Concerted Motion Research Articles

Few-femtosecond time-resolved study of the UV-induced dissociative dynamics of iodomethane

Ultraviolet (UV) light that penetrates our atmosphere initiates various photochemical and photobiological processes. However, the absence of extremely short UV pulses has so far hindered our ability to fully capture the mechanisms at the very early stages of such processes. This is important because the concerted motion of electrons and nuclei in the first few femtoseconds often determines molecular reactivity. Here we investigate the dissociative dynamics of iodomethane following UV photoexcitation, utilizing mass spectrometry with a 5 fs time resolution. The short duration of the UV pump pulse (4.2 fs) allows the ultrafast dynamics to be investigated in the absence of any external field, from well before any significant vibrational displacement occurs until dissociation has taken place. The experimental results combined with semi-classical trajectory calculations provide the identification of the main dissociation channels and indirectly reveal the signature of a conical intersection in the time-dependent yield of the iodine ion. Furthermore, we demonstrate that the UV-induced breakage of the C-I bond can be prevented when the molecule is ionized by the probe pulse within 5 fs after the UV excitation, showcasing an ultrafast stabilization scheme against dissociation.

Self-aggregation and microhydration mechanisms of monoethanolamine: Far-infrared identification of large-amplitude hydrogen bond libration.

The strong tendency for self-aggregation together with an intriguing mechanism for the microhydration of monoethanolamine (MEA) have been explored by low-temperature far-infrared cluster spectroscopy in doped neon "quantum" matrices at 4K complemented by high-level quantum chemical modeling. In addition to the assignment of new mid-infrared perturbed intramolecular transitions, a distinct far-infrared transition is unambiguously assigned to the concerted large-amplitude hydrogen bond librational motion of the MEA homodimer. This observation confirms a global "head-to-head" intermolecular potential energy minimum associated with the formation of a compact doubly intermolecular OH⋯N hydrogen-bonded cyclic structure, where both monomeric intramolecular OH⋯N hydrogen bonds are broken upon complexation. By means of relative mixing ratio dependencies, dedicated annealing procedures, and selective complexation between MEA and isotopic H216O and H218O samples, distinct far-infrared transitions associated with large-amplitude intra-molecular hindered OH torsional motion and inter-molecular H2O librational (hindered c-type overall rotational) motion of the MEA monohydrate are furthermore assigned unambiguously for the first time. These spectroscopic observations reveal an intriguing metastable conformation, where H2O acts as a OH⋯O hydrogen bond donor to the hydroxy group instead of the amino group of MEA upon microhydration in the cryogenic neon environment, where the microhydration strengthens the intramolecular OH⋯N hydrogen bond of MEA due to hydrogen bond cooperativity.

Molecular determinants of neuropeptide-mediated activation mechanisms in tachykinin NK1 and NK2 receptors

Substance P and neurokinin A are closely related neuropeptides belonging to the tachykinin family. Their receptors are neurokinin 1 receptor (NK1R) and neurokinin 2 receptor (NK2R), G protein-coupled receptors that transmit Gs and Gq-mediated downstream signaling. We investigate the importance of sequence differences at the bottom of the receptor orthosteric site for activity and selectivity, focusing on residues that closely interact with the C-terminal methionine of the peptide ligands. We identify a conserved serine (NK1R-S2977.45) and the position of the tryptophan residue within the canonical “toggle switch” motif, CWxP of TM6, neighboring a phenylalanine in NK1R (NK1R-F2646.51) and a tyrosine in NK2R (NK2R-Y2666.51), giving rise to distinct micro-environments for the neuropeptide C-terminals. Mutating these residues results in dramatic activity changes in both NK1R and NK2R due to a close interaction between the ligand and toggle switch. Structural analysis of active and inactive NKR structures suggest only a minor change in sidechain rotation of toggle switch residues upon activation. However, extensive molecular dynamics simulations of receptor:neuropeptide:G protein complexes indicate that a major, concerted motion happens in the toggle switch tryptophan indole group and the sidechains of the micro-switch motif PIF. This rotation establishes a tight hydrogen bond interaction from the tryptophan indole to the conserved serine (NK1R-S2977.45) and a mainchain carbonyl (NK1R-A2947.41) in the kink of TM7. This interaction facilitates communication with the NPxxY micro-switch motif of TM7, resulting in stabilization of the G protein binding region. NK1R-S2977.45 is consequently identified as a central hub for the activation of NKRs.

Few-femtosecond electron transfer dynamics in photoionized donor-π-acceptor molecules.

The exposure of molecules to attosecond extreme-ultraviolet (XUV) pulses offers a unique opportunity to study the early stages of coupled electron-nuclear dynamics in which the role played by the different degrees of freedom is beyond standard chemical intuition. We investigate, both experimentally and theoretically, the first steps of charge-transfer processes initiated by prompt ionization in prototype donor-π-acceptor molecules, namely nitroanilines. Time-resolved measurement of this process is performed by combining attosecond XUV-pump/few-femtosecond infrared-probe spectroscopy with advanced many-body quantum chemistry calculations. We show that a concerted nuclear and electronic motion drives electron transfer from the donor group on a sub-10-fs timescale. This is followed by a sub-30-fs relaxation process due to the probing of the continuously spreading nuclear wave packet in the excited electronic states of the molecular cation. These findings shed light on the role played by electron-nuclear coupling in donor-π-acceptor systems in response to photoionization.

Heavy-Atom Tunneling in Ring-Closure Reactions of Beryllium Ozonide Complexes.

Quantum mechanical tunneling (QMT) has long been recognized as crucial for understanding chemical reaction mechanisms, particularly in reactions involving light atoms like hydrogen. However, recent findings have expanded this understanding to include heavy-atom tunneling reactions. In this report, we present the observation of two heavy-atom tunneling reactions involving the spontaneous conversions from end-on bonded beryllium ozonide complexes, OBeOOO (A) and BeOBeOOO (C), to their corresponding side-on bonded ozonide isomers, OBe(η2-O3) (B) and BeOBe(η2-O3) (D), respectively, in a cryogenic neon matrix. This discovery is supported by the weak temperature dependence of the rate constants and unusually large 16O/18O kinetic isotope effects. Quantum chemistry calculations reveal extremely low barriers (<1 kcal/mol) for both ring-closure reactions. Additionally, instanton theory calculations on both reactions unveil that the tunneling processes involve the concerted motion of all four oxygen atoms.

Reused Protein Segments Linked to Functional Dynamics.

Protein space is characterized by extensive recurrence, or "reuse," of parts, suggesting that new proteins and domains can evolve by mixing-and-matching of existing segments. From an evolutionary perspective, for a given combination to persist, the protein segments should presumably not only match geometrically but also dynamically communicate with each other to allow concerted motions that are key to function. Evidence from protein space supports the premise that domains indeed combine in this manner; we explore whether a similar phenomenon can be observed at the sub-domain level. To this end, we use Gaussian Network Models (GNMs) to calculate the so-called soft modes, or low-frequency modes of motion for a dataset of 150 protein domains. Modes of motion can be used to decompose a domain into segments of consecutive amino acids that we call "dynamic elements", each of which belongs to one of two parts that move in opposite senses. We find that, in many cases, the dynamic elements, detected based on GNM analysis, correspond to established "themes": Sub-domain-level segments that have been shown to recur in protein space, and which were detected in previous research using sequence similarity alone (i.e. completely independently of the GNM analysis). This statistically significant correlation hints at the importance of dynamics in evolution. Overall, the results are consistent with an evolutionary scenario where proteins have emerged from themes that need to match each other both geometrically and dynamically, e.g. to facilitate allosteric regulation.

Computational Characterization of the On-Surface Synthesis of Low-Dimensional Nanostructures

On-surface chemistry represents a fast-growing field allowing to synthesize molecular structures not available by traditional wet chemistry. In this context, high-resolution scanning probe microscopy techniques are able to provide unprecedented spatial resolution, allowing to precisely identify individual products of the reactions. Nevertheless, a deep understanding of the reaction mechanism under the conditions imposed by the substrate remains unknown.Nowadays, various computational strategies are employed to characterize the optimal reaction pathways of the chemical processes that take place on the surfaces of solids. For example, one of the most popular approaches is the nudged elastic band (NEB) as well as different transition state theory methods beyond it. These approaches had demonstrated their capability to characterize the potential energy landscape of the reaction pathways [1-2]. Another approach that had attracted the interest of the on-surface synthesis community is the application of molecular dynamics (MD) methods, within the canonical ensemble, and based on the QM/MM (quantum mechanics/molecular mechanics) of the interatomic forces [3-4]. This approach, which combines Density functional theory (DFT) and empirical force fields to describe the interaction forces, allows to simulate very large systems, at a very low computational cost while still accounting for the crucial quantum mechanics interactions. Also, such temperature-dependent simulations include the effect of entropy, vibrations modes, concerted motion, etc.I will present the experimental and computational results of different projects in which we have made use of the aforementioned computational approaches to achieve a better understanding of the on-surface synthesis experiments performed by the group. For example, the rationalization of the selective cyclodehydrogenation of non-benzenoid nanographenes deposited on a Au(111) substrate by means of temperature-dependent MD calculations and the analysis of the obtained vibrational modes (See Figure 1a). The group had also studied the stepwise transformation of coronene-based organometallic networks into two-dimensional covalent patches through intermolecular homocoupling (See Figure 1b). We had as well investigated the transformation of indenyl precursors, through a triple C-H cleavage followed by a peripheral directed homocoupling, to form a polyacetylene backboned polymer that features a parity dependent and highly delocalized soliton in-gap state (See Figure 1c).

Direct Observation of HOON Intermediate in the Photochemistry of HONO.

The photochemistry of nitrous acid (HONO), encompassing dissociation into OH and NO as well as the reverse association reaction, plays a pivotal role in atmospheric chemistry. Here, we report the direct observation of nitrosyl-O-hydroxide (HOON) in the photochemistry of HONO, employing matrix-isolation IR and UV-vis spectroscopy. Despite a barrier of approximately 30 kJ/mol, HOON undergoes spontaneous rearrangement to the more stable HONO isomer through quantum mechanical tunneling, with a half-life of 28 min at 4 K. Kinetic isotope effects and instanton theory calculations reveal that the tunneling process involves the concerted motion of the NO moiety (65.2%) and the hydrogen atom (32.3%). Our findings underscore the significance of HOON as a key intermediate in the photolytic dissociation-association cycle of HONO at low temperatures.

Mapping the molecular motions of 5-HT3 serotonin-gated channel by voltage-clamp fluorometry.

The serotonin-gated ion channel (5-HT3R) mediates excitatory neuronal communication in the gut and the brain. It is the target for setrons, a class of competitive antagonists widely used as antiemetics, and is involved in several neurological diseases. Cryo-electron microscopy (cryo-EM) of the 5-HT3R in complex with serotonin or setrons revealed that the protein has access to a wide conformational landscape. However, assigning known high-resolution structures to actual states contributing to the physiological response remains a challenge. In the present study, we used voltage-clamp fluorometry (VCF) to measure simultaneously, for 5-HT3R expressed at a cell membrane, conformational changes by fluorescence and channel opening by electrophysiology. Four positions identified by mutational screening report motions around and outside the serotonin-binding site through incorporation of cysteine-tethered rhodamine dyes with or without a nearby quenching tryptophan. VCF recordings show that the 5-HT3R has access to four families of conformations endowed with distinct fluorescence signatures: 'resting-like' without ligand, 'inhibited-like' with setrons, 'pre-active-like' with partial agonists, and 'active-like' (open channel) with partial and strong agonists. Data are remarkably consistent with cryo-EM structures, the fluorescence partners matching respectively apo, setron-bound, 5-HT bound-closed, and 5-HT-bound-open conformations. Data show that strong agonists promote a concerted motion of all fluorescently labeled sensors during activation, while partial agonists, especially when loss-of-function mutations are engineered, stabilize both active and pre-active conformations. In conclusion, VCF, though the monitoring of electrophysiologically silent conformational changes, illuminates allosteric mechanisms contributing to signal transduction and their differential regulation by important classes of physiological and clinical effectors.

Mapping the molecular motions of 5-HT3 serotonin-gated channel by voltage-clamp fluorometry

The serotonin-gated ion channel (5-HT3R) mediates excitatory neuronal communication in the gut and the brain. It is the target for setrons, a class of competitive antagonists widely used as antiemetics, and is involved in several neurological diseases. Cryo-electron microscopy (cryo-EM) of the 5-HT3R in complex with serotonin or setrons revealed that the protein has access to a wide conformational landscape. However, assigning known high-resolution structures to actual states contributing to the physiological response remains a challenge. In the present study, we used voltage-clamp fluorometry (VCF) to measure simultaneously, for 5-HT3R expressed at a cell membrane, conformational changes by fluorescence and channel opening by electrophysiology. Four positions identified by mutational screening report motions around and outside the serotonin-binding site through incorporation of cysteine-tethered rhodamine dyes with or without a nearby quenching tryptophan. VCF recordings show that the 5-HT3R has access to four families of conformations endowed with distinct fluorescence signatures: ‘resting-like’ without ligand, ‘inhibited-like’ with setrons, ‘pre-active-like’ with partial agonists, and ‘active-like’ (open channel) with partial and strong agonists. Data are remarkably consistent with cryo-EM structures, the fluorescence partners matching respectively apo, setron-bound, 5-HT bound-closed, and 5-HT-bound-open conformations. Data show that strong agonists promote a concerted motion of all fluorescently labeled sensors during activation, while partial agonists, especially when loss-of-function mutations are engineered, stabilize both active and pre-active conformations. In conclusion, VCF, though the monitoring of electrophysiologically silent conformational changes, illuminates allosteric mechanisms contributing to signal transduction and their differential regulation by important classes of physiological and clinical effectors.

Synaptic ribbon dynamics after noise exposure in the hearing cochlea

Moderate noise exposure induces cochlear synaptopathy, the loss of afferent ribbon synapses between cochlear hair cells and spiral ganglion neurons, which is associated with functional hearing decline. Prior studies have demonstrated noise-induced changes in the distribution and number of synaptic components, but the dynamic changes that occur after noise exposure have not been directly visualized. Here, we describe a live imaging model using RIBEYE-tagRFP to enable direct observation of pre-synaptic ribbons in mature hearing mouse cochleae after synaptopathic noise exposure. Ribbon number does not change, but noise induces an increase in ribbon volume as well as movement suggesting unanchoring from synaptic tethers. A subgroup of basal ribbons displays concerted motion towards the cochlear nucleus with subsequent migration back to the cell membrane after noise cessation. Understanding the immediate dynamics of synaptic damage after noise exposure may facilitate identification of specific target pathways to treat cochlear synaptopathy.

Solid State Machinery of Multiple Dynamic Elements in a Metal-Organic Framework.

Engineering coordinated rotational motion in porous architectures enables the fabrication of molecular machines in solids. A flexible two-fold interpenetrated pillared Metal-Organic Framework precisely organizes fast mobile elements such as bicyclopentane (BCP) (107 Hz regime at 85 K), two distinct pyridyl rotors and E-azo group involved in pedal-like motion. Reciprocal sliding of the two sub-networks, switched by chemical stimuli, modulated the sizes of the channels and finally the overall dynamical machinery. Actually, iodine-vapor adsorption drives a dramatic structural rearrangement, displacing the two distinct subnets in a concerted piston-like motion. Unconventionally, BCP mobility increases, exploring ultra-fast dynamics (107 Hz) at temperatures as low as 44 K, while the pyridyl rotors diverge into a faster and slower dynamical regime by symmetry lowering. Indeed, one pillar ring gained greater rotary freedom as carried by the azo-group in a crank-like motion. A peculiar behavior was stimulated by pressurized CO2, which regulates BCP dynamics upon incremental site occupation. The rotary dynamics is intrinsically coupled to the framework flexibility as demonstrated by complementary experimental evidence (multinuclear solid-state NMR down to very low temperatures, synchrotron radiation XRD, gas sorption) and computational modelling, which helps elucidate the highly sophisticated rotor-structure interplay.

Oxygen-evolving photosystem II structures during S1–S2–S3 transitions

Photosystem II (PSII) catalyses the oxidation of water through a four-step cycle of Si states (i = 0–4) at the Mn4CaO5 cluster1–3, during which an extra oxygen (O6) is incorporated at the S3 state to form a possible dioxygen4–7. Structural changes of the metal cluster and its environment during the S-state transitions have been studied on the microsecond timescale. Here we use pump-probe serial femtosecond crystallography to reveal the structural dynamics of PSII from nanoseconds to milliseconds after illumination with one flash (1F) or two flashes (2F). YZ, a tyrosine residue that connects the reaction centre P680 and the Mn4CaO5 cluster, showed structural changes on a nanosecond timescale, as did its surrounding amino acid residues and water molecules, reflecting the fast transfer of electrons and protons after flash illumination. Notably, one water molecule emerged in the vicinity of Glu189 of the D1 subunit of PSII (D1-E189), and was bound to the Ca2+ ion on a sub-microsecond timescale after 2F illumination. This water molecule disappeared later with the concomitant increase of O6, suggesting that it is the origin of O6. We also observed concerted movements of water molecules in the O1, O4 and Cl-1 channels and their surrounding amino acid residues to complete the sequence of electron transfer, proton release and substrate water delivery. These results provide crucial insights into the structural dynamics of PSII during S-state transitions as well as O–O bond formation.

Correlated proton dynamics in hydrogen bonding networks: the benchmark case of 3-hydroxyglutaric acid.

Proton and hydrogen-bonded networks sustain a broad range of structural and charge transfer processes in supramolecular materials. The modelling of proton dynamics is however challenging and demands insights from prototypical benchmark systems. The intramolecular H-bonding networks induced by either protonation or deprotonation of 3-hydroxyglutaric acid provide intriguing case studies of correlated proton dynamics. The vibrational signatures associated with the fluxional proton bonding and its coupling with the hydroxyglutaric backbone are investigated here with infrared action ion spectroscopy experiments and Born-Oppenheimer molecular dynamics (BOMD) computations. Despite the formally similar symmetry of protonated and deprotonated hydroxyglutaric acid, the relative proton affinities of the oxygen centers of the carboxylic and carboxylate groups with respect to that of the central hydroxyl group lead to distinct proton dynamics. In the protonated acid, a tautomeric arrangement of the type HOCO·[HOH]+·OCOH is preferred with the proton binding tighter to the central hydroxyl moiety and the electronic density being shared between the two nearly symmetric H-bonds with the carboxylic end groups. In the deprotonated acid, the asymmetric [OCO]-·HO·HOCO configuration is more stable, with a stronger H-bonding on the bare carboxylate end. Both systems display active backbone dynamics and concerted Grothuss-like proton motions, leading to diffuse band structures in their vibrational spectra. These features are accurately reproduced by the BOMD computations.

Mechanism of drug resistance in HIV-1 protease subtype C in the presence of Atazanavir

AIDS is one of the deadliest diseases in the history of humankind caused by HIV. Despite the technological development, curtailing the viral infection inside human host still remains a challenge. Therapies such as HAART uses a combination of drugs to inhibit the viral activity. One of the important targets includes HIV protease and inhibiting its activity will minimize the production of mature structural proteins. However, the genetic diversity and the occurrence of drug resistant mutations adds complexity to effective drug design. In this study, we aimed at understanding the drug binding mechanism of one such subtype, namely subtype C and its insertion variant L38HL. We performed multiple molecular dynamics simulations along with binding free energy analysis of wild-type and L38HL bound to Atazanavir (ATV). From the analysis, we revealed that the insertion alters the hydrogen bond and hydrophobic interaction networks. The alterations in the interaction networks increase flexibility at the hinge-fulcrum interface. Further, the effects of these changes affect flap tip curling. Moreover, the changes in the hinge-fulcrum-cantilever interface alters the concerted motion of the functional regions leading to change in the direction of flap movement thus causing a subtle change in the active site volume. Additionally, formation of intramolecular hydrogen bonds in the ATV docked to L38HL restricted the movement of R1 and R2 groups thereby altering the interactions. Overall, the changes in the flexibility of flap together with the changes in the active site volume and compactness of the ligand provide insights for increased binding affinity of ATV with L38HL.

Formation of compounds with diverse polyelectrolyte morphologies and nonlinear ion conductance in a two-dimensional nanofluidic channel.

Aqueous electrolytes subjected to angstrom-scale confinement have recently attracted increasing interest because of their distinctive structural and transport properties, as well as their promising applicability in bioinspired nanofluidic iontronics and ion batteries. Here, we performed microsecond-scale molecular dynamics simulations, which provided evidence of nonlinear ionic conductance under an external lateral electric field due to the self-assembly of cations and anions with diverse polyelectrolyte morphologies (e.g., extremely large ion clusters) in aqueous solutions within angstrom-scale slits. Specifically, we found that the cations and anions of Li2SO4 and CaSO4 formed chain-like polyelectrolyte structures, whereas those of Na2SO4 and MgSO4 predominantly formed a monolayer of hydrated salt. Additionally, the cations and anions of K2SO4 assembled into a hexagonal anhydrous ionic crystal. These ion-dependent diverse polyelectrolyte morphologies stemmed from the enhanced Coulomb interactions, weakened hydration and steric constraints within the angstrom-scale slits. More importantly, once the monolayer hydrated salt or ionic crystal structure was formed, the field-induced ion current exhibited an intriguing gating effect at a low field strength. This abnormal ion transport was attributed to the concerted movement of cations and anions within the solid polyelectrolytes, leading to the suppression of ion currents. When the electric field exceeded a critical strength, however, the ion current surged rapidly due to the dissolution of many cations and anions within a few nanoseconds in the aqueous solution.

(Invited) A Dive into the Complex Mechanisms That May or May Not Increase Li/Na Mobility in Solid State Conductors

The conductivity of Li and Na has achieved remarkably high values in some materials, higher than what has been achieved in liquid electrolytes. Because there is no mobile solvation shell in solid-state conductors, the maximum of conductivity is essentially unlimited. I will discuss our current understanding of the compositional and structural elements that contribute to very high alkali ion mobility. This will include a discussion, of activated complexes that create concerted motion, possible high-entropy effects, the effect of (poly)anions, and structural topology.

Nanoscale one-dimensional close packing of interfacial alkali ions driven by water-mediated attraction.

The permeability and selectivity of biological and artificial ion channels correlate with the specific hydration structure of single ions. However, fundamental understanding of the effect of ion-ion interaction remains elusive. Here, via non-contact atomic force microscopy measurements, we demonstrate that hydrated alkali metal cations (Na+ and K+) at charged surfaces could come into close contact with each other through partial dehydration and water rearrangement processes, forming one-dimensional chain structures. We prove that the interplay at the nanoscale between the water-ion and water-water interaction can lead to an effective ion-ion attraction overcoming the ionic Coulomb repulsion. The tendency for different ions to become closely packed follows the sequence K+ > Na+ > Li+, which is attributed to their different dehydration energies and charge densities. This work highlights the key role of water molecules in prompting close packing and concerted movement of ions at charged surfaces, which may provide new insights into the mechanism of ion transport under atomic confinement.

Atomistic Simulations of Sarcomere Proteins.

Concerted atomic motions are requisite for sarcomere protein function and may become disrupted in HCM pathologies. Computational approaches such as molecular dynamics simulation can resolve such dynamics with unrivalled spatial and temporal resolution. This chapter describes methods to model structural and dynamical changes in biomolecules with HCM-associated perturbations.

N → π* Interaction Enabling Transient Inversion of Chirality.

This study reports the observation and characterization of two isomers of the acrolein dimer by using high-resolution rotational spectroscopy in pulsed jets. The first isomer is stabilized by two hydrogen bonds, adopting a planar configuration, and is energetically favored over the second isomer, which exhibits a dominant n → π* interaction in a nearly orthogonal arrangement. Surprisingly, the n → π* interaction was revealed to enable a concerted tunneling motion of two moieties along the carbonyl group. This motion leads to the inversion of transient chirality associated with the exchange of donor-acceptor roles, as revealed by the spectral feature of quadruplets. Inversion of transient chirality is a fundamental phenomenon in quantum mechanics and commonly observed for only inversional motions of protons. It is the first discovery, to the best of our knowledge, that such heavy moieties can also undergo chirality inversion.