Kinetics from indirectly detected hyperpolarized NMR spectroscopy by using spatially selective coherence transfers

An important recent development in NMR spectroscopy is the advent of ex situ dynamic nuclear polarization (DNP) approaches, which are capable of yielding liquid‐state sensitivities that exceed considerably those afforded by the highest‐field spectrometers. This increase in sensitivity has triggered new research avenues, particularly concerning the in vivo monitoring of metabolism and disease by NMR spectroscopy. So far such gains have mainly materialized for experiments that focus on nonprotonated, low‐γ nuclei; targets favored by relatively long relaxation times T₁, which enable them to withstand the transfer from the cryogenic hyperpolarizer to the reacting centers of interest. Recent studies have also shown that transferring this hyperpolarization to protons by indirectly detected methods could successfully give rise to ¹H NMR spectra of hyperpolarized compounds with a high sensitivity. The present study demonstrates that, when merged with spatially encoded methods, indirectly detected ¹H NMR spectroscopy can also be exploited as time‐resolved hyperpolarized spectroscopy. A methodology is thus introduced that can successfully deliver a series of hyperpolarized ¹H NMR spectra over a minutes‐long timescale. The principles and opportunities presented by this approach are exemplified by following the in vitro phosphorylation of choline by choline kinase, a potential metabolic marker of cancer; and by tracking acetylcholine’s hydrolysis by acetylcholine esterase, an important enzyme partaking in synaptic transmission and neuronal degradation.     

Probing Cooperativity of N-Terminal Domain Orientations in the p97 Molecular Machine: Synergy Between NMR Spectroscopy and Cryo-EM

The hexameric p97 enzyme plays an integral role in cellular homeostasis. Large changes to the orientation of its N-terminal domains (NTDs), corresponding to NTD-down (p97-ADP) or NTD-up (p97-ATP), accompany ATP hydrolysis. The NTDs in a series of p97 disease mutants interconvert rapidly between up and down conformations when p97 is in the ADP-bound state. While the populations of up and down NTDs can be determined from bulk measurements, information about the cooperativity of the transition between conformations is lacking. Here we use cryo-EM to determine populations of the 14 unique up/down NTD states of the homo-hexameric R95G disease-causing p97 ring, showing that NTD orientations do not depend on those of neighboring subunits. In contrast, NMR studies establish that inter-protomer cooperativity is important for regulating the orientation of NTDs in p97 particles comprising mixtures of different subunits, such as wild-type and R95G, emphasizing the synergy between cryo-EM and NMR in establishing how the components of p97 function.     

Solvation Dynamics of a Single Water Molecule Probed by Infrared Spectra—Theory Meets Experiment

The dynamics and energetics of water at interfaces or in biological systems plays a fundamental role in all solvation and biological phenomena in aqueous solution. In particular, the migration of water molecules is the first step that controls the overall process in the time domain. Experimentally, the dynamics of individual water molecules is nearly impossible to follow in solution, because signals from molecules in heterogeneous environments overlap. Although molecular dynamics simulations do not have this restriction, there is a lack of experimental data to validate the calculated dynamics. Here, we demonstrate a new strategy, in which the calculated dynamics are verified by measured time‐resolved infrared spectra. The coexistence of fast and slow migrations of water molecules around a CONH peptide linkage is revealed for a model system representative of a hydrate peptide.     

Phenylene Ethynylene‐Tethered Perylene Bisimide Folda‐Dimer and Folda‐Trimer: Investigations on Folding Features in Ground and Excited States

In this work, we have elucidated in detail the folding properties of two perylene bisimide (PBI) foldamers composed of two and three PBI units, respectively, attached to a phenylene ethynylene backbone. The folding behaviors of these new PBI folda‐dimer and trimer have been studied by solvent‐dependent UV/Vis absorption and 1D and 2D NMR spectroscopy, revealing facile folding of both systems in tetrahydrofuran (THF). In CHCl₃ the dimer exists in extended (unfolded) conformation, whereas partially folded conformations are observed in the trimer. Temperature‐dependent ¹H NMR spectroscopic studies in [D₈]THF revealed intramolecular dynamic processes for both PBI foldamers due to, on the one hand, hindered rotation around C?N imide bonds and, on the other hand, backbone flapping; the latter process being energetically more demanding as it was observed only at elevated temperature. The structural features of folded conformations of the dimer and trimer have been elucidated by different 2D‐NMR spectroscopy (e.g., ROESY and DOSY) in [D₈]THF. The energetics of folding processes for the PBI dimer and trimer have been assessed by calculations applying various methods, particularly the semiempirical PM6‐DH2 and the more sophisticated B97D approach, in which relevant dispersion corrections are included. These calculations corroborate the results of NMR spectroscopic studies. Folding features in the excited states of these PBI foldamers have been characterized by using time‐resolved fluorescence and transient absorption spectroscopy in THF and CHCl₃, exhibiting similar solvent‐dependent behavior as observed for the ground state. Interestingly, photoinduced electron transfer (PET) process from electron‐donating backbone to electron‐deficient PBI core for extended, but not for folded, conformations was observed, which can be explained by a fast relaxation of excited PBI stacks in the folded conformation into fluorescent excimer states.     

Ultrafast Dynamics of o‐Bromofluorobenzene Studied by Time‐Resolved Photoelectron Imaging

Photodissociation dynamics and rotational wave packet coherences of o‐bromofluorobenzene are studied by femtosecond time‐resolved photoelectron imaging (see figure). The decay of different photoelectron rings shows the population decay of states from which the lifetimes of different states are determined. The variation of photoelectron angular distributions reflects the evolution of rotational coherences.

     

A Sharp Thermal Transition of Fast Aromatic‐Ring Dynamics in Ubiquitin

Aromatic amino acid side chains have a rich role within proteins and are often central to their structure and function. Suitable isotopic‐labelling strategies enable studies of sub‐nanosecond aromatic‐ring dynamics using solution NMR relaxation methods. Surprisingly, it was found that the three aromatic side chains in human ubiquitin show a sharp thermal dynamical transition at approximately 312 K. Hydrostatic pressure has little effect on the low‐temperature behavior, but somewhat decreases the amplitude of motion in the high‐temperature regime. Therefore, below the transition temperature, ring motion is largely librational. Above this temperature, a complete ring‐rotation process that is fully consistent with a continuous diffusion not requiring the transient creation of a large activated free volume occurs. Molecular dynamics simulations qualitatively corroborate this view and reinforce the notion that the dynamical character of the protein interior has much more liquid‐alkane‐like properties than previously appreciated.     

The Excited‐State Dynamics of Phycocyanobilin in Dependence on the Excitation Wavelength

The primary light‐induced processes of phycocyanobilin were studied by means of transient‐grating spectroscopy, whereby the excitation wavelength was varied over the spectral region of the ground‐state absorption. On the basis of the results obtained, both the rate of the photoreaction in phycocyanobilin and the ratio of the decay of different excited‐state species via two decay channels depend on the excitation wavelength. Furthermore, the formation of the photoreaction product is also dependent on the pump color. These data support a recently established model for the primary photoprocesses in phycocyanobilin. In addition, phycocyanobilin protonated at the basic pyrrolenine‐type nitrogen atom was included in the transient absorption study. The decay behavior was found to be almost unchanged when compared with the unprotonated form, and this suggests that protonation of the tetrapyrrole ring structure has no effect on the overall photochemistry.     

Isomerization‐ and Temperature‐Jump‐Induced Dynamics of a Photoswitchable β‐Hairpin

Conformational changes in proteins and peptides can be initiated by diverse processes. This raises the question how the variation of initiation mechanisms is connected to differences in folding or unfolding processes. In this work structural dynamics of a photoswitchable β‐hairpin model peptide were initiated by two different mechanisms: temperature jump (T‐jump) and isomerization of a backbone element. In both experiments the structural changes were followed by time‐resolved IR spectroscopy in the nanosecond to microsecond range. When the photoisomerization of the azobenzene backbone switch initiated the folding reaction, pronounced absorption changes related to folding into the hairpin structure were found with a time constant of about 16 μs. In the T‐jump experiment kinetics with the same time constant were observed. For both initiation processes the reaction dynamics revealed the same strong dependence of the reaction time on temperature. The highly similar transients in the microsecond range show that the peptide dynamics induced by T‐jump and isomerization are both determined by the same mechanism and exclude a downhill‐folding process. Furthermore, the combination of the two techniques allows a detailed model for folding and unfolding to be presented: The isomerization‐induced folding process ends in a transition‐state reaction scheme, in which a high energetic barrier of 48 kJ mol^?1 separates unfolded and folded structures.     

Picosecond Structural Relaxation of Abietic Acid Based Amine End Capped Para‐Phenylenevinylene Trimers in Solution

The synthesis and photophysical properties of six new abietic acid based amine end‐capped p‐phenylenevinylene trimers (AECPV3) in their lowest excited singlet states are presented. The AECPV3 compounds show a large red‐shift of both the absorption (25–30 nm) and emission (37–42 nm) maxima with respect to those of the corresponding trimers. Picosecond time‐resolved fluorescence data reveal the presence of a fast conformational relaxation process (40–62 ps) of the initially excited compounds, leading to more planar conformers. The conformational relaxation time is proportional to the volume of both the side chain and the amine groups.     

Molecular Structure and Dynamics of Water at the Water–Air Interface Studied with Surface‐Specific Vibrational Spectroscopy

Water interfaces provide the platform for many important biological, chemical, and physical processes. The water–air interface is the most common and simple aqueous interface and serves as a model system for water at a hydrophobic surface. Unveiling the microscopic (<1 nm) structure and dynamics of interfacial water at the water–vapor interface is essential for understanding the processes occurring on the water surface. At the water interface the network of very strong intermolecular interactions, hydrogen‐bonds, is interrupted and the density of water is reduced. A central question regarding water at interfaces is the extent to which the structure and dynamics of water molecules are influenced by the interruption of the hydrogen‐bonded network and thus differ from those of bulk water. Herein, we discuss recent advances in the study of interfacial water at the water–air interface using laser‐based surface‐specific vibrational spectroscopy.     

Ultrafast Vibrational Population Transfer Dynamics in 2‐Acetylcyclopentanone Studied by 2D IR Spectroscopy

2‐Acetylcyclopentanone (2‐ACP), which is a β‐dicarbonyl compound, undergoes keto–enol isomerization, and its enol tautomers are stabilized by a cyclic intramolecular hydrogen bond. 2‐ACP (keto form) has symmetric and asymmetric vibrational modes of the two carbonyl groups at 1748 and 1715 cm^?1, respectively, which are well separated from the carbonyl modes of its enol tautomers in the FTIR spectrum. We have investigated 2‐ACP dissolved in carbon tetrachloride by 2D IR spectroscopy and IR pump–probe spectroscopy. Vibrational population transfer dynamics between the two carbonyl modes were observed by 2D IR spectroscopy. To extract the population exchange dynamics (i.e., the down‐ and uphill population transfer rate constants), we used the normalized volumes of the cross‐peaks with respect to the diagonal peaks at the same emission frequency and the survival and conditional probability functions. As expected, the downhill population transfer time constant (3.2 ps) was measured to be smaller than the uphill population transfer time constant (3.8 ps). In addition, the vibrational population relaxation dynamics of the two carbonyl modes were observed to be the same within the experimental error and were found to be much slower than vibrational population transfer between two carbonyl modes.     

Studies on the Solvation Dynamics of Coumarin 153 in 1‐Ethyl‐3‐Methylimidazolium Alkylsulfate Ionic Liquids: Dependence on Alkyl Chain Length

Steady‐state and time‐resolved fluorescence behavior of coumarin 153 (C153) is investigated in a series of 1‐ethyl‐3‐methylimidazolium alkylsulfate ([C₂mim][C_nOSO₃]) ionic liquids differing only in the length of the linear alkyl chain (n=4, 6, and 8) in the anion. The aim of the present study is to understand the role of alkyl chain length in solute rotation and solvation dynamics of C153 in these ionic liquids. The blueshift observed in the steady‐state absorption and emission maxima of C153 on going from the C₄OSO₃ to the C₈OSO₃ system indicates increasing nonpolar character of the microenvironment of the solute with increasing length of the alkyl side chain of the anion of the ionic liquids. The average solvation time is also found to increase on changing the substituent from butyl to octyl, and this is attributed to the increase in the bulk viscosity of the ILs. A steady blueshift of the time‐zero maximum of the fluorescence spectrum with increasing alkyl chain length also indicates that the probe molecule experiences a less polar environment in the early part of the dynamics. Rotational dynamics of C153 are also analyzed by using the Stokes–Einstein–Debye (SED), Gierer–Wirtz (GW), and Dote–Kivelson–Schwartz (DKS) theories. Analyses of the results seem to suggest decoupling of the rotational motion of the probe from solvent viscosity.     

SAM‐II Riboswitch Samples at least Two Conformations in Solution in the Absence of Ligand: Implications for Recognition

Conformational equilibria are increasingly recognized as pivotal for biological function. Traditional structural analyses provide a static image of conformers in solution that sometimes present conflicting views. From ¹³C and ¹H chemical exchange saturation transfer experiments, in concert with ligation and selective labeling strategies, we show that in the absence of metabolite, a Mg²⁺ (0–0.5 mm )‐bound apo SAM‐II riboswitch RNA exists in a minor (≈10 %) partially closed state that rapidly exchanges with a predominantly (≈90 %) open form with a lifetime of ≈32 ms. The base and sugar (H6,C6, H1′,C1′) chemical shifts of C43 for the dominant conformer are similar to those of a free CMP, but those of the minor apo species are comparable to shifts of CMPs in helical RNA regions. Our results suggest that these transient, low populated states stabilized by Mg²⁺ will likely enhance rapid ligand recognition and, we anticipate, will play potentially ubiquitous roles in RNA signaling.     

The Role of Conformations in the Interplay of Structure and Dynamics in Macromolecular and Supramolecular Systems

Summary: Following Paul J. Flory, the role of local chain conformation in determining the structure and dynamics of macromolecules is elucidated, employing advanced solid state NMR spectroscopy supported by X-ray scattering and dielectric spectroscopy. Topics covered include the local conformation in amorphous polymers, conformational memory, chain organization and dynamics in semicrystalline polymers, polypeptides, and rod-coil copolymers.