistry.chemical_compound ,Electron transfer ,Colloid and Surface Chemistry ,Intramolecular force ,Excited state ,540 Chemistry ,Kinetic isotope effect ,Proton-coupled electron transfer ,Acetonitrile - Abstract
The photochemistry of a molecular pentad composed of a central anthraquinone (AQ) acceptor flanked by two Ru(bpy)32+ photosensitizers and two peripheral triarylamine (TAA) donors was investigated by transient IR and UV–vis spectroscopies in the presence of 0.2 M p-toluenesulfonic acid (TsOH) in deaerated acetonitrile. In ∼15% of all excited pentad molecules, AQ is converted to its hydroquinone form (AQH2) via reversible intramolecular electron transfer from the two TAA units (τ = 65 ps), followed by intermolecular proton transfer from TsOH (τ ≈ 3 ns for the first step). Although the light-driven accumulation of reduction equivalents occurs through a sequence of electron and proton transfer steps, the resulting photoproduct decays via concerted PCET (τ = 4.7 μs) with an H/D kinetic isotope effect of 1.4 ± 0.2. Moreover, the reoxidation of AQH2 seems to take place via a double electron transfer step involving both TAA+ units rather than sequential single electron transfer events. Thus, the overall charge-recombination reaction seems to involve a concerted proton-coupled two-electron oxidation of AQH2. The comparison of experimental data obtained in neat acetonitrile with data from acidic solutions suggests that the inverted driving-force effect can play a crucial role for obtaining long-lived photoproducts resulting from multiphoton, multielectron processes. Our pentad provides the first example of light-driven accumulation of reduction equivalents stabilized by PCET in artificial molecular systems without sacrificial reagents. Our study provides fundamental insight into how light-driven multielectron redox chemistry, for example the reduction of CO2 or the oxidation of H2O, can potentially be performed without sacrificial reagents.
- Published
- 2017
26. Kinetic response of a photoperturbed allosteric protein
- Author
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Reto Walser, Peter Hamm, Sandra Steiner, Rolf Pfister, Mateusz L. Donten, Steven A. Waldauer, Oliver Zerbe, Nicolas Blöchliger, Brigitte Buchli, Amedeo Caflisch, University of Zurich, and Hamm, Peter
- Subjects
Models, Molecular ,10120 Department of Chemistry ,Magnetic Resonance Spectroscopy ,Time Factors ,Spectrophotometry, Infrared ,Photochemistry ,Protein Conformation ,Allosteric regulation ,PDZ domain ,Protein Tyrosine Phosphatase, Non-Receptor Type 13 ,Molecular Dynamics Simulation ,01 natural sciences ,03 medical and health sciences ,Molecular dynamics ,chemistry.chemical_compound ,Protein structure ,Allosteric Regulation ,540 Chemistry ,0103 physical sciences ,10019 Department of Biochemistry ,Humans ,030304 developmental biology ,1000 Multidisciplinary ,0303 health sciences ,Multidisciplinary ,010304 chemical physics ,biology ,Photoswitch ,Lasers ,Water ,Nuclear magnetic resonance spectroscopy ,Kinetics ,Allosteric enzyme ,Azobenzene ,chemistry ,Physical Sciences ,biology.protein ,Biophysics ,570 Life sciences ,Azo Compounds - Abstract
By covalently linking an azobenzene photoswitch across the binding groove of a PDZ domain, a conformational transition, similar to the one occurring upon ligand binding to the unmodified domain, can be initiated on a picosecond timescale by a laser pulse. The protein structures have been characterized in the two photoswitch states through NMR spectroscopy and the transition between them through ultrafast IR spectroscopy and molecular dynamics simulations. The binding groove opens on a 100-ns timescale in a highly nonexponential manner, and the molecular dynamics simulations suggest that the process is governed by the rearrangement of the water network on the protein surface. We propose this rearrangement of the water network to be another possible mechanism of allostery.
- Published
- 2013
27. Light-driven electron accumulation in a molecular pentad
- Author
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Oliver S. Wenger, Martin Kuss-Petermann, Margherita Orazietti, Peter Hamm, University of Zurich, and Hamm, Peter
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10120 Department of Chemistry ,010405 organic chemistry ,Chemistry ,1503 Catalysis ,UFSP13-6 Solar Light to Chemical Energy Conversion ,1600 General Chemistry ,General Chemistry ,010402 general chemistry ,Photochemistry ,01 natural sciences ,7. Clean energy ,Redox ,Acceptor ,Catalysis ,0104 chemical sciences ,Artificial photosynthesis ,Electron transfer ,540 Chemistry ,Energy transformation ,Time-resolved spectroscopy ,Visible spectrum - Abstract
Accumulation and temporary storage of redox equivalents with visible light as an energy input is of pivotal importance for artificial photosynthesis because key reactions, such as CO2 reduction or water oxidation, require the transfer of multiple redox equivalents. We report on the first purely molecular system, in which a long-lived charge-separated state (τ≈870 ns) with two electrons accumulated on a suitable acceptor unit can be observed after excitation with visible light. Importantly, no sacrificial reagents were employed.
- Published
- 2016
28. Photocontrol of Reversible Amyloid Formation with a Minimal-Design Peptide
- Author
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Beatrice Paoli, Peter Hamm, Riccardo Pellarin, Paul M. Donaldson, Steven A. Waldauer, Shabir Hassan, Amedeo Caflisch, Rolf Pfister, University of Zurich, and Hamm, Peter
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10120 Department of Chemistry ,Amyloid ,Photoisomerization ,Ultraviolet Rays ,Stereochemistry ,Peptide ,Sequence (biology) ,Molecular Dynamics Simulation ,010402 general chemistry ,01 natural sciences ,Protein Structure, Secondary ,03 medical and health sciences ,Molecular dynamics ,chemistry.chemical_compound ,Isomerism ,540 Chemistry ,10019 Department of Biochemistry ,Materials Chemistry ,Ultraviolet light ,Physical and Theoretical Chemistry ,2505 Materials Chemistry ,030304 developmental biology ,chemistry.chemical_classification ,0303 health sciences ,2508 Surfaces, Coatings and Films ,Hydrogen Bonding ,Fluorescence ,0104 chemical sciences ,Surfaces, Coatings and Films ,Cross-Linking Reagents ,chemistry ,Azobenzene ,570 Life sciences ,biology ,Peptides ,1606 Physical and Theoretical Chemistry ,Azo Compounds - Abstract
Amyloid aggregates are highly ordered fibrillar assemblies of polypeptides involved in a number of neurodegenerative diseases. Very little is known on the pathways of self-assembly of peptides into the final amyloid fibrils, which is due in part to the difficulty of triggering the aggregation process in a controlled manner. Here we present the design and validation of a cross-linked hexapeptide that reversibly aggregates and dissociates under ultraviolet light irradiation control. First molecular dynamics simulations were carried out to identify, among hundreds of possible sequences, those with the highest propensity to form ordered (β-sheet) oligomers in the trans state of the azobenzene cross-linker, and at the same time with the highest solubility in the cis state. In the simulations, the peptides were observed to spontaneously form ordered oligomers with cross-β contacts when the cross-linker was in the trans state, whereas in the cis state they self-assemble into amorphous aggregates. For the most promising sequence emerging from the simulations (Ac-Cys-His-Gly-Gln-Cys-Lys-NH(2) cross-linked at the two cysteine residues), the photoisomerization of the azobenzene group was shown to induce reversible aggregation by time-resolved light scattering and fluorescence measurements. The amyloid-like fibrillar topology was confirmed by electron microscopy. Potential applications of minimally designed peptides with photoswitchable amyloidogenic propensity are briefly discussed.
- Published
- 2012
29. Photocatalytic H2 production with a Rhenium/Cobalt system in water under acidic conditions
- Author
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Marco Brandstätter, Christian Buchwalder, Alexander Rodenberg, Benjamin Probst, Miguel Guttentag, Peter Hamm, René Kopelent, Roger Alberto, University of Zurich, and Hamm, Peter
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Green chemistry ,10120 Department of Chemistry ,010405 organic chemistry ,1604 Inorganic Chemistry ,chemistry.chemical_element ,Homogeneous catalysis ,Rhenium ,010402 general chemistry ,Photochemistry ,01 natural sciences ,0104 chemical sciences ,3. Good health ,Catalysis ,Inorganic Chemistry ,chemistry.chemical_compound ,chemistry ,Pyridine ,540 Chemistry ,Photocatalysis ,Dehydroascorbic acid ,Cobalt ,Nuclear chemistry - Abstract
In photocatalytic H2 formation, tertiary amines are commonly used as sacrificial electron donors, thereby limiting the pH range for studies in water and the concentration of free protons. We found that ascorbate rapidly reductively quenches the excited state of [Re(CO)3(bipy)(py)]+ (bpy = 2,2′-bipyridyl; py = pyridine). In combination with the water reduction catalyst (WRC) [Co{(DO)(DOH)pn}Br2] [(DO)(DOH)pn = N2,N2′-propanediylbis(2,3-butanedione 2-imine 3-oxime)], this system produces H2 upon irradiation with light under acidic conditions (pH range 2–6) and with significantly enhanced turnover numbers. Furthermore, we observed that, in contrast to similar systems with tertiary amines, oxidized ascorbate (dehydroascorbic acid) is slowly re-reduced during the course of photocatalysis.
- Published
- 2012
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30. Transition from IVR limited vibrational energy transport to bulk heat transport
- Author
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Peter Hamm, Marco Schade, University of Zurich, and Hamm, Peter
- Subjects
10120 Department of Chemistry ,Length scale ,010304 chemical physics ,Vibrational energy ,Chemistry ,General Physics and Astronomy ,02 engineering and technology ,021001 nanoscience & nanotechnology ,01 natural sciences ,Molecular physics ,3100 General Physics and Astronomy ,Hot band ,Propagation rate ,Molecular vibration ,540 Chemistry ,0103 physical sciences ,Vibrational energy relaxation ,Energy density ,Physical and Theoretical Chemistry ,Atomic physics ,1606 Physical and Theoretical Chemistry ,0210 nano-technology ,Energy transport - Abstract
In a previous paper [M. Schade, P. Hamm, Vibrational energy transport in the presence of intrasite vibrational energy redistribution, J. Chem. Phys. 131 (2009) 044511], it has been shown that on ultrashort length and time scales, the speed of vibrational energy transport along a molecular chain is limited by intra site vibrational relaxation rather than the actual inter site propagation. However, since intra site vibrational relaxation is length independent, the inter site propagation rate is expected to become rate-limiting at some length scale, where propagation approaches the bulk limit. In the present paper, we investigate the transition between both regimes. The response of different types of modes may be very different at early times, depending on how much they contribute directly to energy transport. Surprisingly though, when averaging the energy content over all vibrational modes of the various chain sites, the complexity of the intra site vibrational relaxation process is completely hidden so that energy transport on the nanoscale can be described by an effective propagation rate, that equals the bulk value, even at short times.
- Published
- 2012
31. Temperature Dependence of the Heat Diffusivity of Proteins
- Author
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Jan Helbing, Michael Devereux, Karin Nienhaus, Markus Meuwly, Peter Hamm, G. Ulrich Nienhaus, University of Zurich, and Hamm, Peter
- Subjects
10120 Department of Chemistry ,Male ,Hot Temperature ,Hemeprotein ,Infrared Rays ,Protein Conformation ,Heme ,02 engineering and technology ,Molecular Dynamics Simulation ,Thermal diffusivity ,Vibration ,01 natural sciences ,7. Clean energy ,Molecular dynamics ,chemistry.chemical_compound ,540 Chemistry ,0103 physical sciences ,Libration ,Animals ,Molecule ,Physical and Theoretical Chemistry ,Carbon Monoxide ,010304 chemical physics ,Myoglobin ,Anharmonicity ,Whales ,Water ,021001 nanoscience & nanotechnology ,Spermatozoa ,Kinetics ,Energy Transfer ,chemistry ,Chemical physics ,Mutation ,Solvents ,Thermodynamics ,Physical chemistry ,1606 Physical and Theoretical Chemistry ,0210 nano-technology ,Excitation ,Protein Binding - Abstract
In a combined experimental-theoretical study, we investigated the transport of vibrational energy from the surrounding solvent into the interior of a heme protein, the sperm whale myoglobin double mutant L29W-S108L, and its dependence on temperature from 20 to 70 K. The hindered libration of a CO molecule that is not covalently bound to any part of the protein but is trapped in one of its binding pockets (the Xe4 pocket) was used as the local thermometer. Energy was deposited into the solvent by IR excitation. Experimentally, the energy transfer rate increased from (30 ps)(-1) at 20 K to (8 ps)(-1) at 70 K. This temperature trend is opposite to what is expected, assuming that the mechanism of heat transport is similar to that in glasses. In order to elucidate the mechanism and its temperature dependence, nonequilibrium molecular dynamics (MD) simulations were performed, which, however, predicted an essentially temperature-independent rate of vibrational energy flow. We tentatively conclude that the MD potentials overestimate the coupling between the protein and the CO molecule, which appears to be the rate-limiting step in the real system at low temperatures. Assuming that this coupling is anharmonic in nature, the observed temperature trend can readily be explained.
- Published
- 2011
32. Ultrafast, Multidimensional Attenuated Total Reflectance Spectroscopy of Adsorbates at Metal Surfaces
- Author
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Davide Lotti, Peter Hamm, Jan Philip Kraack, University of Zurich, and Hamm, Peter
- Subjects
10120 Department of Chemistry ,Infrared ,Chemistry ,Analytical chemistry ,2500 General Materials Science ,Characterization (materials science) ,Chemical physics ,Attenuated total reflection ,540 Chemistry ,Femtosecond ,Physics::Atomic and Molecular Clusters ,Vibrational energy relaxation ,Molecule ,General Materials Science ,Physics::Chemical Physics ,Physical and Theoretical Chemistry ,1606 Physical and Theoretical Chemistry ,Spectroscopy ,Refractive index - Abstract
Ultrafast dynamics of molecules at solid–liquid interfaces are of outstanding importance in chemistry and physics due to their involvement in processes of heterogeneous catalysis. We present a new spectroscopic approach to resolve coherent, time-resolved, 2D vibrational spectra as well as ultrafast vibrational relaxation dynamics of molecules adsorbed on metallic thin films in contact with liquids. The setup is based on the technique of attenuated total reflectance (ATR) spectroscopy, which is used at interfaces between materials that exhibit different refractive indices. As a sample molecule, we consider carbon monoxide adsorbed in different binding configurations on different metals and resolve its femtosecond vibrational dynamics. It is presented that mid-infrared, multidimensional ATR spectroscopy allows for obtaining a surface-sensitive characterization of adsorbates’ vibrational relaxation, spectral diffusion dynamics, and sample inhomogeneity on the femtosecond time scale.
- Published
- 2015
33. 2D attenuated total reflectance infrared spectroscopy reveals ultrafast vibrational dynamics of organic monolayers at metal-liquid interfaces
- Author
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Jan Philip Kraack, Peter Hamm, Davide Lotti, University of Zurich, and Hamm, Peter
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10120 Department of Chemistry ,chemistry.chemical_classification ,Chemistry ,Infrared ,Analytical chemistry ,General Physics and Astronomy ,Infrared spectroscopy ,3100 General Physics and Astronomy ,Spectral line ,Condensed Matter::Soft Condensed Matter ,Attenuated total reflection ,Molecular vibration ,540 Chemistry ,Monolayer ,Vibrational energy relaxation ,Physical and Theoretical Chemistry ,1606 Physical and Theoretical Chemistry ,Alkyl - Abstract
We present two-dimensional infrared (2D IR) spectra of organic monolayers immobilized on thin metallic films at the solid liquid interface. The experiments are acquired under Attenuated Total Reflectance (ATR) conditions which allow a surface-sensitive measurement of spectral diffusion, sample inhomogeneity, and vibrational relaxation of the monolayers. Terminal azide functional groups are used as local probes of the environment and structural dynamics of the samples. Specifically, we investigate the influence of different alkyl chain-lengths on the ultrafast dynamics of the monolayer, revealing a smaller initial inhomogeneity and faster spectral diffusion with increasing chain-length. Furthermore, by varying the environment (i.e., in different solvents or as bare sample), we conclude that the most significant contribution to spectral diffusion stems from intra- and intermolecular dynamics within the monolayer. The obtained results demonstrate that 2D ATR IR spectroscopy is a versatile tool for measuring interfacial dynamics of adsorbed molecules.
- Published
- 2015
34. Fast infrared spectroscopy of protein dynamics: advancing sensitivity and selectivity
- Author
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Peter Hamm, Klemens L. Koziol, Philip J. M. Johnson, Steven A. Waldauer, Brigitte Stucki-Buchli, University of Zurich, and Hamm, Peter
- Subjects
Models, Molecular ,10120 Department of Chemistry ,Spectrophotometry, Infrared ,Chemistry ,Protein Conformation ,Protein dynamics ,Infrared spectroscopy ,Proteins ,Reproducibility of Results ,Nanotechnology ,Sensitivity and Specificity ,1315 Structural Biology ,Structural Biology ,540 Chemistry ,1312 Molecular Biology ,Sensitivity (control systems) ,Spectroscopy ,Selectivity ,Molecular Biology ,Ultrashort pulse - Abstract
2D-IR spectroscopy has matured to a powerful technique to study the structure and dynamics of peptides, but its extension to larger proteins is still in its infancy, the major limitations being sensitivity and selectivity. Site-selective information requires measuring single vibrational probes at sub-millimolar concentrations where most proteins are still stable, which is a severe challenge for conventional (FT)IR spectroscopy. Besides its ultrafast time-resolution, a so far largely underappreciated potential of 2D-IR spectroscopy lies in its sensitivity gain. The present paper sets the goals and outlines strategies how to use that sensitivity gain together with properly designed vibrational labels to make IR spectroscopy a versatile tool to study a wide class of proteins.
- Published
- 2015
35. Mechanism of photocatalytic hydrogen generation by a polypyridyl-based cobalt catalyst in aqueous solution
- Author
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Alexander Rodenberg, Peter Hamm, Benjamin Probst, Roger Alberto, Cyril Bachmann, Margherita Orazietti, Kim K. Baldridge, University of Zurich, and Hamm, Peter
- Subjects
10120 Department of Chemistry ,Hydrogen ,Inorganic chemistry ,chemistry.chemical_element ,Electron donor ,010402 general chemistry ,Photochemistry ,7. Clean energy ,01 natural sciences ,Catalysis ,Inorganic Chemistry ,chemistry.chemical_compound ,540 Chemistry ,medicine ,Physical and Theoretical Chemistry ,Hydrogen production ,Quenching (fluorescence) ,Aqueous solution ,1604 Inorganic Chemistry ,010405 organic chemistry ,0104 chemical sciences ,chemistry ,13. Climate action ,Triethanolamine ,1606 Physical and Theoretical Chemistry ,Cobalt ,medicine.drug - Abstract
The mechanism of photocatalytic hydrogen production was studied with a three-component system consisting of fac-[Re(py)(CO)3bipy](+) (py = pyridine, bipy = 2,2'-bipyridine) as photosensitizer, [Co(TPY-OH)(OH2)](2+) (TPY-OH = 2-bis(2-pyridyl)(hydroxy)methyl-6-pyridylpyridine), a polypyridyl-based cobalt complex, as water reduction catalyst (WRC), and triethanolamine (TEOA) as sacrificial electron donor in aqueous solution. A detailed mechanistic picture is provided, which covers all processes from excited state quenching on the time scale of a few nanoseconds to hydrogen release taking place between seconds and minutes at moderately basic reaction conditions. Altogether these processes span 9 orders of magnitude in time. The following reaction sequence was found to be the dominant pathway for hydrogen generation: After reductive quenching by TEOA, the reduced photosensitizer (PS) transfers an electron to the Co(II)-WRC. Protonation of Co(I) yields Co(III)H which is reduced in the presence of excess Co(I). Co(II)H releases hydrogen after a second protonation step, which is detected time-resolved by a clark-type hydrogen electrode. Aside from these productive steps, the role of side and back reactions involving TEOA-derived species is assessed, which is particularly relevant in laser flash photolysis measurements with significantly larger transient concentrations of reactive species as compared to continuous photolysis experiments. Most notable is an equilibrium reaction involving Co(I), which is explained by a nucleophilic addition of Co(I) to the oxidation product of TEOA, an electrophilic iminium ion. Quantum chemical calculations indicate that the reaction is energetically feasible. The calculated spectra of the adduct are consistent with the spectroscopic observations.
- Published
- 2014
36. Effect of viscogens on the kinetic response of a photoperturbed allosteric protein
- Author
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Steven A. Waldauer, Lukas Frey, Brigitte Stucki-Buchli, Peter Hamm, University of Zurich, and Hamm, Peter
- Subjects
Glycerol ,10120 Department of Chemistry ,Conformational change ,Protein Folding ,Sucrose ,Light ,Kinetics ,Allosteric regulation ,Protein Tyrosine Phosphatase, Non-Receptor Type 13 ,General Physics and Astronomy ,PDZ Domains ,Molecular Dynamics Simulation ,Chemical kinetics ,Viscosity ,Molecular dynamics ,540 Chemistry ,Molecule ,Humans ,Physical and Theoretical Chemistry ,Chemistry ,Energy landscape ,Photochemical Processes ,3100 General Physics and Astronomy ,Biophysics ,Physical chemistry ,1606 Physical and Theoretical Chemistry - Abstract
By covalently binding a photoswitchable linker across the binding groove of the PDZ2 domain, a small conformational change can be photo-initiated that mimics the allosteric transition of the protein. The response of its binding groove is investigated with the help of ultrafast pump-probe IR spectroscopy from picoseconds to tens of microseconds. The temperature dependence of that response is compatible with diffusive dynamics on a rugged energy landscape without any prominent energy barrier. Furthermore, the dependence of the kinetics on the concentration of certain viscogens, sucrose, and glycerol, has been investigated. A pronounced viscosity dependence is observed that can be best fit by a power law, i.e., a fractional viscosity dependence. The change of kinetics when comparing sucrose with glycerol as viscogen, however, provides strong evidence that direct interactions of the viscogen molecule with the protein do play a role as well. This conclusion is supported by accompanying molecular dynamics simulations.
- Published
- 2014
37. Response of villin headpiece-capped gold nanoparticles to ultrafast laser heating
- Author
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Marco Schade, Peter Hamm, Shabir Hassan, Christopher P. Shaw, Raphaël Lévy, University of Zurich, and Hamm, Peter
- Subjects
10120 Department of Chemistry ,Circular dichroism ,Chemistry ,Hydrogen bond ,Circular Dichroism ,Lasers ,Microfilament Proteins ,Solvation ,2508 Surfaces, Coatings and Films ,Infrared spectroscopy ,Metal Nanoparticles ,Surfaces, Coatings and Films ,Blueshift ,Crystallography ,Colloidal gold ,Temperature jump ,Spectroscopy, Fourier Transform Infrared ,540 Chemistry ,Materials Chemistry ,Denaturation (biochemistry) ,Spectrophotometry, Ultraviolet ,Gold ,Physical and Theoretical Chemistry ,1606 Physical and Theoretical Chemistry ,2505 Materials Chemistry - Abstract
The integrity of a small model protein, the 36-residue villin headpiece HP36, attached to gold nanoparticles (AuNP) is examined, and its response to laser excitation of the AuNPs is investigated. To that end, it is first verified by stationary IR and CD spectroscopy, together with denaturation experiments, that the folded structure of the protein is fully preserved when attached to the AuNP surface. It is then shown by time-resolved IR spectroscopy that the protein does not unfold, even upon the highest pump fluences that lead to local temperature jumps on the order of 1000 K of the phonon system of the AuNPs, since that temperature jump persists for too short a time of a few nanoseconds only to be destructive. Judged from a blue shift of the amide I band, indicating destabilized or a few broken hydrogen bonds, the protein either swells, becomes more unstructured from the termini, or changes its degree of solvation. In any case, it recovers immediately after the excess energy dissipates into the bulk solvent. The process is entirely reversible for millions of laser shots without any indication of aggregation of the protein or the AuNPs and with only a minor fraction of broken protein-AuNP thiol bonds. The work provides important cornerstones in designing laser pulse parameters for maximal heating with protein-capped AuNPs without destroying the capping layer.
- Published
- 2014
38. Testing for memory-free spectroscopic coordinates by 3D IR exchange spectroscopy
- Author
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Peter Hamm, Fivos Perakis, Joanna Borek, University of Zurich, and Hamm, Peter
- Subjects
10120 Department of Chemistry ,1000 Multidisciplinary ,Multidisciplinary ,Infrared ,Computer science ,Kinetics ,Astrophysics::Cosmology and Extragalactic Astrophysics ,computer.software_genre ,Solvent ,chemistry.chemical_compound ,Molecular dynamics ,chemistry ,540 Chemistry ,Physical Sciences ,Physical chemistry ,Phenol ,Critical test ,Data mining ,Physics::Chemical Physics ,Benzene ,computer ,Two-dimensional nuclear magnetic resonance spectroscopy ,Astrophysics::Galaxy Astrophysics - Abstract
Using 3D infrared (IR) exchange spectroscopy, the ultrafast hydrogen-bond forming and breaking (i.e., complexation) kinetics of phenol to benzene in a benzene/CCl4 mixture is investigated. By introducing a third time point at which the hydrogen-bonding state of phenol is measured (in comparison with 2D IR exchange spectroscopy), the spectroscopic method can serve as a critical test of whether the spectroscopic coordinate used to observe the exchange process is a memory-free, or Markovian, coordinate. For the system under investigation, the 3D IR results suggest that this is not the case. This conclusion is reconfirmed by accompanying molecular dynamics simulations, which furthermore reveal that the non-Markovian kinetics is caused by the heterogeneous structure of the mixed solvent.
- Published
- 2014
39. Vibrational conical intersections in the water dimer
- Author
-
Gerhard Stock, Peter Hamm, University of Zurich, and Hamm, Peter
- Subjects
10120 Department of Chemistry ,Water dimer ,3104 Condensed Matter Physics ,Chemistry ,Intermolecular force ,Biophysics ,Conical intersection ,Condensed Matter Physics ,Adiabatic theorem ,Normal mode ,Intramolecular force ,540 Chemistry ,Vibrational energy relaxation ,1312 Molecular Biology ,Physics::Chemical Physics ,Physical and Theoretical Chemistry ,Atomic physics ,Adiabatic process ,1606 Physical and Theoretical Chemistry ,Molecular Biology ,1304 Biophysics - Abstract
A recent paper by Hamm and Stock [Phys. Rev. Lett. 109, 173201 (2012)] has introduced the concept of vibrational conical intersections as a potential source of ultrafast vibrational relaxation, using the coupling between high-frequency OH modes and low-frequency intramolecular hydrogen bonding modes of malonaldehyde as an example. Here, the question is addressed whether such conical intersections may also appear for intermolecular hydrogen bonds. To that end, the water dimer [(H2O)2] is studied as a minimal model for the hydrogen bonding in liquid water. Although a significant separation of time scales between intramolecular and intermolecular degrees of freedom exists in (H2O)2, a standard normal-mode description is found to lead to a complete breakdown of the adiabatic ansatz. This is due to strong nonlinear couplings between high- and low-frequency normal modes, which in turn give rise to large overall non-adiabatic couplings. A valid adiabatic picture is obtained, on the other hand, when internal coor...
- Published
- 2013
40. Two-dimensional infrared spectroscopy of isotope-diluted low density amorphous ice
- Author
-
Fivos Perakis, Andrey Shalit, Peter Hamm, University of Zurich, and Hamm, Peter
- Subjects
10120 Department of Chemistry ,Chemistry ,Phonon ,Anharmonicity ,2508 Surfaces, Coatings and Films ,Astrophysics::Cosmology and Extragalactic Astrophysics ,Surfaces, Coatings and Films ,Amorphous solid ,Two-dimensional infrared spectroscopy ,Phase (matter) ,Excited state ,Amorphous ice ,540 Chemistry ,Materials Chemistry ,Fermi resonance ,Physical and Theoretical Chemistry ,Atomic physics ,1606 Physical and Theoretical Chemistry ,2505 Materials Chemistry - Abstract
We present two-dimensional (2D) infrared (IR) spectra of isotope diluted ice in its low density amorphous form. Amorphous ice, which is structurally more similar to liquid water than to crystalline ice, provides higher resolution spectra of the hydrogen bond potentials because all motion is frozen. In the case of OD vibration of HOD in H2O, diagonal and off-diagonal (intermode) anharmonicity as well as the relaxation rate of the first excited state increase with hydrogen bond strength in a consistent way. For the OH vibration of HOD in D2O, additional more specific couplings need to be taken into account to explain the 2D IR response, that is, a Fermi resonance with the HOD bend vibration and couplings to phonon modes that lead to quantum beating. The lifetime of the fist excited state, 240 fs, is the shortest ever reported for any phase of isotope diluted water.
- Published
- 2013
41. pH-jump induced α-helix folding of poly-l-glutamic acid
- Author
-
Peter Hamm, Mateusz L. Donten, University of Zurich, and Hamm, Peter
- Subjects
chemistry.chemical_classification ,10120 Department of Chemistry ,Biomolecule ,Kinetics ,General Physics and Astronomy ,Glutamic acid ,3100 General Physics and Astronomy ,Crystallography ,Residue (chemistry) ,chemistry ,540 Chemistry ,Jump ,Physical and Theoretical Chemistry ,1606 Physical and Theoretical Chemistry - Abstract
pH jumps are a truly biomimetic technique to initiate non-equilibrium dynamics of biomolecules. In this work, the pH jump induced α-helix folding of poly- l -glutamic acid is investigated upon proton release from o-nitrobenzaldehyde. The aim of this work is twofold: On the one hand, design criteria of pH jump experiments are discussed, on the other hand, the folding mechanism of poly- l -glutamic acid is clarified by probing the IR response of the amide I band. Its folding kinetics is studied in dependence of the starting pD, the size of the pD jump and the length of the helix. While no dependence on the first two parameters could be detected, the folding time varies from 0.6 μs to 1.8 μs for helix lengths of 20 residue to 440 residue, respectively. It converges to a long-length limit at about 50 residue, a result which is attributed to a nucleation–propagation mechanism.
- Published
- 2013
42. A highly stable polypyridyl-based cobalt catalyst for homo- and heterogeneous photocatalytic water reduction
- Author
-
Roger Alberto, Alexander Rodenberg, Cyril Bachmann, Miguel Guttentag, Anna Senn, Peter Hamm, University of Zurich, and Hamm, Peter
- Subjects
10120 Department of Chemistry ,010405 organic chemistry ,Chemistry ,1604 Inorganic Chemistry ,Inorganic chemistry ,chemistry.chemical_element ,010402 general chemistry ,Heterogeneous catalysis ,7. Clean energy ,01 natural sciences ,0104 chemical sciences ,Inorganic Chemistry ,Cobalt catalyst ,Chemical engineering ,Homogeneous ,540 Chemistry ,Photocatalysis ,Cobalt ,Hydrogen production - Abstract
Synthesis, characterization and activity in homogeneous photocatalytic hydrogen production of a cobalt polypyridyl complex are reported. TONs up to 9000 H(2)/Co could be achieved. Immobilization of the complex on a swellable resin yielded a recyclable heterogeneous catalyst.
- Published
- 2012
43. Two-dimensional infrared spectroscopy of neat ice Ih
- Author
-
Fivos Perakis, Peter Hamm, University of Zurich, and Hamm, Peter
- Subjects
10120 Department of Chemistry ,Chemistry ,Infrared ,Exciton ,Isotropy ,Analytical chemistry ,General Physics and Astronomy ,Ice Ih ,Molecular physics ,3100 General Physics and Astronomy ,Two-dimensional infrared spectroscopy ,Excited state ,540 Chemistry ,Astrophysics::Earth and Planetary Astrophysics ,Physical and Theoretical Chemistry ,Anisotropy ,Spectroscopy ,1606 Physical and Theoretical Chemistry - Abstract
The OH stretch line shape of ice Ih exhibits distinct peaks, the assignment of which remains controversial. We address this longstanding question using two dimensional infrared (2D IR) spectroscopy of the OH stretch of H(2)O and the OD stretch of D(2)O of ice Ih at T = 80 K. The isotropic response is dominated by a 2D line shape component which does not depend on the pump pulse frequency. The decay time of the component that does depend on the pump frequency is calculated using singular value decomposition (bi-exponential decay H(2)O: 30 fs, 490 fs; D(2)O: 40 fs, 690 fs). The anisotropic contribution exhibits on-diagonal peaks, which decay on a very fast timescale (H(2)O: 85 fs; D(2)O: 65 fs), with no corresponding anisotropic cross-peaks. Both isotropic and anisotropic results indicate that randomization of excited dipoles occurs with a very rapid rate, just like in neat liquid water. We conclude that the underlying mechanism relates to the complex interplay between exciton migration and exciton-phonon coupling.
- Published
- 2012
44. Note: Inverted time-ordering in two-dimensional-Raman-terahertz spectroscopy of water
- Author
-
Junichi Ono, Janne Savolainen, Yoshitaka Tanimura, Peter Hamm, University of Zurich, and Hamm, Peter
- Subjects
10120 Department of Chemistry ,Chemistry ,Terahertz radiation ,General Physics and Astronomy ,Pulse sequence ,3100 General Physics and Astronomy ,Pulse (physics) ,Terahertz spectroscopy and technology ,symbols.namesake ,Dipole ,540 Chemistry ,symbols ,Physical and Theoretical Chemistry ,Atomic physics ,1606 Physical and Theoretical Chemistry ,Raman spectroscopy ,Spectroscopy ,Coherence (physics) - Abstract
In a previous paper [P. Hamm and J. Savolainen, J. Chem. Phys. 136, 094516 (2012)]10.1063/1.3691601, we have studied the 2D-Raman-THz response of liquid water, based on an all-atom molecular dynamics simulation. In the pulse sequence we investigated a near-infraredlaser pulse excites a vibrational coherence through a Raman process that switches it into another coherence by a THz pulse after some time, and finally read out by the emission of a THz field.In the present note, we explore the inverted time-ordered pulse sequence, in which the first coherence is generated by a direct THz excitation, while the switching of coherences is achieved by a Raman interaction. Since the dependence of the polarizibility on the nuclear coordinates is more nonlinear compared to that of the dipole moment, this pulse sequence reveals more of the couplings and correlations between the various degrees of freedom of water. Compared to 2D-Raman spectroscopy and the original pulse sequence, this pulse sequence reveals the cleares...
- Published
- 2012
45. Azide–water intermolecular coupling measured by two-color two-dimensional infrared spectroscopy
- Author
-
Felix Kläsi, Fivos Perakis, Sean Garrett-Roe, Peter Hamm, Joanna Borek, University of Zurich, and Hamm, Peter
- Subjects
Ions ,10120 Department of Chemistry ,Azides ,education.field_of_study ,Spectrophotometry, Infrared ,Absorption spectroscopy ,Chemistry ,Intermolecular force ,Population ,Analytical chemistry ,Color ,Water ,General Physics and Astronomy ,Infrared spectroscopy ,3100 General Physics and Astronomy ,Two-dimensional infrared spectroscopy ,Excited state ,540 Chemistry ,Stimulated emission ,Physical and Theoretical Chemistry ,Absorption (chemistry) ,1606 Physical and Theoretical Chemistry ,education - Abstract
We utilize two-color two-dimensional infrared spectroscopy to measure the intermolecular coupling between azide ions and their surrounding water molecules in order to gain information about the nature of hydrogen bonding of water to ions. Our findings indicate that the main spectral contribution to the intermolecular cross-peak comes from population transfer between the asymmetric stretch vibration of azide and the OD-stretch vibration of D(2)O. The azide-bound D(2)O bleach/stimulated emission signal, which is spectrally much narrower than its linear absorption spectrum, shows that the experiment is selective to solvation shell water molecules for population times up to ~500 fs. The waters around the ion are present in an electrostatically better defined environment. Afterwards, ~1 ps, the sample thermalizes and selectivity is lost. On the other hand, the excited state absorption signal of the azide-bound D(2)O is much broader. The asymmetry in spectral width between bleach/stimulated emission versus excited absorption has been observed in very much the same way for isotope-diluted ice Ih, where it has been attributed to the anharmonicity of the OD potential.
- Published
- 2012
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