Molecular Translational Motion Research Articles

Foldaxanes: Rotaxane-like Architectures from Foldamers.

Mechanically interlocked molecules such as rotaxanes and catenanes contain free-moving components that cannot dissociate and have enabled the investigation and control of various translational and rotational molecular motions. The architecture of pseudo-rotaxanes and of some kinetically labile rotaxanes is comparable to that of rotaxanes but their components are reversibly associated and not irreversibly interlocked. In other words, pseudo-rotaxanes may fall apart. This Account focuses on a peculiar family of rotaxane-like architectures termed foldaxanes.Foldaxanes consist of a helically folded oligomer wound around a rod-like dumbbell-shaped guest. Winding of the helix around the rod thus entails an unwinding-rewinding process that creates a kinetic barrier. It follows that foldaxanes, albeit reversibly assembled, have significant lifetimes and may not fall apart while defined molecular motions are triggered. Foldaxanes based on helically folded aromatic oligoamide hosts and oligo(alkyl carbamate) guests can be designed rationally through the inclusion of complementary binding motifs on the rod and at the inner rim of the helix so that helix length and rod length match. Single helical foldaxanes (bimolecular species) and double helical foldaxanes (trimolecular species) have thus been produced as well as poly[n]foldaxanes, in which several helices bind to long rods with multiple binding stations. When the binding stations differ and are organized in a certain sequence, a complementary sequence of different stacked helices, each matching with their binding station, can be assembled, thus reproducing in an artificial system a sort of translation process.Foldaxane helix handedness may be controlled by stereogenic centers on the rod-like guest. Handedness can also be transmitted from helix to helix in polyfoldaxanes. Foldaxane formation has drastic consequences for the rod properties, including its stiffening and the restriction of the mobility of a macrocycle already interlocked on the rod. Fast translation (without dissociation) of helices along rod-like guests has been demonstrated. Because of the helical nature of the hosts, translation may be accompanied by rotation in various sorts of screw-like motions. The possibility, on longer time scales, for the helix to dissociate from and reassociate to the rod has allowed for the design of complex, kinetically controlled supramolecular pathways of a helix on a rod. Furthermore, the design of helices with a directionality, that is, with two distinct termini, that bind to nonsymmetrical rod-like guests in a defined orientation makes it possible to also control the orientation of molecular motion. Altogether, foldaxanes constitute a distinct and full-of-potential family of rotaxane-like architectures that possess designer structures and allow orchestration of the time scales of various supramolecular events.

Translational and reorientational dynamics in deep eutectic solvents.

We performed rheological measurements of the typical deep eutectic solvents (DESs) glyceline, ethaline, and reline in a very broad temperature and dynamic range, extending from the low-viscosity to the high-viscosity supercooled-liquid regime. We find that the mechanical compliance spectra can be well described by the random free-energy barrier hopping model, while the dielectric spectra on the same materials involve significant contributions arising from reorientational dynamics. The temperature-dependent viscosity and structural relaxation time, revealing non-Arrhenius behavior typical for glassy freezing, are compared to the ionic dc conductivity and relaxation times determined by broadband dielectric spectroscopy. For glyceline and ethaline, we find essentially identical temperature dependences for all dynamic quantities. These findings point to a close coupling of the ionic and molecular translational and reorientational motions in these systems. However, for reline, the ionic charge transport appears decoupled from the structural and reorientational dynamics, following a fractional Walden rule. In particular, at low temperatures, the ionic conductivity in this DES is enhanced by about one decade compared to expectations based on the temperature dependence of the viscosity. The results for all three DESs can be understood without invoking a revolving-door mechanism previously considered as a possible charge-transport mechanism in DESs.

Effect of transverse dissipative particle dynamics on dynamic properties of nanometer-thick liquid films on solid surfaces

ABSTRACT To ascertain the effect of transverse dissipative particle dynamics (DPD), which includes lateral dissipative forces in addition to the central ones in the standard DPD, on dynamics of systems involving interfaces, we compare dynamic properties derived from coarse-grained (CG) molecular dynamics simulations with the standard and transverse DPD for nanometer-thick liquid films on solid surfaces. The dynamic properties include relaxation times of the film thickness distribution and molecular rotational motion, and transport properties associated with molecular translational motion. Our results show that these dynamic properties are tuneable by changing friction coefficients in the transverse DPD, whereas this is not the case in the standard DPD. We also confirm that the transverse DPD applied to liquid–solid CG bead pairs can tune dynamic properties of nanometer-thick liquid films on solid surfaces, though it is less effective than when applied to liquid–liquid CG bead pairs. Moreover, we reveal that the dissipative forces are isotropic in transverse DPD, whereas the liquid–solid dissipative forces are highly anisotropic and nearly along the direction perpendicular to solid surfaces in standard DPD. This suggests that the transverse liquid–solid DPD might be crucial for modelling the in-plane energy dissipation at liquid–solid interfaces.

Molecular mechanism of thermal sensitization effect of potential materials for microwave hyperthermia

ABSTRACT The materials susceptible to microwave irradiation has the potential to improve the heating efficiency of microwave tumour ablation. A molecular dynamics simulation was performed to investigate the mechanisms of thermal sensitisation of the potential susceptible materials including pure water, normal saline, hydrogel, sodium alginate and calcium alginate under microwave heating conditions. The comparison result of the temperature rises of these materials indicated that calcium alginate gels was the highest and that of pure water was lowest. The reasons were analysed by calculating the variations in translational and rotational kinetic energies, dielectric constant and energy contribution of the components of the materials in the presence of an external electromagnetic field of 2.45 GHz. It is found that the rapid translational molecular motion of salt ions leads to higher temperature rise of normal saline compared with pure water. The polymeric network structure of hydrogel can trap the water molecules in a small space and pack the surrounding water molecules more closely, and the temperature rise increases nonlinearly with the increase of the density of the water molecules. A combination of the heating mechanisms of normal saline and hydrogel induces the highest temperature rise of the alginates among all of the investigated materials.

Energy transfer within the hydrogen bonding network of water following resonant terahertz excitation.

Energy dissipation in water is very fast and more efficient than in many other liquids. This behavior is commonly attributed to the intermolecular interactions associated with hydrogen bonding. Here, we investigate the dynamic energy flow in the hydrogen bond network of liquid water by a pump-probe experiment. We resonantly excite intermolecular degrees of freedom with ultrashort single-cycle terahertz pulses and monitor its Raman response. By using ultrathin sample cell windows, a background-free bipolar signal whose tail relaxes monoexponentially is obtained. The relaxation is attributed to the molecular translational motions, using complementary experiments, force field, and ab initio molecular dynamics simulations. They reveal an initial coupling of the terahertz electric field to the molecular rotational degrees of freedom whose energy is rapidly transferred, within the excitation pulse duration, to the restricted translational motion of neighboring molecules. This rapid energy transfer may be rationalized by the strong anharmonicity of the intermolecular interactions.

Microscopic molecular translational dynamics in cholesteric and cholesteric blue phases

In the nematic (N) phase, the molecular symmetry axis orients on average along one direction denoted as the director. The cholesteric (Ch) phase shows similar orientational order locally. However, the average molecular direction in the Ch phase rotates continuously around a direction perpendicular to the director. The cholesteric blue phase (ChBP) shows a double-twist orientational order that differs from the single-twist order of the Ch phase and also shows self-assembled three-dimensional lattice structure of defect lines of the orientational order in the mesoscopic spatial scale. The helical structure of the molecular orientation in ChBP brings the structural colour and photonic band gap into the wavelength range of visible light. Therefore, ChBP has been studied for applications to photonic elements and fast-response displays. We measured the molecular translational dynamics along the molecular long axis in the Ch phase, ChBP and the isotropic (Iso) liquid phase of the mixture system of the nematic liquid crystal 4′-heptyloxy-4-biphenylcarbonitrile and the chiral dopant (S)-4′-(2-methylbutyl)-4-biphenylcarbonitrile directly at the nanometric molecular scale by using quasi-elastic scattering spectroscopy using Mossbauer gamma ray. We successfully determined the timescale of the molecular translational motion in the Ch phase to be 40 ns, which is similar to the timescale of the N phase of 4′-n-octyl-4-cyanobiphenyl. In the ChBP and Iso phase, molecular motions occur on timescales similar to those of the Ch phase, suggesting that the molecular dynamics is insensitive to the presence of orientational order, the helical structure, and higher-order structure. Our results demonstrate that the molecular dynamics in both the Ch phase and ChBP can be measured by quasi-elastic gamma-ray-scattering spectroscopy, in addition to the time scales of molecular motions in the N and smectic phases. The present results greatly expand the possibility of using this spectroscopic technique for molecular-mobility studies of industrial liquid-crystalline materials, because Ch liquid crystals are widely used for display systems in addition to N liquid crystals.

Dielectric and structural relaxation in water and some monohydric alcohols.

Relaxation times of the principal (Debye-type) relaxation terms in the dielectric spectra of water and normal alcohols have been evaluated in order to eliminate the effect of multi-molecular cross-correlations and to thus yield reorientation times of the molecular electric dipole moments. The reorientation times have been compared to relaxation times from ultraviolet and X-ray Brillouin spectra as well as from broadband ultrasonic spectra, which are considered as the structure relaxation times characterizing the density fluctuations of the liquid hydrogen bond networks. With some alcohols, shear impedance spectra indicate the network fluctuations to be tightly associated with shear viscosity relaxation. Within the limits of uncertainty, the molecular dipole moment reorientation times and the structure relaxation times feature close correlations. This finding suggests a coupling between translational and orientational molecular motions, and it is discussed in the light of the wait-and-switch model of dielectric relaxation.

Properties of immobile hydrogen confined in microporous carbon

We report results of vibrational neutron spectroscopy investigation aimed to identify the state of hydrogen adsorbed in ultramicroporous carbon. The mobility of hydrogen confined in carbon pores was probed as a function of temperature and pressure using inelastic neutron scattering, and the molecular translational and rotational motions were studied. At low loading rotation of H2 molecules adsorbed in the smallest carbon pores (∼4–5 Å) is severely hindered, suggesting that the interaction between H2 and the host matrix is anisotropic. At higher loading, H2 molecules behave as a nearly free rotor, implying lower anisotropic interactions with adsorption sites. At 77 K where bulk H2 is a gas, deconvolution of elastic/quasielastic signal provide evidence of pressure-dependent fractions of immobile (solid-like) and partially mobile (liquid-like) hydrogen, which correlate with the excess adsorption isotherm at 77 K. Effective H2 density in pores changes from solid-like to liquid-like with increasing pressure at 77 K. Surprisingly, immobile and partially mobile H2 is present even at temperatures as high as ∼110 K where bulk hydrogen exists only in gas form.

Complex Surface Diffusion Mechanisms of Cobalt Phthalocyanine Molecules on Ag(100)

We used time-lapsed scanning tunneling microscopy between 43 and 50 K and density functional theory (DFT) to explore the basic surface diffusion steps of cobalt phthalocyanine (CoPc) molecules on the Ag(100) surface. We show that the CoPc molecules translate and rotate on the surface in the same temperature range. Both processes are associated with similar activation energies; however, the translation is more frequently observed. Our DFT calculations provide the activation energies for the translation of the CoPc molecule between the nearest hollow sites and the rotation at both the hollow and the bridge sites. The activation energies are only consistent with the experimental findings, if the surface diffusion mechanism involves a combined translational and rotational molecular motion. Additionally, two channels of motion are identified: the first provides only a channel for translation, while the second provides a channel for both the translation and the rotation. The existence of the two channels explains a higher rate for the translation determined in experiment.

Abstract 19843: Myocardial Microcirculation Induces Anisotropic Diffusion-like Magnetic Resonance Contrast

Introduction: The magnetic resonance (MR) signal in the presence of a magnetic field gradient is highly sensitive to the aggregate translational molecular motion of water. In highly vascularized tissues, diffusion-like contrast induced by microcirculation has been used to characterize blood flow in heart. The effect in tissues with random capillary orientations has been modeled as intravoxel incoherent motion (IVIM), but is not completely understood in organized tissues. Hypothesis: We hypothesize that blood flow in organized tissues will manifest as speed- and orientation- dependent “pseudo” diffusion coefficient D*. Methods: For Gaussian-distributed flow with mean speed vm in parallel capillaries as a function of the relative encoding angle θ, it can be shown that D* is proportional to the square power of both vm and cos(θ), which is then incorporated into a generalized formulation of anisotropic tissue diffusion and flow with a tensor entity D* to characterize the flow pseudo diffusivity in 3D space using the familiar diffusion tensor imaging (DTI) notation. Validation experiments were conducted on isolated, perfused, guinea pig hearts (n=7) in a Langendorff setup and imaged with Bruker (7T) MRI scanner under normal and low flow conditions. Statistical analyses were conducted via 1-way ANOVA with Bonferroni post-hoc multiple-comparison correction (P<0.05 considered statistically significant). Results: Figure 1A-C show representative diffusion-weighted MR images encoded at perpendicular directions, and Fig 1D shows the flow-speed and angular dependence (or anisotropy) of the fitted D* component at high flow and low flow. D* significantly decreased by 63% only in the parallel direction to myocytes (or capillaries) (P<0.05). Conclusions: These findings suggest that the DTI formalism of anisotropic spin motion can be incorporated into the classical IVIM theory to describe the MR signal arising from diffusion and microcirculation in organized tissues.

Molecular dynamics analysis of incoherent neutron scattering from light water via the Van Hove space–time self-correlation function with a new quantum correction

In this paper, we propose a general method for evaluating the neutron incoherent scattering cross-section of light water by molecular dynamics (MD) analysis of the Van Hove space–time self-correlation function (STSCF) with a newly developed quantum correction named as Gaussian approximation-assisted quantum correction (GAAQC). The self-intermediate scattering function (SISF) by GAAQC satisfies the detailed balance condition and sum rules up to second order adequately, and approaches for long times the one obtained directly from MD trajectory data. These features are desirable for the evaluation of the neutron scattering cross-section over a wide range of energy and momentum transfer. From the analysis of quasi-elastic scattering, the self-scattering law by GAAQC shows the jump-diffusive behavior of the molecular translational motion, which is not reproduced by Gaussian approximation (GA). As compared with GA, double differential and total cross-sections by GAAQC show better agreement with experimental data, particularly below the cold neutron region where the non-Gaussian property of the SISF becomes apparent. Thus, the present method, namely, the direct analysis of the STSCF with GAAQC will serve for improving the evaluation of the neutron scattering cross-section for light water.

Tribochemistry of Phosphoric Acid Sheared between Quartz Surfaces: A Reactive Molecular Dynamics Study

Tribochemical processes have profound consequences on tribological performance. In the present paper, the tribochemical mechanism of low friction state in the silica/phosphoric acid system is elucidated by reactive molecular dynamics (ReaxFF) simulations. The friction coefficient is found having strong positive correlation with the number of interfacial hydrogen bonds, which suggests that a weaker interfacial hydrogen bond network would favor a lower friction. The friction reduction mechanisms have been analyzed in two temperature regimes: For 300 ≤ T ≤ 600 K, no indication of tribochemical reaction is observed, and the friction coefficient decreases because of the accelerated molecular rotational and translational motion and the corresponding weakened hydrogen bond network. For 800 K ≤ T ≤ 1400 K, the occurrence of tribochemical reactions leads to a clustering and polymerization of the phosphoric acid molecules and generation of a considerable quantity of water molecules distributed mainly in the sliding...

Accelerating the Phase Separation in Aqueous Poly(N-isopropylacrylamide) Solutions by Slight Modification of the Polymer Stereoregularity: A Single Molecule Fluorescence Study

We discovered for aqueous thermoresponsive polymer solutions that only a slight change in stereoregularity of the polymer can drastically accelerate phase separation. Single molecule fluorescence tracking (SMT) for an isotactic-slight-rich (meso-diad-rich) polymer sample solution revealed an interpolymer nanonetwork even before phase separation, and also revealed a novel phase in which translational molecular motion was frozen after phase separation. For such systems, fluorescence correlation spectroscopy (FCS) provided quantitative information on molecular diffusion. The results on FCS well agreed with the interpolymer nanonetwork model that was proposed on the basis of SMT measurement. We demonstrate such a novel method to control phase separation dynamics and also the interpolymer nanonetwork model.

Excess heat capacity in glass-forming liquid systems containing molecules

Excess heat capacities at glass transition temperature in two types of glass-forming systems of [xNaNO3·(1−x)KNO3]60·[Ca(NO3)2]40 (0 ⩽ x ⩽ 1) and Ca(NO3)2·yH2O (4⩽y⩽13) are studied. In the former system, with the replacement of K+ cation with Na+ cation, the excess heat capacity is around 65.1 J·mol−1·K−1, while the excess increases by 38.9 J·mol−1·K−1 upon one molar H2O content in latter system. A quantitative description to the excess heat capacity is built up with the thermal effects of atomic and molecular translational motion in liquids. The results might offer a further understanding to the glass transition.

Solid-State NMR in Macromolecular Systems: Insights on How Molecular Entities Move

The function of synthetic and natural macromolecularsystems critically depends on the packing and dynamics of the individual components of a given system. Not only can solid-state NMR provide structural information with atomic resolution, but it can also provide a way to characterize the amplitude and time scales of motions over broad ranges of length and time. These movements include molecular dynamics, rotational and translational motions of the building blocks, and also the motion of the functional species themselves, such as protons or ions. This Account examines solid-state NMR methods for correlating dynamics and function in a variety of chemical systems. In the early days, scientists thought that the rotationalmotions reflected the geometry of the moving entities. They described these phenomena as jumps about well-defined axes, such as phenyl flips, even in amorphous polymers. Later, they realized that conformational transitions in macromolecules happen in a much more complex way. Because the individual entities do not rotate around well-defined axes, they require much less space. Only recently researchers have appreciated the relative importance of large angle fluctuations of polymers over rotational jumps. Researchers have long considered that cooperative motions might be at work, yet only recently they have clearly detected these motions by NMR in macromolecular and supramolecular systems. In correlations of dynamics and function, local motions do not always provide the mechanism of long-range transport. This idea holds true in ion conduction but also applies to chain transport in polymer melts and semicrystalline polymers. Similar chain motions and ion transport likewise occur in functional biopolymers, systems where solid-state NMR studies are also performed. In polymer science, researchers have appreciated the unique information on molecular dynamics available from advanced solid-state NMR at times, where their colleagues in the biomacromolecular sciences have emphasized structure. By contrast, following X-ray crystallographers, researchers studying proteins using solution NMR introduced the combination of NMR with computer simulation before that became common practice in solid-state NMR. Today's simulation methods can handle partially ordered or even disordered systems common in synthetic polymers. Thus, the multitechnique approaches employed in NMR of synthetic and biological macromolecules have converged. Therefore, this Account will be relevant to both researchers studying synthetic macromolecular and supramolecular systems and those studying biological complexes.

Transport coefficients of the TIP4P-2005 water model

A detailed understanding of the dynamics of liquid water at molecular level is of fundamental importance as well as have applications in many branches of science and technology. In this work, the diffusion of the TIP4P-2005 model of water is systematically investigated in liquid phase in the temperature range 210-310 K. The translational and rotational diffusions, as well as correlations between them, are examined. The effects of system size and shape are also probed in this study. The results suggest the presence of a temperature of dynamical arrest of molecular translations in the range of 150-180 K and of molecular rotations in the range of 80-130 K, depending on specific direction. A substantial change in the preferred directions of translations and rotations relative to the molecular coordinate system is observed slightly below (≈15 K) the melting temperature of the model. It is shown that there is a correlation between translational and rotational molecular motions essential for diffusion in the liquid. The presence of hydrodynamic size effects is confirmed and quantified; it is also shown that using a non-cubic simulation box for a liquid system leads to an anisotropic splitting in the diffusion tensor. The findings of this study enhance our general understanding of models of water, specifically the TIP4P-2005 model, as well as provide evidences of the direct connection between thermodynamics of liquid water and dynamics of its molecules.

3.0T MR diffusion-weighted imaging: evaluating diagnosis potency of pulmonary solid benign lesions and malignant tumors and optimizing b value

背景与目的磁共振扩散加权成像（diffusion-weighted imaging, DWI）是唯一能在活体检测组织内水分子扩散运动的无创影像检查技术，能在宏观成像中反映活体组织中水分子的微观扩散运动。本研究旨在探讨3.0T磁共振成像（magnetic resonance imaging, MRI）DWI联合相控阵线圈和并行阵列采集空间敏感度编码技术（array spatial sensitivity encoding technique, ASSET）对肺实性良恶性病变的鉴别诊断效能，并优化最佳b值。方法经病理或临床随访证实的20例肺良性病变和96例肺恶性肿瘤（共120个病灶）在3.0T MR扫描仪上行T2加权像（T2 weighted imaging, T2WI）、T1加权像（T1 weighted imaging, T1WI）、脂肪抑制T2WI以及不同b值DWI（200 s/mm2、500 s/mm2、800 s/mm2、1, 000 s/mm2）扫描，得到各b值的DWI图和表观扩散系数（apparent diffusion coefficient, ADC）图，分别测量各b值下病变的DWI信号强度、ADC值，比较各b值组的信噪比（signal-to-noise ratio, SNR）、对比噪声比（contrast-to-noise ratio, CNR）、ADC值，并绘制各b值的受试者操作特征曲线（receiver operating characteristic curve, ROC），得出ADC值对肺实性良恶性病变的鉴别诊断效能，优化DWI诊断肺部实性良恶性病变的最佳b值。结果不同b值组间SNR、CNR差异均有统计学意义（P < 0.001, P=0.002）。肺良性和恶性病变组ADC值均随b值增加而逐渐变小，差异有统计学意义（P < 0.001, P < 0.001）。4组不同b值的ROC曲线下面积（area under curve, AUC）分别为0.831、0.876、0.813、0.785，均有诊断意义（AUC > 0.5）；b=500 s/mm2时获得的ADC值的诊断效能最大，鉴别良恶性病变的最佳阈值为1.473×10-3 mm2/s，敏感度和特异度分别为80%和84%。结论3.0T MR DWI联合相控阵线圈和ASSET技术对肺实性良恶性病变的鉴别诊断有较高价值，b=500 s/mm2时获得的ADC值诊断效能较高。

Intermolecular Electron Density Modulations in Water and Their Effects on the Far-Infrared Spectral Profiles at 6 THz

The modulations in the electron density induced by molecular motions are analyzed theoretically for tetrahedrally hydrogen-bonded water molecules. Those modulations are represented as the electron density derivatives, and their forms are examined by the use of the one- and two-dimensional integrated plots. It is shown that intermolecular flux of electrons, called intermolecular charge flux, is induced by the molecular translation modes in water, leading to the infrared intensity at 6 THz. This means that the molecular translational and electronic motions are strongly coupled, and this coupling is observable through this vibrational band. A comparison is made with the case of the OH stretching mode. A method to incorporate this effect in spectral simulations based on classical molecular dynamics is also shown. These results provide a way to correct understanding of dynamics in, for example, aqueous solutions of biomolecules from analyses of their vibrational spectra in the terahertz frequency region. A general idea on how we can perform reasonable calculations and analyses of the vibrational spectral profiles of liquid systems is also discussed.

Enhancement of photoacoustic emission through terahertz-field-driven electron motions

We report the study of enhanced photoacoustic emission from a laser-induced plasma under the influence of the terahertz field up to 100 kV/cm. We theoretically and experimentally investigate the energy transfer from terahertz radiation to molecular translational motion, through terahertz-field-driven electron motion and inelastic electron-molecule collision. The enhanced photoacoustic emission in the frequency range of 1-140 kHz is quadratically dependent on the incident terahertz field. We also demonstrate, as an application, that the enhancement of photoacoustic emission from gases asymmetrically ionized by two-color laser field can be used for coherent terahertz wave detection.

Nanopumping molecules via a carbon nanotube

We demonstrate the feasibility of using a carbon nanotube to nanopump molecules. Molecular dynamics simulations show that the transport and ejection of a C20 molecule via a single-walled carbon nanotube (SWNT) can be achieved by a sustained mechanical actuation driven by two oscillating tips. The optimal condition for nanopumping is found when the tip oscillation frequency and magnitude correlate to form quasi steady-state mechanical wave propagation in the SWNT, so that the energy transfer process is optimal leading to maximal molecular translational motion and minimal rotational motion. Our finding provides a potentially useful mechanism for using an SWNT as a vehicle to deliver large drug molecules.