Rotational dynamics and transition mechanisms of surface-adsorbed proteins.

Assembly of biomolecules at solid­water interfaces requires molecules to traverse complex orientation-dependent energy landscapes through processes that are poorly understood, largely due to the dearth of in situ single-molecule measurements and statistical analyses of the rotational dynamics that define directional selection. Emerging capabilities in high-speed atomic force microscopy and machine learning have allowed us to directly determine the orientational energy landscape and observe and quantify the rotational dynamics for protein nanorods on the surface of muscovite mica under a variety of conditions. Comparisons with kinetic Monte Carlo simulations show that the transition rates between adjacent orientation-specific energetic minima can largely be understood through traditional models of in-plane Brownian rotation across a biased energy landscape, with resulting transition rates that are exponential in the energy barriers between states. However, transitions between more distant angular states are decoupled from barrier height, with jump-size distributions showing a power law decay that is characteristic of a nonclassical Levy-flight random walk, indicating that large jumps are enabled by alternative modes of motion via activated states. The findings provide insights into the dynamics of biomolecules at solid­liquid interfaces that lead to self-assembly, epitaxial matching, and other orientationally anisotropic outcomes and define a general procedure for exploring such dynamics with implications for hybrid biomolecular­inorganic materials design.

Nonlinear rotational spectroscopy reveals many-body interactions in water molecules.

Because of their central importance in chemistry and biology, water molecules have been the subject of decades of intense spectroscopic investigations. Rotational spectroscopy of water vapor has yielded detailed information about the structure and dynamics of isolated water molecules, as well as water dimers and clusters. Nonlinear rotational spectroscopy in the terahertz regime has been developed recently to investigate the rotational dynamics of linear and symmetric-top molecules whose rotational energy levels are regularly spaced. However, it has not been applied to water or other lower-symmetry molecules with irregularly spaced levels. We report the use of recently developed two-dimensional (2D) terahertz rotational spectroscopy to observe high-order rotational coherences and correlations between rotational transitions that were previously unobservable. The results include two-quantum (2Q) peaks at frequencies that are shifted slightly from the sums of distinct rotational transitions on two different molecules. These results directly reveal the presence of previously unseen metastable water complexes with lifetimes of 100 ps or longer. Several such peaks observed at distinct 2Q frequencies indicate that the complexes have multiple preferred bimolecular geometries. Our results demonstrate the sensitivity of rotational correlations measured in 2D terahertz spectroscopy to molecular interactions and complexation in the gas phase.

Switchable Xe/Kr Selectivity in a Hofmann-Type Metal-Organic Framework via Temperature-Responsive Rotational Dynamics.

The development of adsorbents for Kr and Xe separation is essential to meet industrial demands and for energy conservation. Although a number of previous studies have focused on Xe-selective adsorbents, stimuli-responsive Xe/Kr-selective adsorbents still remain underdeveloped. Herein, a Hofmann-type framework Co(DABCO)[Ni(CN)4 ] (referred to as CoNi-DAB; DABCO = 1,4-diazabicyclo[2,2,2]octane) that provides a temperature-dependent switchable Xe/Kr separation performance is reported. CoNi-DAB showed high Kr/Xe (0.8/0.2) selectivity with significant Kr adsorption at 195 K as well as high Xe/Kr (0.2/0.8) selectivity with superior Xe adsorption at 298 K. Such adsorption features are associated with the temperature-dependent rotational configuration of the DABCO ligand, which affects the kinetic gate-opening temperature of Xe and Kr. The packing densities of Xe (2.886 g cm-3 at 298 K) and Kr (2.399 g  cm-3 at 195 K) inside the framework are remarkable and comparable with those of liquid Xe (3.057 g cm-3 ) and liquid Kr (2.413 g cm-3 ), respectively. Breakthrough experiments confirm the temperature-dependent reverse separation performance of CoNi-DAB at 298 K under dry and wet (88% relative humidity) conditions and at 195 K under dry conditions. The unique adsorption behavior is also verified through van der Waals (vdW)-corrected density functional theory (DFT) calculations and nudged elastic band (NEB) simulations.

Tracking the rotation of single CdS nanorods during photocatalysis with surface plasmon resonance microscopy.

While rotational dynamics of anisotropic nanoobjects has often been limited in plasmonic and fluorescent nanomaterials, here we demonstrate the capability of a surface plasmon resonance microscopy (SPRM) to determine the orientation of all kinds of anisotropic nanomaterials. By taking CdS nanorods as an example, it was found that two-dimensional Fourier transform of the asymmetrical wave-like SPRM image resulted in a peak in its angular spectrum in k space. Consistency between the peak angle and the geometrical orientation of the nanorod was validated by both in situ scanning electron microscope characterizations and theoretical calculations. Real-time monitoring of the rotational dynamics of single CdS nanorods further revealed the accelerated rotation under appropriate reaction conditions for photocatalyzed hydrogen generation. The driving force was attributed to the asymmetric production of hydrogen molecules as a result of inhomogeneous distribution of reactive sites within the nanorod. The present work not only builds the experimental and theoretical connections between the orientation of anisotropic nanomaterials and its SPRM images; the general suitability of SPRM also sheds light on broad types of nonfluorescent and nonplasmonic anisotropic nanoobjects from semiconductors to bacteria and viruses.

The Brownian and Flow-Driven Rotational Dynamics of a Multicomponent DNA Origami-Based Rotor.

Nanomechanical devices are becoming increasingly popular due to the very diverse field of potential applications, including nanocomputing, robotics, and drug delivery. DNA is one of the most promising building materials to realize complex 3D structures at the nanoscale level. Several mechanical DNA origami structures have already been designed capable of simple operations such as a DNA box with a controllable lid, bipedal walkers, and cargo sorting robots. However, the nanomechanical properties of mechanically interlinked DNA nanostructures that are in general highly deformable have yet to be extensively experimentally evaluated. In this work, a multicomponent DNA origami-based rotor is created and fully characterized by electron microscopy under negative stain and cryo preparations. The nanodevice is further immobilized on a microfluidic chamber and its Brownian and flow-driven rotational behaviors are analyzed in real time by single-molecule fluorescence microscopy. The rotation in previous DNA rotors based either on strand displacement, electric field or Brownian motion. This study is the first to attempt to manipulate the dynamics of an artificial nanodevice with fluidic flow as a natural force.

Dynamics of Hydrogen Bonding in Three-Component Nanorotors.

The dynamics of hydrogen bonding do not only play an important role in many biochemical processes but also in Nature's multicomponent machines. Here, a three-component nanorotor is presented where both the self-assembly and rotational dynamics are guided by hydrogen bonding. In the rate-limiting step of the rotational exchange, two phenolic O-H-N,N(phenanthroline) hydrogen bonds are cleaved, a process that was followed by variable-temperature 1 H NMR spectroscopy. Activation data (ΔG≠ 298 =46.7 kJ mol-1 at 298 K, ΔH≠ =55.3 kJ mol-1 , and ΔS≠ =28.8 J mol-1 K-1 ) were determined, furnishing a rotational exchange frequency of k298 =40.0 kHz. Fully reversible disassembly/assembly of the nanorotor was achieved by addition of 5.0 equivalents of trifluoroacetic acid (TFA)/1,8-diazabicyclo[5.4.0]undec-7-ene (DBU) over three cycles.

Nonlinear two-dimensional terahertz photon echo and rotational spectroscopy in the gas phase.

Ultrafast 2D spectroscopy uses correlated multiple light-matter interactions for retrieving dynamic features that may otherwise be hidden under the linear spectrum; its extension to the terahertz regime of the electromagnetic spectrum, where a rich variety of material degrees of freedom reside, remains an experimental challenge. We report a demonstration of ultrafast 2D terahertz spectroscopy of gas-phase molecular rotors at room temperature. Using time-delayed terahertz pulse pairs, we observe photon echoes and other nonlinear signals resulting from molecular dipole orientation induced by multiple terahertz field-dipole interactions. The nonlinear time domain orientation signals are mapped into the frequency domain in 2D rotational spectra that reveal J-state-resolved nonlinear rotational dynamics. The approach enables direct observation of correlated rotational transitions and may reveal rotational coupling and relaxation pathways in the ground electronic and vibrational state.

Radiation-driven rotational motion of nanoparticles.

Focused synchrotron beams can influence a studied sample via heating, or radiation pressure effects due to intensity gradients. The high angular sensitivity of rotational X-ray tracking of crystalline particles via their Bragg reflections can detect extremely small forces such as those caused by field gradients. By tracking the rotational motion of single-crystal nanoparticles embedded in a viscous or viscoelastic medium, the effects of heating in a uniform gradient beam and radiation pressure in a Gaussian profile beam were observed. Changes in viscosity due to X-ray heating were measured for 42 µm crystals in glycerol, and angular velocities of 10-6 rad s-1 due to torques of 10-24 N m were measured for 340 nm crystals in a colloidal gel matrix. These results show the ability to quantify small forces using rotation motion of tracer particles.

Electron spin resonance of spin-labeled lipid assemblies and proteins.

Spin-label electron spin resonance (ESR) spectroscopy is a valuable means to study molecular mobility and interactions in biological systems. This paper deals with conventional, continuous wave ESR of nitroxide spin-labels at 9-GHz providing an introduction to the basic principles of the technique and applications to self-assembled lipid aggregates and proteins. Emphasis is given to segmental lipid chain order and rotational dynamics of lipid structures, environmental polarity of membranes and proteins, structure and conformational dynamics of proteins.

Rotational Diffusion of a New Large Non Polar Dye Molecule in Alkanes.

Rotational reorientation times of a newly synthesized 2,5-bis(phenylethynyl)1,4-bis(dodecyloxy) benzene (DDPE) are experimentally determined in series of n-alkanes by employing steady state and time resolved fluorescence depolarization technique with a view to understand rotational dynamics of large non-polar solute molecule in non-polar solvents and few general solvents of different sizes and varying viscosity. It is observed that rotational reorientation times vary linearly as function of viscosity. The hydrodynamic stick condition describes the experimental results at low viscosities while the results tend to deviate significantly from it at higher viscosities. This is attributed to the possibility of long chains in solvents hosting a variety of chain defects (end-gauche, double-gauche, all-trans, kink, etc.) thereby reducing the effective length of the molecule, leading to a slightly reduced friction. The experimental results are compared with the predictions of Stokes-Einstein-Debye (SED) hydrodynamic theory as well as the quasi-hydrodynamic theories of Gierer-Wirtz (GW) and Dote-Kivelson-Shwartz (DKS). The predictions from these theories underestimate τr in the solvents employed in the study.

Comparison of the dielectric and NMR results for liquid crystals: dynamic aspects.

Critical analysis of the results of studies of molecular rotational dynamics in liquid crystalline substances with the aid of the dielectric spectroscopy (DS) and nuclear magnetic resonance (NMR) is given. Both methods are known to be sensitive to different aspects of molecular rotations: the polarization vector and the relaxation time τ(DS) in the case of DS, a tensor describing a nuclear interaction and the correlation time τ(NMR) for NMR method. Furthermore, both methods provide correlation functions with different rank values. A common basis for the comparison between τ(DS) and τ(NMR) is postulated. Several examples of the temperature dependence of the correlation times coming from the two spectroscopic methods are presented. Qualitative agreements of the correlation times were achieved in most cases.

Mass distribution and shape influence the perceived weight of objects.

Research suggests that the rotational dynamics of an object underpins our perception of its weight. We examine the generalisability of that account using a more ecologically valid way of manipulating an object's mass distribution (mass concentrated either at the top, bottom, centre, near the edges or evenly distributed throughout the object), shape (cube or sphere), and lifting approach (lifting directly by the hand or indirectly using a handle or string). The results were in line with our predictions. An interaction effect was found where the mass distribution and lifting approach both associated with the lowest rotational dynamics made the stimulus appear lighter compared to other combinations. These findings demonstrate rotational dynamic effects in a more run-of-the-mill experience of weight perception than what has been demonstrated before using cumbersome stimuli.

Role of Gemini Surfactants with Variable Spacers and SiO2 Nanoparticles in ct-DNA Compaction and Applications toward In Vitro/In Vivo Gene Delivery.

Compaction of calf thymus DNA (ct-DNA) by two cationic gemini surfactants, 12-4-12 and 12-8-12, in the absence and presence of negatively charged SiO2 nanoparticles (NPs) (∼100 nm) has been explored using various techniques. 12-8-12 having a longer hydrophobic spacer induces a greater extent of ct-DNA compaction than 12-4-12, which becomes more efficient with SiO2 NPs. While 50% ct-DNA compaction in the presence of SiO2 NPs occurs at ∼77 nM of 12-8-12 and ∼130 nM of 12-4-12, but a conventional counterpart surfactant, DTAB, does it at its concentration as high as ∼7 µM. Time-resolved fluorescence anisotropy measurements show changes in the rotational dynamics of a fluorescent probe, DAPI, and helix segments in the condensed DNA. Fluorescence lifetime data and ethidium bromide exclusion assays reveal the binding sites of surfactants to ct-DNA. 12-8-12 with SiO2 NPs has shown the highest cell viability (≥90%) and least cell death in the human embryonic kidney (HEK) 293 cell lines in contrast to the cell viability of ≤80% for DTAB. These results show that 12-8-12 with SiO2 NPs has the highest time and dose-dependent cytotoxicity compared to 12-8-12 and 12-4-12 in the murine breast cancer 4T1 cell line. Fluorescence microscopy and flow cytometry are performed for in vitro cellular uptake of YOYO-1-labeled ct-DNA with surfactants and SiO2 NPs using 4T1 cells after 3 and 6 h incubations. The in vivo tumor accumulation studies are carried out using a real-time in vivo imaging system after intravenous injection of the samples into 4T1 tumor-bearing mice. 12-8-12 with SiO2 has delivered the highest amount of ct-DNA in cells and tumors in a time-dependent manner. Thus, the application of a gemini surfactant with a hydrophobic spacer and SiO2 NPs in compacting and delivering ct-DNA to the tumor is proven, warranting its further exploration in nucleic acid therapy for cancer treatment.

Thermodynamics of translational and rotational dynamics of C9 hydrocarbons in the pores of zeolite-beta.

There has been a growing interest in the separation of aromatic hydrocarbon molecules from the petroleum stream using zeolite-based technologies. This led to numerous experimental and molecular simulation studies of the structural and dynamical properties of aromatic hydrocarbons under the confinement of microporous materials like zeolites. The understanding of the behavior of the isomers of the trimethylbenzene under confinement is crucial for their separation and purification from industrial streams. Here, we investigate the translational and rotational dynamics and associated thermodynamics of three isomers of trimethyl benzene, namely, 1,2,3-trimethyl benzene (1,2,3-TMB), 1,2,4-trimethyl benzene (1,2,4-TMB), and 1,3,5-trimethylbenzene (1,3,5-TMB) under the confinement of zeolite-beta (BEA) using molecular dynamics (MD) simulations. The trends in the diffusion coefficients of the TMB isomers calculated from our MD simulation data are in good agreement with the data already available in the literature. Analysis of dynamics and associated thermodynamic properties indicate that 1,2,4-TMB is translationally more facile than the other two isomers. The rotational motion of TMB isomers is largely anisotropic and it is relatively more significant for both 1,2,4-TMB and 1,3,5-TMB. The thermodynamic properties reveal that the distinguishability in the dynamic properties among these three isomers is essentially caused by entropy. These results are not only critical to engineer the separation process of TMB isomers across the zeolite beds but also to understand the different catalytic processes such as trans-alkylation, conversion, cracking etc.

Rotational Dynamics of The Transmembrane Domains Play an Important Role in Peptide Dynamics of Viral Fusion and Ion Channel Forming Proteins-A Molecular Dynamics Simulation Study.

Focusing on the transmembrane domains (TMDs) of viral fusion and channel-forming proteins (VCPs), experimentally available and newly generated peptides in an ideal conformation of the S and E proteins of severe acute respiratory syndrome coronavirus type 2 (SARS-CoV-2) and SARS-CoV, gp41 and Vpu, both of human immunodeficiency virus type 1 (HIV-1), haemagglutinin and M2 of influenza A, as well as gB of herpes simplex virus (HSV), are embedded in a fully hydrated lipid bilayer and used in multi-nanosecond molecular dynamics simulations. It is aimed to identify differences in the dynamics of the individual TMDs of the two types of viral membrane proteins. The assumption is made that the dynamics of the individual TMDs are decoupled from their extra-membrane domains, and that the mechanics of the TMDs are distinct from each other due to the different mechanism of function of the two types of proteins. The diffusivity coefficient (DC) of the translational and rotational diffusion is decreased in the oligomeric state of the TMDs compared to those values when calculated from simulations in their monomeric state. When comparing the calculations for two different lengths of the TMD, a longer full peptide and a shorter purely TMD stretch, (i) the difference of the calculated DCs begins to level out when the difference exceeds approximately 15 amino acids per peptide chain, and (ii) the channel protein rotational DC is the most affected diffusion parameter. The rotational dynamics of the individual amino acids within the middle section of the TMDs of the fusion peptides remain high upon oligomerization, but decrease for the channel peptides, with an increasing number of monomers forming the oligomeric state, suggesting an entropic penalty on oligomerization for the latter.

Effect of increasing speed on whole-body angular momentum during stepping in the elderly.

Recent evidence suggests that older adults may have difficulty controlling whole-body angular momentum (H) during volitional stepping, which could impose a major challenge for balance control and result in potential falls. However, it is not known if and how H is influenced by speed when stepping. This study aimed to investigate the effect on H of increasing speed during step initiation in older adults. Twenty-seven healthy individuals over 60 were enrolled in the current study and were instructed to perform a series of step initiations with their dominant leg under two speed conditions: at preferred speed and as fast as possible. Two force plates and a motion-capture system were used to record H and the components of the net external moment (moment arms and ground reaction forces) during the double support and step execution phases of stepping. Results revealed that increasing speed of stepping affected H differently in both stepping phases and in the different planes. H ranges in all three planes increased with speed during the double support phase. During the step execution phase, while H ranges in frontal and transversal planes decreased, sagittal plane H range significantly increased with speed. This increased H range in the sagittal plane, which may result from the task demands, could impose a greater challenge for balance control in the elderly.

Excitation of Tumbling in Phobos and Deimos.

Mass-spring model simulations are used to investigate past spin states of a viscoelastic Phobos and Deimos. From an initially tidally locked state, we find crossing of a spin-orbit resonance with Mars or a mean motion resonance with each other does not excite tumbling in Phobos or Deimos. However, once tumbling our simulations show that these moons can remain so for an extended period and during this time their orbital eccentricity can be substantially reduced. We attribute the tendency for simulations of an initially tumbling viscoelastic body to drop into spin-synchronous state at very low eccentricity to the insensitivity of the tumbling chaotic zone volume to eccentricity. After a tumbling body enters the spin synchronous resonance, it can exhibit long lived non-principal axis rotation and this too can prolong the period of time with enhanced tidally generated energy dissipation. The low orbital eccentricities of Phobos and Deimos could in part be due to spin excitation by nearly catastrophic impacts rather than tidal evolution following orbital resonance excitation.

Revealing the dynamics and energetics of interaction of a cationic biological photosensitizer within a bile salt aggregate.

The present investigation reports a detailed characterization of the interaction of a cationic photosensitizer, phenosafranin (PSF) with sodium deoxycholate (NaDC) bile salt aggregates based on spectroscopic and calorimetric techniques. Our explicit spectroscopic results not only establish the occurrence of PSF-NaDC binding interaction, but also reveal marked lowering of micropolarity at the interaction site (ET(30) = 55.97 kcal mol-1 in the presence of NaDC as compared to ET(30) = 63.1 kcal mol-1 in bulk aqueous buffer). A thorough mathematical analysis of the fluorescence depolarization results based on the two-step and wobbling in cone model yields critical insight into the complex rotational relaxation dynamics of the bound drug. The impartation of motional restriction on the PSF molecules within the bile salt aggregates is evidenced from enhancement of average rotational correlation time from <τr> = 136 ps in aqueous buffer to 1.11 ns with added NaDC (8.0 mM). This is further supported from a high value of the generalized order parameter (S = 0.81) as well as the diffusion coefficient (Dw = 1.40 × 1012 s-1). Furthermore, our extensive calorimetric investigation unveils the complicated thermodynamics of the interaction process in terms of predominant entropic contribution over the enthalpic part in the lower temperature regime (TΔS = 18.84 ±â€¯1.13 kJ mol-1, ΔH = -5.82 ±â€¯0.35 kJ mol-1 at 288 K) with subsequent reversal of the relative contributions with increasing temperature (TΔS = 7.54 ±â€¯0.39 kJ mol-1, ΔH = - 17.09 ±â€¯0.90 kJ mol-1 at 318 K). The instrumental role of the hydrophobic effect underlying the PSF-NaDC interaction is characterized by a negative heat capacity change (ΔCp = -364 J mol-1 K-1). An intriguing thermodynamic feature in terms of enthalpy-entropy compensation (with increasing temperature ΔG remains almost constant while ΔH and TΔS vary significantly) aptly corroborates the aforesaid argument and establishes an appreciable hydrophobic contribution to the overall binding energies.

Static Characteristics of a New Three-Dimensional Linear Homeomorphic Saccade Model.

A linear homeomorphic saccade model that produces 3D saccadic eye movements consistent with physiological and anatomical evidence is introduced. Central to the model is the implementation of a time-optimal controller with six linear muscles and pulleys that represent the saccade oculomotor plant. Each muscle is modeled as a parallel combination of viscosity [Formula: see text] and series elasticity [Formula: see text] connected to the parallel combination of active-state tension generator [Formula: see text], viscosity element [Formula: see text], and length tension elastic element [Formula: see text]. Additionally, passive tissues involving the eyeball include a viscosity element [Formula: see text], elastic element [Formula: see text], and moment of inertia [Formula: see text]. The neural input for each muscle is separately maintained, whereas the effective pulling direction is modulated by its respective mid-orbital constraint from the pulleys. Initial parameter values for the oculomotor plant are based on anatomical and physiological evidence. The oculomotor plant uses a time-optimal, 2D commutative neural controller, together with the pulley system that actively functions to implement Listing's law during both static and dynamic conditions. In a companion paper, the dynamic characteristics of the saccade model is analyzed using a time domain system identification technique to estimate the final parameter values and neural inputs from saccade data. An excellent match between the model estimates and the data is observed, whereby a total of 20 horizontal, 5 vertical, and 64 oblique saccades are analyzed.