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The allosteric protein MCL-1 and its natural inhibitors, the BH3-only proteins PUMA, BIM, and NOXA regulate apoptosis by interacting promiscuously within an entangled binding network. Little is known about the transient processes and dynamic conformational fluctuations that are the basis for the formation and stability of the MCL-1/BH3-only complex. In this study, we designed photoswitchable versions of MCL-1/PUMA and MCL-1/NOXA, and investigated the protein response after an ultrafast photo-perturbation with transient infrared spectroscopy. We observed partial α-helical unfolding in all cases, albeit on strongly varying timescales (1.6 ns for PUMA, 9.7 ns for the previously studied BIM, and 85 ns for NOXA). These differences are interpreted as a BH3-only-specific "structural resilience" to defy the perturbation while remaining in MCL-1's binding pocket. Thus, the presented insights could help to better understand the differences between PUMA, BIM, and NOXA, the promiscuity of MCL-1, in general, and the role of the proteins in the apoptotic network. [ABSTRACT FROM AUTHOR]

Theoretical calculations of the low-frequency anharmonic couplings of the β-phase of crystalline bromoform are presented based on density functional theory quantum chemistry calculations. The electrical and mechanical anharmonicities between intra- and intermolecular modes are calculated, revealing that the electrical anharmonicity dominates the cross-peak intensities in the 2D Raman–THz response and crystalline, as well as liquid, bromoform. Furthermore, the experimentally observed difference in relative cross-peak intensities between the two intramolecular modes of bromoform and the intermolecular modes can be explained by the C3v-symmetry of bromoform in combination with orientational averaging. The good agreement with the experimental results provides further evidence for our interpretation that the 2D Raman–THz response of bromoform is, indeed, related to the anharmonic coupling between the intra- and intermolecular modes. [ABSTRACT FROM AUTHOR]

Protein dynamics form a critical bridge between protein structure and function, yet the impact of evolution on ultrafast processes inside proteins remains enigmatic. This study delves deep into nanosecond-scale protein dynamics of a structurally and functionally conserved protein across species separated by almost a billion years, investigating ten homologs in complex with their ligand. By inducing a photo-triggered destabilization of the ligand inside the binding pocket, we resolved distinct kinetic footprints for each homolog via transient infrared spectroscopy. Strikingly, we found a cascade of rearrangements within the protein complex which manifest in time points of increased dynamic activity conserved over hundreds of millions of years within a narrow window. Among these processes, one displays a subtle temporal shift correlating with evolutionary divergence, suggesting reduced selective pressure in the past. Our study not only uncovers the impact of evolution on molecular processes in a specific case, but has also the potential to initiate a field of scientific inquiry within molecular paleontology, where species are compared and classified based on the rapid pace of protein dynamic processes; a field which connects the shortest conceivable time scale in living matter (10-9 s) with the largest ones (1016 s). [ABSTRACT FROM AUTHOR]

Two-dimensional (2D) Raman-THz spectroscopy in the frequency of up to 7 THz has been applied to study the crystalline β-phase of bromoform (CHBr3). As for liquid CHBr3, cross peaks are observed, which, however, sharpen up in the crystalline sample and split into assignable sub-contributions. In the Raman dimension, the frequency positions of these cross peaks coincide with the intramolecular bending modes of the CHBr3 molecules and in the THz dimension with the IR-active lattice modes of the crystal. This work expands the applicability of this new 2D spectroscopic technique to solid samples at cryogenic temperatures. Furthermore, it provides new experimental evidence that the cross peaks, indeed, originate from the coupling between intra- and intermolecular vibrational modes. [ABSTRACT FROM AUTHOR]

We present a 2D-Raman-terahertz (THz) setup with multichannel (single-shot) THz detection, utilizing two crossed echelons, in order to reduce the acquisition time of typical 2D-Raman-THz experiments from days to a few hours. This speed-up is obtained in combination with a high repetition rate (100 kHz) Yb-based femtosecond laser system and a correspondingly fast array detector. The wavelength of the Yb-laser (1030 nm) is advantageous, since it assures almost perfect phase matching in GaP for THz generation and detection and since the dispersion in the transmissive echelons is minimal. 2D-Raman-THz test measurements on liquid bromoform (CHBr3) are reported. An enhancement of a factor ∼5.8 in signal-to-noise ratio is obtained for single-shot detection when compared to conventional step-scanning measurements in the THz time domain, corresponding to a speed-up of acquisition time of ∼34. [ABSTRACT FROM AUTHOR]

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. [ABSTRACT FROM AUTHOR]

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. [ABSTRACT FROM AUTHOR]

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. 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 are usually highly complex. Linking the spectral response to specific molecular events is a major obstacle. Here, we investigate a cyanobacteriochrome 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 regimes. 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. [ABSTRACT FROM AUTHOR]

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 Förster 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. [ABSTRACT FROM AUTHOR]

The 2D-Raman-THz response in all possible time-orderings (Raman-THz-THz, THz-Raman-THz, and THz-THz-Raman) of amorphous water ice is calculated in two ways: from atomistic molecular dynamics simulations and with the help of a Feynman diagram model, the latter of which power-expands the potential energy surface and the dipole and polarizability surfaces up to leading order. Comparing both results allows one to dissect the 2D-Raman-THz response into contributions from mechanical anharmonicity, as well as electrical dipole and polarizability anharmonicities. Mechanical anharmonicity dominates the 2D-Raman-THz response of the hydrogen-bond stretching and hydrogen-bond bending bands of water, and dipole anharmonicity dominates that of the librational band, while the contribution of polarizability anharmonicity is comparably weak. A distinct echo of the hydrogen-bond stretching band is observed for the THz-Raman-THz pulse sequence, again dominated by mechanical anharmonicity. A peculiar mechanism is discussed, which is based on the coupling between the many normal modes within the hydrogen-bond stretching band and which will inevitably generate such an echo for an amorphous structure. [ABSTRACT FROM AUTHOR]

Binding affinity measured by fluorescence quenching In ref. [1], we measured the binding affinity by fluorescence quenching. We kept the concentration of the peptide constant (15 M), varied that of the protein between 0 and 50 M, and fitted the resulting fluorescence signal to a two-state binding equilibrium. 2a in ref. [1]), we measured the binding affinities of a small pentapeptide in the I cis i and the I trans i -state of the azobenzene moiety with the help of fluorescence quenching experiments (Fig. That assumption is inherently wrong for a protein-ligand association, as discussed in a number of publications.[4]-[6] In fact, in order to verify the new binding affinities measured by fluorescence depolarization (Fig. [Extracted from the article]

A three-point velocity correlation function ⟨ v (t1 + t2) v 2 (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. [ABSTRACT FROM AUTHOR]

2D-Raman-THz spectroscopy of liquid water, which has been presented recently [J. Savolainen et al., Proc. Natl. Acad. Sci. U. S. A. 110, 20402 (2013)], directly probes the intermolecular degrees of freedom of the hydrogen-bond network. However, being a relatively new technique, its information content is not fully explored to date. While the spectroscopic signal can be simulated based on molecular dynamics simulation in connection with a water force field, it is difficult to relate spectroscopic signatures to the underlying microscopic features of the force field. Here, a completely different approach is taken that starts from an as simple as possible model, i.e., a single vibrational mode with electrical and mechanical anharmonicity augmented with homogeneous and inhomogeneous broadening. An intuitive Feynman diagram picture is developed for all possible pulse sequences of hybrid 2D-Raman-THz spectroscopy. It is shown that the model can explain the experimental data essentially quantitatively with a very small set of parameters, and it is tentatively concluded that the experimental signal originates from the hydrogen-bond stretching vibration around 170 cm−1. Furthermore, the echo observed in the experimental data can be quantified by fitting the model. A dominant fraction of its linewidth is attributed to quasi-inhomogeneous broadening in the slow-modulation limit with a correlation time of 370 fs, reflecting the lifetime of the hydrogen-bond networks giving rise to the absorption band. [ABSTRACT FROM AUTHOR]

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 parametrizations and with full 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. The hydrophobic character of the CF-group is particularly relevant for applications in pharmaceutical chemistry with a focus on local hydration and interaction with the surrounding protein. [ABSTRACT FROM AUTHOR]

A polarizable water model is presented which has been calibrated against experimental THz and Raman spectra of bulk water. These low-frequency spectra directly probe the dynamics, and thereby intermolecular interactions, on time scales relevant to molecular motions. The model is based on the TL4P force field developed recently by Tavan and co-workers [J. Phys. Chem. B 117, 9486 (2013)], which has been designed to be transferable between different environments; in particular, to correctly describe the electrostatic properties of both the isolated water molecule in the gas-phase and the liquid water at ambient conditions. Following this design philosophy, TL4P was amended with charge transfer across hydrogen-bonded dimers as well as an anisotropic polarizability in order to correctly reproduce the THz and Raman spectra. The thermodynamic and structural properties of the new model are of equal quality as those of TL4P, and at the same time, an almost quantitative agreement with the spectroscopic data could be achieved. Since TL4P is a rigid model with a single polarizable site, it is computationally very efficient, while the numerical overhead for the addition of charge transfer and the anisotropic polarizability is minor. Overall, the model is expected to be well suited for, e.g., large scale simulations of 2D-Raman-THz spectra or biomolecular simulations. [ABSTRACT FROM AUTHOR]

The response of water re-solvating a charge-transfer dye (deprotonated Coumarin 343) after photoexcitation has been measured by means of transient THz spectroscopy. Two steps of increasing THz absorption are observed, a first ∼10 ps step on the time scale of Debye relaxation of bulk water and a much slower step on a 3.9 ns time scale, the latter of which reflecting heating of the bulk solution upon electronic relaxation of the dye molecules from the S1 back into the S0 state. As an additional reference experiment, the hydroxyl vibration of water has been excited directly by a short IR pulse, establishing that the THz signal measures an elevated temperature within ∼1 ps. This result shows that the first step upon dye excitation (10 ps) is not limited by the response time of the THz signal; it rather reflects the reorientation of water molecules in the solvation layer. The apparent discrepancy between the relatively slow reorientation time and the general notion that water is among the fastest solvents with a solvation time in the sub-picosecond regime is discussed. Furthermore, non-equilibrium molecular dynamics simulations have been performed, revealing a close-to-quantitative agreement with experiment, which allows one to disentangle the contribution of heating to the overall THz response from that of water orientation. [ABSTRACT FROM AUTHOR]

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 hydrogenbonded network. For the transmission 2D IR spectroscopy, a novel method had to be developed for the preparation of ultrathin films (1-2 μm) 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. [ABSTRACT FROM AUTHOR]

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 lawis applied. [ABSTRACT FROM AUTHOR]

Recently, various spectroscopic techniques have been developed, which can measure the 2D response of the inter-molecular degrees of freedom of liquids in the THz regime. By employing hybrid Raman-THz pulse sequences, the inherent experimental problems of 2D-Raman spectroscopy are circumvented completely, culminating in the recent measurement of the 2D-Raman-THz responses of water and aqueous salt solutions. This review article focuses on the possibility to observe echoes in such experiments, which would directly reveal the inhomogeneity of the typically extremely blurred THz bands of liquids, and hence the heterogeneity of local structures that are transiently formed, in particular, in a hydrogen-bonding liquid such as water. The generation mechanisms of echoes in 2D-Raman-THz spectroscopy are explained, which differ from those in "conventional" 2D-IR spectroscopy in a subtle but important manner. Subsequently, the circumstances are discussed, under which echoes are expected, revealing a physical picture of the information content of an echo. That is, the echo decay reflects the lifetime of local structures in the liquid on a length scale that equals the delocalization length of the intermolecular modes. Finally, recent experimental results are reviewed from an echo perspective. [ABSTRACT FROM AUTHOR]

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. [ABSTRACT FROM AUTHOR]

A stop-flow sample delivery system for transient spectroscopy is presented, which is, in particular, suited for laser-based instruments (quantum-cascade lasers or amplified femtosecond lasers) with excitation pulse repetition rates in the range 10–100 Hz. Two pulsing micro-valves are mounted onto a flow cuvette designed for transient IR spectroscopy, which is integrated into a flow cycle driven by a peristaltic pump. The performance of the system is demonstrated with transient IR experiments of the trans-to-cis photoisomerization of a water-soluble azobenzene derivative. The sample stands still when the micro-valves are closed and is pushed out from the probe beam focus on a 1 ms timescale when opening the micro-valves. The setup is extremely sample efficient. It needs only small sample volumes, and at the same time, it enables excitation of a large fraction of molecules in solution. [ABSTRACT FROM AUTHOR]

Based on extensive ab initio calculations and the time-propagation of the nuclear Schrödinger equation, we study the vibrational relaxation dynamics and resulting spectral signatures of the OH stretch vibration of a hydrogen-bonded complex, HCO2- · H2O. Despite their smallness, it has been shown experimentally by Johnson and coworkers that the gas-phase infrared spectra of these types of complexes exhibit much of the complexity commonly observed for hydrogen-bonded systems. That is, the OH stretch band exhibits a significant red shift together with an extreme broadening and a pronounced substructure, which reflects its very strong anharmonicity. Employing an adiabatic separation of time scales between the three intramolecular high-frequency modes of the water molecule and the three most important intermolecular low-frequency modes of the complex, we calculate potential energy surfaces (PESs) of the ground and the first excited states of the high-frequency modes and identify a vibrational conical intersection between the PESs of the OH stretch fundamental and the HOH bend overtone. By performing a time-dependent propagation of the resulting system, we show that the conical intersection affects a coherent population transfer between the two states, the first step of which being ultrafast (60 fs) and irreversible. The subsequent relaxation of vibrational energy into the HOH bend and ground state occurs incoherently but also quite fast (1 ps), although the corresponding PESs are well separated in energy. Owing to the smaller effective mass difference between light and heavy degrees of freedom, the adiabatic ansatz is consequently less significant for vibrations than in the electronic case. Based on the model, we consider several approximations to calculate the measured Ar-tag action spectrum of HCO2- · H2O and achieve semiquantitative agreement with the experiment. [ABSTRACT FROM AUTHOR]

Based on extensive ab initio calculations and the time-propagation of the nuclear Schrödinger equation, we study the vibrational relaxation dynamics and resulting spectral signatures of the OH stretch vibration of a hydrogen-bonded complex, HCO2- · H2O. Despite their smallness, it has been shown experimentally by Johnson and coworkers that the gas-phase infrared spectra of these types of complexes exhibit much of the complexity commonly observed for hydrogen-bonded systems. That is, the OH stretch band exhibits a significant red shift together with an extreme broadening and a pronounced substructure, which reflects its very strong anharmonicity. Employing an adiabatic separation of time scales between the three intramolecular high-frequency modes of the water molecule and the three most important intermolecular low-frequency modes of the complex, we calculate potential energy surfaces (PESs) of the ground and the first excited states of the high-frequency modes and identify a vibrational conical intersection between the PESs of the OH stretch fundamental and the HOH bend overtone. By performing a time-dependent propagation of the resulting system, we show that the conical intersection affects a coherent population transfer between the two states, the first step of which being ultrafast (60 fs) and irreversible. The subsequent relaxation of vibrational energy into the HOH bend and ground state occurs incoherently but also quite fast (1 ps), although the corresponding PESs are well separated in energy. Owing to the smaller effective mass difference between light and heavy degrees of freedom, the adiabatic ansatz is consequently less significant for vibrations than in the electronic case. Based on the model, we consider several approximations to calculate the measured Ar-tag action spectrum of HCO2- · H2O and achieve semiquantitative agreement with the experiment. [ABSTRACT FROM AUTHOR]

The solvent dynamics around fluorinated acetonitrile is characterized by 2-dimensional infrared spectroscopy and atomistic simulations. The lineshape of the linear infrared spectrum is better captured by semiempirical (density functional tight binding) mixed quantum mechanical/molecular mechanics simulations, whereas force field simulations with multipolar interactions yield lineshapes that are significantly too narrow. For the solvent dynamics, a relatively slow time scale of 2 ps is found from the experiments and supported by the mixed quantum mechanical/molecular mechanics simulations. With multipolar force fields fitted to the available thermodynamical data, the time scale is considerably faster--on the 0.5 ps time scale. The simulations provide evidence for a well established CF-HOH hydrogen bond (population of 25%) which is found from the radial distribution function g(r) from both, force field and quantum mechanics/molecular mechanics simulations. [ABSTRACT FROM AUTHOR]

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. [ABSTRACT FROM AUTHOR]

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. [ABSTRACT FROM AUTHOR]

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. [ABSTRACT FROM AUTHOR]

Recently, re-purposing of cyanobacterial photoreceptors as optogentic actuators enabled light-regulated protein expression in different host systems. These new bi-stable optogenetic tools enable interesting new applications, but their light-driven working mechanism remains largely elusive on a molecular level. Here, we study the optogenetic cyanobacteriochrome Am1-c0023g2 with isotope labeling and two dimensional infrared (2D-IR) spectroscopy. Isotope labeling allows us to isolate two site-specific carbonyl marker modes from the overwhelming mid-IR signal of the peptide backbone vibrations. Unlike conventional difference-FTIR spectroscopy, 2D-IR is sensitive to homogeneous and inhomogeneous broadening mechanisms of these two vibrational probes in the different photostates of the protein. We analyse the 2D-IR line shapes in the context of available structural models and find that they reflect the hydrogen-bonding environment of these two marker groups. [ABSTRACT FROM AUTHOR]

Isotopic substitutions largely affect the dielectric relaxation dynamics of hydrogen-bonded liquid water; yet, the role of the altered molecular masses and nuclear quantum effects has not been fully established. To disentangle these two effects we study the dielectric relaxation of light (H216O), heavy (D216O) and heavy-oxygen (H218O) water at temperatures ranging from 278 to 338 K. Upon 16O/18O exchange, we find that the relaxation time of the collective orientational relaxation mode of water increases by 4–5%, in quantitative agreement with the enhancement of viscosity. Despite the rotational character of dielectric relaxation, the increase is consistent with a translational mass factor. For H/D substitution, the slow-down of the relaxation time is more pronounced and also shows a strong temperature dependence. In addition to the classical mass factor, the enhancement of the relaxation time for D216O can be described by an apparent temperature shift of 7.2 K relative to H216O, which is higher than the 6.5 K shift reported for viscosity. As this shift accounts for altered zero-point energies, the comparison suggests that the underlying thermally populated states relevant to the activation of viscous flow and dielectric relaxation differ. [ABSTRACT FROM AUTHOR]

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. [ABSTRACT FROM AUTHOR]

We apply two-dimensional infrared spectroscopy to differentiate between the two polyamorphous forms of glassy water, low-density (LDA) and high-density (HDA) amorphous ices, that were obtained by slow vapor deposition at 80 and 11 K, respectively. Both the vibrational lifetime and the bandwidth of the 1-2 transition of the isolated OD stretch vibration of HDO in H2O exhibit characteristic differences when comparing hexagonal (Ih), LDA, and HDA ices, which we attribute to the different local structures - in particular the presence of interstitial waters in HDA ice - that cause different delocalization lengths of intermolecular phonon degrees of freedom. Moreover, temperature dependent measurements show that the vibrational lifetime closely follows the structural transition between HDA and LDA phases. [ABSTRACT FROM AUTHOR]

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 are 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 ∼1 ns to ∼10 µs, can be rationalized by a remodeling of its rugged free-energy landscape, with very 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. [ABSTRACT FROM AUTHOR]

Using classical molecular dynamics simulations, the 2D infrared (IR) spectroscopy of CN- solvated in D2O is investigated. Depending on the force field parametrizations, most of which are based on multipolar interactions for the CN- molecule, the frequency-frequency correlation function and observables computed from it differ. Most notably, models based on multipoles for CN- and TIP3P for water yield quantitatively correct results when compared with experiments. Furthermore, the recent finding that T1 times are sensitive to the van der Waals ranges on the CN- is confirmed in the present study. For the linear IR spectrum, the best model reproduces the full widths at half maximum almost quantitatively (13.0 cm-1 vs. 14.9 cm-1) if the rotational contribution to the linewidth is included. Without the rotational contribution, the lines are too narrow by about a factor of two, which agrees with Raman and IR experiments. The computed and experimental tilt angles (or nodal slopes) α as a function of the 2D IR waiting time compare favorably with the measured ones and the frequency fluctuation correlation function is invariably found to contain three time scales: a sub-ps, 1 ps, and one on the 10-ps time scale. These time scales are discussed in terms of the structural dynamics of the surrounding solvent and it is found that the longest time scale (≈10 ps) most likely corresponds to solvent exchange between the first and second solvation shell, in agreement with interpretations from nuclear magnetic resonance measurements. [ABSTRACT FROM AUTHOR]

Free-energy landscape theory is often used to describe complex molecular systems. Here, a microscopic description of water structure and dynamics based on configuration-space-networks and molecular dynamics simulations of the TIP4P/2005 model is applied to investigate the free-energy landscape of water. The latter is built on top of a large set of water microstates describing the kinetic stability of local hydrogen-bond arrangements up to the second solvation shell. In temperature space, the landscape displays three different regimes. At around ambient conditions, the free-energy surface is characterized by many short-lived basins of attraction which are structurally well-defined (inhomogeneous regime). At lower temperatures instead, the liquid rapidly becomes homogeneous. In this regime, the free energy is funneled-like, with fully coordinated water arrangements at the bottom of the funnel. Finally, a third regime develops below the temperature of maximal compressibility (Widom line) where the funnel becomes steeper with few interconversions between microstates other than the fully coordinated ones. Our results present a way to manage the complexity of water structure and dynamics, connecting microscopic properties to its ensemble behavior. [ABSTRACT FROM AUTHOR]

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 D2O. The azide-bound D2O 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 D2O 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. [ABSTRACT FROM AUTHOR]

We discuss the hybrid 2D-Raman-THz spectroscopy of liquid water. This two-dimensional spectroscopy is designed to directly work in the low-frequency range of the intermolecular degrees of freedom. The information content of 2D-Raman-THz spectroscopy is similar to 2D-Raman or 2D-THz spectroscopy, but its experimental implementation should be easier. That is, 2D-Raman-THz spectroscopy is a 3rd-order nonlinear spectroscopy and as such completely avoids cascading of consecutive 3rd-order signals, which turned out to be a major difficulty in 5th-order 2D-Raman spectroscopy. On the other hand, it does not require any intense THz pump-pulse, the lack of which limits 2D-THz spectroscopy to the study of semiconductor quantum wells as the currently available pulse energies are too low for molecular systems. In close analogy to 2D-Raman spectroscopy, the 2D-Raman-THz response of liquid water is simulated from an all-atom molecular dynamics simulation, and the expected spectral features are discussed. [ABSTRACT FROM AUTHOR]

We present experimental 2D IR spectra of isotope diluted ice Ih (i.e., the OH stretch mode of HOD in D2O and the OD stretch mode of HOD in H2O) at T = 80 K. The main spectral features are the extremely broad 1-2 excited state transition, much broader than the corresponding 0-1 groundstate transition, as well as the presence of quantum beats. We do not observe any inhomogeneous broadening that might be expected due to proton disorder in ice Ih. Complementary, we perform simulations in the framework of the Lippincott-Schroeder model, which qualitatively reproduce the experimental observations. We conclude that the origin of the observed line shape features is the coupling of the OH-vibrational coordinate with crystal phonons and explain the beatings as a coherent oscillation of the O···O hydrogen bond degree of freedom. [ABSTRACT FROM AUTHOR]

The mechanism of vibrational energy flow is studied in a regime where a diffusion equation is likely to break down, i.e., on length scales of a few chemical bonds and time scales of a few picoseconds. This situation occurs, for example, during photochemical reactions in protein environment. To that end, a toy model is introduced that on the one hand mimics the vibrational normal mode distribution of proteins, and on the other hand is small enough to numerically time propagate the system fully quantum mechanically. Comparing classical and quantum-mechanical results, the question is addressed to what extent the classical nature of the molecular dynamics simulations (which would be the only choice for the modeling of a real molecular system) affects the vibrational energy flow mechanism. Small differences are found which are due to the different ways classical and quantum mechanics distribute thermal energy over vibrational modes. In either case, a ballistic and a diffusive phase can be identified. For these small length and time scales, the latter is governed by intrasite vibrational energy redistribution, since vibrational energy does not necessarily thermalize completely within individual peptide units. Overall, the model suggests a picture that unifies many of the observations made recently in experiments. [ABSTRACT FROM AUTHOR]

We demonstrate a method to collect purely absorptive three-dimensional (3D) fifth-order vibrational spectra on the model system CO2 in H2O. The six beam interferometer is described, as well as a method to experimentally determine the phase of the 3D spectrum. The measured spectra agree very well with simulations of the data based on the cumulant expansion. There are five peaks corresponding to different paths up and down the vibrational ladder. The positions, signs, and amplitudes of the peaks agree with theoretical predictions, and the intensities of the peaks scale linearly with concentration. Based on the concentration dependence and agreement between the simulations and measurements, we conclude that cascaded lower order signals contribute negligibly to the observed signal. [ABSTRACT FROM AUTHOR]

Intramolecular vibrational energy relaxation (IVR) in nitrous acid (HONO) is studied with the help of ultrafast two-color pump-probe spectroscopy. In a previous paper [V. Botan et al., J. Chem. Phys. 124, 234511 (2006)], it has been observed that trans-HONO cools through a cascade of overtones of one specific mode after pumping the OH stretch vibration. We had suggested that this cooling mode is the ONO bend vibration. Furthermore, molecules that have initially been excited by the OH stretch vibration of cis-HONO and then underwent isomerization follow the same relaxation pathway. In the present study, we extend the investigation of IVR of cis- and trans-HONO to the N=O stretch and HON bend spectral regions, finding further evidence that the bottleneck of trans cooling is indeed the ONO bend vibration. In combination with information on the anharmonic coupling constants of different modes, the energy relaxation dynamics preceding this cooling cascade can also be followed in unprecedented detail. [ABSTRACT FROM AUTHOR]

With the help of ultrafast time-resolved infrared spectroscopy, we investigate the temperature dependence of the IR driven cis→trans isomerization of nitrous acid (HONO) in solid Kr. We find that the lifetime of the OH-stretch vibration, as well as the final cooling into the matrix, is affected only minimally (if at all) by temperature. Nevertheless, the quantum yield of the cis→trans isomerization reaction increases by ≈30% to a total of 50%–70% when lowering the temperature from 30 to 15 K, whereas the trans→cis back yield is reduced by ≈40%. The results are discussed in analogy to Marcus theory of nonadiabatic electron transfer for the essentially barrierless case. We present a unified view of this important prototype proton transfer reaction that can explain the high cis→trans quantum yield of close to 1. [ABSTRACT FROM AUTHOR]

With the help of ultrafast time-resolved infrared spectroscopy, we investigate rotational diffusion of cis- and trans-nitrous acid (HONO) in solid Kr at 30 K, as well as its reorientation upon the IR-driven cis→trans isomerization. We find different mobilities for the two isomers: cis-HONO is pinned to the matrix with no decay of the anisotropy on the 100 ns time scale, whereas trans-HONO rotates around its long axis, reducing its anisotropy partially on that time scale. The long axis itself, defined by the terminal oxygen and hydrogen atoms of HONO, stays fixed on even a minute time scale. Accompanying molecular dynamics simulations reproduce the anisotropic rotational diffusion of trans-HONO correctly, although on a completely wrong time scale, whereas they would predict complete reorientation of cis-HONO within ≈10 ps, in harsh disagreement with the experiment. We attribute the mismatch of orientational time scales to either too soft interaction potentials or to the fact that HONO occupies an interstitial rather than a monosubstitutional matrix site. The experiments furthermore show that the direction of the OH bond hardly changes during the IR-driven cis→trans isomerization, in contrast to the intuitive picture that it is mostly the light hydrogen which moves. Rather, it is the two central nitrogen and oxygen atoms that are removed during isomerization in a hula hoop fashion, whereas the terminal atoms are still pinned to the matrix cage. [ABSTRACT FROM AUTHOR]

Characterizing the dynamics of the OH stretch in isotopically substituted liquid water (HOD in D2O) in terms of three-point frequency fluctuation correlation functions and joint probability densities shows that dynamics during hydrogen bond rearrangements occur primarily along a coordinate which is perpendicular to the spectroscopic coordinate. Molecular dynamics simulations show that three-point correlation functions are sensitive to this motion, unlike two-point correlation functions, and can select sets of trajectories which linger in the area of the transition state. Three-dimensional-infrared correlation spectroscopy could potentially measure these dynamics, though motional narrowing significantly changes the shape of the resulting spectra. [ABSTRACT FROM AUTHOR]

In a recent paper [R. Schanz et al., J. Chem. Phys. 122, 044509 (2005)], we investigated the IR-driven cis-trans isomerization of HONO in a Kr matrix with the help of femtosecond IR spectroscopy. We found that isomerization occurs on a 20 ps time scale, however, with a cis→trans quantum yield of only 10% that is significantly below the value reported in the literature (close to 100%). At the same time, we concluded that vibrational energy has not completely dissipated out of the molecule at the maximum delay time we reached in this study (500 ps). In order to verify whether additional, slower reaction channels exist, we extend the study here to delay times up to 100 ns. At a temperature of 32 K, we indeed find an additional isomerization channel on a 2 ns timescale, which increases the total cis→trans quantum yield to ≈30%. The trans→cis quantum yield is ≈7%. There is still a discrepancy between the quantum yields we observe and the literature values, however, we provide experimental evidence that this discrepancy is due to the different temperatures of our study. Vibrational cooling occurs on a 20 ns time scale, and cascades in a highly nonstatistical manner through one single normal mode (most likely the ONO bending mode ν5). Intermolecular energy dissipation into the rare gas matrix is more efficient than intramolecular vibrational energy redistribution and the matrix environment can certainly not be considered a weak perturbation. [ABSTRACT FROM AUTHOR]

Three-dimensional-IR spectroscopy is proposed as a new spectroscopic technique that is sensitive to three-point frequency fluctuation correlation functions. This will be important when the statistics of the underlying stochastic process is non-Gaussian, and hence when the system does not follow the linear response hypothesis. Furthermore, a very general classification of nonlinear spectroscopy in terms of higher order frequency fluctuation correlation functions is introduced, according to which certain moments of a multidimensional spectrum are related to certain frequency fluctuation correlation functions. The classification is rigorous in the so-called inhomogenous limit, but remains valid approximately also when motional narrowing becomes important. The work also puts a recent paper [J. Bredenbeck et al., Phys. Rev. Lett. 95, 083201 (2005)] onto solid theoretical grounds, where we have shown for the first time that fifth-order spectroscopy—in this case transient two-dimensional spectroscopy—is indeed sensitive to the three-point frequency fluctuation correlation function. [ABSTRACT FROM AUTHOR]