37 results on '"Hamm, Peter"'
Search Results
2. Transient CO desorption from thin Pt films induced by mid-IR pumping
- Author
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Tek, Gökçen, Hamm, Peter, University of Zurich, and Hamm, Peter
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10120 Department of Chemistry ,Aqueous solution ,Materials science ,010304 chemical physics ,UFSP13-6 Solar Light to Chemical Energy Conversion ,Analytical chemistry ,General Physics and Astronomy ,Photon energy ,010402 general chemistry ,01 natural sciences ,Fluence ,3100 General Physics and Astronomy ,0104 chemical sciences ,Wavelength ,Adsorption ,Desorption ,540 Chemistry ,0103 physical sciences ,Vibrational energy relaxation ,Physical and Theoretical Chemistry ,1606 Physical and Theoretical Chemistry ,Spectroscopy - Abstract
Resonant and off-resonant mid-infrared pump–probe spectroscopy is used to measure the vibrational dynamics of CO adsorbed to thin (0.2 nm, 2 nm, and 10 nm) heterogeneous Pt layers in an aqueous solution. The transient signals observed with resonant pumping are dominated by vibrational relaxation of the CO internal stretch vibration with a lifetime of T1 ∼ 3 ps in all cases. Off-resonant pumping suppresses that contribution to the signal and singles out a signal, which is attributed to heating of the metal layer as well as transient desorption of the CO molecules. Due to the small photon energy (0.2 eV) used as pump pulses, the mechanism of desorption must be thermal, in which case the desorption yield depends exclusively on the fluence of absorbed light and not its wavelength. The thin Pt layers facilitate CO desorption, despite a relatively low pump pulse fluence, as they concentrate the absorbed energy in a small volume.
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- 2021
3. 2D Raman–THz Spectroscopy of Binary CHBr3–MeOH Solvent Mixture
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Shalit, Andrey, Mousavi, Seyyed Jabbar, Hamm, Peter, University of Zurich, and Hamm, Peter
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10120 Department of Chemistry ,Surfaces ,Coatings and Films ,540 Chemistry ,2508 Surfaces, Coatings and Films ,Materials Chemistry ,Physical and Theoretical Chemistry ,1606 Physical and Theoretical Chemistry ,2505 Materials Chemistry - Published
- 2021
4. Shedding Light on the Molecular Surface Assembly at the Nanoscale Level: Dynamics of a Re(I) Carbonyl Photosensitizer with a Coadsorbed Cobalt Tetrapyridyl Water Reduction Catalyst on ZrO2
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Oppelt, Kerstin, Mosberger, Mathias, Ruf, Jeannette, Fernandez-Teran, Ricardo, Probst, Benjamin, Alberto, Roger, Hamm, Peter, University of Zurich, Oppelt, Kerstin, and Hamm, Peter
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10120 Department of Chemistry ,Surfaces ,Coatings and Films ,General Energy ,2100 General Energy ,540 Chemistry ,UFSP13-6 Solar Light to Chemical Energy Conversion ,2508 Surfaces, Coatings and Films ,Electronic ,2504 Electronic, Optical and Magnetic Materials ,Optical and Magnetic Materials ,Physical and Theoretical Chemistry ,1606 Physical and Theoretical Chemistry - Published
- 2020
5. Flexible to rigid: IR spectroscopic investigation of a rhenium-tricarbonyl-complex at a buried interface
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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.
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- 2021
- Full Text
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6. Geminate Recombination versus Cage Escape in the Reductive Quenching of a Re(I) Carbonyl Complex on Mesoporous ZrO2
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Oppelt, Kerstin, Fernández-Terán, Ricardo, Pfister, Rolf, Hamm, Peter, University of Zurich, and Oppelt, Kerstin
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10120 Department of Chemistry ,Surfaces ,Coatings and Films ,General Energy ,2100 General Energy ,540 Chemistry ,2508 Surfaces, Coatings and Films ,Electronic ,2504 Electronic, Optical and Magnetic Materials ,Optical and Magnetic Materials ,Physical and Theoretical Chemistry ,1606 Physical and Theoretical Chemistry - Published
- 2019
7. Nanosecond protein dynamics in a red/green cyanobacteriochrome revealed by transient IR spectroscopy
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Buhrke, David, Oppelt, Kerstin T, Heckmeier, Philipp J, Fernandez-Teran, Ricardo, Hamm, Peter, University of Zurich, and Buhrke, David
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Models, Molecular ,10120 Department of Chemistry ,Materials science ,Protein Conformation ,FOS: Physical sciences ,General Physics and Astronomy ,Infrared spectroscopy ,Cyanobacteria ,010402 general chemistry ,01 natural sciences ,Bacterial Proteins ,540 Chemistry ,0103 physical sciences ,Ultrafast laser spectroscopy ,Physics - Biological Physics ,Physical and Theoretical Chemistry ,Spectroscopy ,010304 chemical physics ,Protein dynamics ,Nanosecond ,3100 General Physics and Astronomy ,3. Good health ,0104 chemical sciences ,Photoexcitation ,Kinetics ,Microsecond ,Biological Physics (physics.bio-ph) ,Chemical physics ,Cyanobacteriochrome ,1606 Physical and Theoretical Chemistry - Abstract
Over the last decades, photoreceptive proteins were extensively studied with biophysical methods to gain a fundamental understanding of their working mechanisms and further guide the development of optogenetic tools from them. Time-resolved infrared (IR) spectroscopy is one of the key methods to access their functional non-equilibrium processes with high temporal resolution, but has the major drawback that experimental data is usually highly complex. Linking the spectral response to specific molecular events is a major obstacle. Here, we investigate a cyanobacteriochrome (CBCR) photoreceptor with a combined approach of transient absorption spectroscopy in the Visible and IR spectral regions. We obtain kinetic information in both spectral regions by analysis with two different fitting methods, global multiexponential fitting and lifetime analysis. We investigate the ground state dynamics that follow photoexcitation in both directions of the bi-stable photocycle (Pr* and Pg*) in the nanosecond and microsecond time regime. We find two ground state intermediates associated with the decay of Pr* and four with Pg* and report the macroscopic time constants of their interconversions. One of these processes is assigned to a structural change in the protein backbone. At later delay times, the spectroscopic responses are stretched out in time, an effect that can be better described by the lifetime analysis than the global fit. We ascribe it to the intrinsic ruggedness of the free energy landscape of proteins., Comment: regular article 12 pages 7 figures and 2 tables
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- 2020
8. Markov state model of the two-state behaviour of water
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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.
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- 2016
9. 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.
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- 2014
10. Hydration dynamics and IR spectroscopy of 4-fluorophenol
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Salehi, Seyedeh Maryam, Käser, Silvan, Töpfer, Kai, Diamantis, Polydefkis, Pfister, Rolf, Hamm, Peter, Rothlisberger, Ursula, Meuwly, Markus, University of Zurich, and Meuwly, Markus
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Chemical Physics (physics.chem-ph) ,10120 Department of Chemistry ,gas-phase ,Spectrophotometry, Infrared ,Phenol ,molecular-dynamics ,water ,FOS: Physical sciences ,General Physics and Astronomy ,atomic fluctuations ,3100 General Physics and Astronomy ,infrared-spectroscopy ,Phenols ,moller-plesset ,Physics - Chemical Physics ,medicinal chemistry ,540 Chemistry ,Solvents ,Quantum Theory ,vibrational-spectra ,Physical and Theoretical Chemistry ,1606 Physical and Theoretical Chemistry ,density-functional theory ,halogen atoms - Abstract
Halogenated groups are relevant in pharmaceutical applications and potentially useful spectroscopic probes for infrared spectroscopy. In this work, the structural dynamics and infrared spectroscopy of $para$-fluorophenol (F-PhOH) and phenol (PhOH) is investigated in the gas phase and in water using a combination of experiment and molecular dynamics (MD) simulations. The gas phase and solvent dynamics around F-PhOH and PhOH is characterized from atomistic simulations using empirical energy functions with point charges or multipoles for the electrostatics, Machine-Learning (ML) based parametrization and with full $\textit{ab initio}$ (QM) and mixed Quantum Mechanical/Molecular Mechanics (QM/MM) simulations with a particular focus on the CF- and OH-stretch region. The CF-stretch band is heavily mixed with other modes whereas the OH-stretch in solution displays a characteristic high-frequency peak around 3600 cm$^{-1}$ most likely associated with the -OH group of PhOH and F-PhOH together with a characteristic progression below 3000 cm$^{-1}$ due to coupling with water modes which is also reproduced by several of the simulations. Solvent and radial distribution functions indicate that the CF-site is largely hydrophobic except for simulations using point charges which renders them unsuited for correctly describing hydration and dynamics around fluorinated sites., Main Manuscript: 41 pages and 6 figures, SI: 10 pages and 10 figures
11. Sequence of Events during Peptide Unbinding from RNase S: A Complete Experimental Description
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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.
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- 2021
12. The Speed of Allosteric Signaling Within a Single-Domain Protein
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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.
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- 2021
13. Transient 2D IR spectroscopy from micro- to milliseconds
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Peter Hamm, University of Zurich, and Hamm, Peter
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10120 Department of Chemistry ,Materials science ,Infrared spectroscopy ,General Physics and Astronomy ,010402 general chemistry ,01 natural sciences ,law.invention ,law ,0103 physical sciences ,540 Chemistry ,Physical and Theoretical Chemistry ,Millisecond ,010304 chemical physics ,biology ,business.industry ,Amplifier ,Bacteriorhodopsin ,Laser ,3100 General Physics and Astronomy ,0104 chemical sciences ,Pulse (physics) ,Femtosecond ,biology.protein ,Optoelectronics ,Transient (oscillation) ,business ,1606 Physical and Theoretical Chemistry - Abstract
A new application of high-repetition rate, femtosecond Yb-laser/amplifier systems is introduced: transient 2D IR spectroscopy covering the time range from micro- to milliseconds. This approach intertwines the measurement of 2D IR spectra with the time separation from an actinic pump pulse and utilizes the high repetition rate of these lasers systems in two ways: by offering a high time resolution (10 µs) and by enabling the measurement of many 2D IR spectra. The well-studied photocycle of bacteriorhodopsin is used as a demonstration object in this proof-of-principle experiment.
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- 2021
14. A closer look into the distance dependence of vibrational energy transfer on surfaces using 2D IR spectroscopy
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Peter Hamm, Ricardo Fernández-Terán, University of Zurich, and Hamm, Peter
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10120 Department of Chemistry ,Materials science ,010304 chemical physics ,fungi ,Intermolecular force ,Infrared spectroscopy ,General Physics and Astronomy ,Percolation threshold ,Nuclear Overhauser effect ,Nuclear magnetic resonance spectroscopy ,010402 general chemistry ,7. Clean energy ,01 natural sciences ,Acceptor ,Molecular physics ,Electron spectroscopy ,3100 General Physics and Astronomy ,0104 chemical sciences ,0103 physical sciences ,540 Chemistry ,Isotopologue ,Physical and Theoretical Chemistry ,1606 Physical and Theoretical Chemistry - Abstract
Vibrational energy transfer (VET) between two isotopologues of [Re(dcb)(CO)3Br] immobilized on a TiO2 surface is studied with the help of 2D IR spectroscopy in dependence of surface coverage. To dilute the molecules on the surface, and thereby control the intermolecular distances, two different diluents have been used: a third isotopologue of the same molecule and 4-cyanobenzoic acid. As expected, the VET rate decreases with dilution. For a quantitative investigation of the distance dependence of the VET rate, we analyze the data based on an excitonic model. This model reveals the typical 1/r6-distance dependence for a dimer of a donor and acceptor, similar to the nuclear Overhauser effect in NMR spectroscopy or Forster resonant energy transfer in electronic spectroscopy. However, VET becomes a collective phenomenon on the surface, with the existence of a network of coupled molecules and its disappearance below a percolation threshold, dominating the concentration dependence of the VET rate.
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- 2020
15. 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.
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- 2017
16. Velocity echoes in water
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Peter Hamm, University of Zurich, and Hamm, Peter
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Physics ,10120 Department of Chemistry ,010304 chemical physics ,Intermolecular force ,General Physics and Astronomy ,Function (mathematics) ,Simple harmonic motion ,010402 general chemistry ,01 natural sciences ,Molecular physics ,3100 General Physics and Astronomy ,0104 chemical sciences ,Dipole ,Correlation function (statistical mechanics) ,0103 physical sciences ,Amorphous ice ,540 Chemistry ,Density of states ,Physical and Theoretical Chemistry ,Langevin dynamics ,1606 Physical and Theoretical Chemistry - Abstract
A three-point velocity correlation function ⟨v(t1 + t2)v2(t1)v(0)⟩ is introduced for a better understanding of the recent 2D-Raman-THz spectroscopy of the intermolecular degrees of freedoms of water and aqueous salt solutions. This correlation function reveals echoes in the presence of inhomogeneous broadening, which are coined “velocity echoes.” In analogy to the well-known two-point velocity correlation function ⟨v(t)v(0)⟩, it reflects the density of states (DOS) of the system under study without having to amend them with transition dipoles and transition polarizabilities. The correlation function can be calculated from equilibrium trajectories and converges extremely quickly. After deriving the theory, the information content of the three-point velocity correlation function is first tested based on a simple harmonic oscillator model with Langevin dynamics. Subsequently, velocity echoes of TIP4P/2005 water are calculated as a function of temperature, covering ambient conditions, the supercooled regime and amorphous ice, as well as upon addition of various salts. The experimentally observed trends can be reproduced qualitatively with the help of computationally very inexpensive molecular dynamics simulations.
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- 2019
17. Signatures of Intra- and Intermolecular Vibrational Coupling in Halogenated Liquids Revealed by Two-Dimensional Raman-Terahertz Spectroscopy
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Gustavo Ciardi, Arian Berger, Andrey Shalit, Peter Hamm, University of Zurich, and Hamm, Peter
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10120 Department of Chemistry ,Materials science ,Physics::Medical Physics ,Physics::Optics ,02 engineering and technology ,01 natural sciences ,Molecular physics ,symbols.namesake ,540 Chemistry ,0103 physical sciences ,General Materials Science ,Physics::Chemical Physics ,Physical and Theoretical Chemistry ,Spectroscopy ,010304 chemical physics ,Condensed Matter::Other ,Intermolecular force ,Degrees of freedom ,Pulse sequence ,021001 nanoscience & nanotechnology ,2500 General Materials Science ,Terahertz spectroscopy and technology ,symbols ,1606 Physical and Theoretical Chemistry ,0210 nano-technology ,Raman spectroscopy ,Rotational–vibrational coupling ,Ultrashort pulse - Abstract
Hybrid two-dimensional (2D) Raman-terahertz spectroscopy with the Raman-terahertz-terahertz (RTT) pulse sequence is used to explore the ultrafast intra- and intermolecular degrees of freedom of liquid bromoform (CHBr
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- 2019
18. Quinones as Reversible Electron Relays in Artificial Photosynthesis
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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.
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- 2016
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. Solvation Layer of Antifreeze Proteins Analyzed with a Markov State Model
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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
21. Characterization of the Platinum-Hydrogen Bond by Surface-Sensitive Time-Resolved Infrared Spectroscopy
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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
22. 2D IR spectroscopy of high-pressure phases of ice
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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
23. 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
- Subjects
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
24. 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
- Subjects
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
25. 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
26. 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
27. 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
28. 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
- Subjects
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
29. 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
30. Effect of viscogens on the kinetic response of a photoperturbed allosteric protein
- Author
-
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
31. Response of villin headpiece-capped gold nanoparticles to ultrafast laser heating
- Author
-
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
32. 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
33. 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
34. 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
35. 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
36. 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
37. 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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