Time Scale Of Molecular Motions Research Articles

Melting and Bubble Formation in a Double-Stranded DNA: Microscopic Aspects of Early Base-Pair Opening Events and the Role of Water.

Despite its rigid structure, DNA is a remarkably flexible molecule. Flexibility is essential for biological functions (such as transcription and gene repair), which require large-amplitude structural changes such as bubble formation. The bubbles thus formed are required to have a certain stability of their own and survive long on the time scale of molecular motions. A molecular understanding of fluctuations leading to quasi-stable structures is not available. Through extensive atomistic molecular dynamics simulations, we identify a sequence of microscopic events that culminate in local bubble formation, which is initiated by base-pair (BP) opening, resulting from the cleavage of native BP hydrogen bonds (HBs). This is followed by the formation of mismatched BPs with non-native contacts. These metastable structures can either revert to their original forms or undergo a flipping transition to form a local bubble that can span across 3-4 BPs. A substantial distortion of the DNA backbone and a disruption of BP stacking are observed because of the structural changes induced by these local perturbations. We also explored how water helps in the entire process. A small number of water molecules undergo rearrangement to stabilize the intermediate states by forming HBs with DNA bases. Water thus acts as a lubricant that counteracts the enthalpic penalty suffered from the loss of native BP contacts. Although the process of bubble formation is reversible, the sequence of steps involved poses an entropic barrier, preventing it from easily retracing the path to the native state.

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.

Ultrafast Nanoscale Raman Thermometry Proves Heating Is Not a Primary Mechanism for Plasmon-Driven Photocatalysis.

Plasmonic materials efficiently convert light to various forms of energies for many applications, including photocatalysis, photovoltaics, and photothermal therapies. In particular, plasmonic photocatalysts hold incredible promise for highly selective sunlight-driven catalysis through the generation of highly energetic holes and electrons used to drive chemical reactions. However, plasmons are also known to generate heat, and the partitioning of photoexcitation energy into hot carriers and heat on molecularly relevant time scales is not well understood, yet plays a crucial role in designing and understanding these photocatalysts. Using an ultrafast surface-enhanced Raman thermometry technique, we probe the effective temperature, equivalent to the mode-specific increase of vibrational kinetic energy, of molecules adsorbed to gold nanoparticle aggregates in the most active hot spots on the picosecond time scale of chemical reactivity. This represents the first measurement of vibrational energy deposition for coupled molecular-plasmonic systems on the picosecond time scale of molecular motion. We find that upon plasmon excitation, the adsorbates in the hot spots undergo an initial energy transfer within several picoseconds that changes the effective temperature of the system by less than 100 K, even at peak flux values 108 times stronger than focused sunlight. The energy quickly dissipates from the adsorbates into the surroundings in less than 5 ps, even at the highest values of photoexcitation. This surprisingly modest energy transfer of the most active regions of the plasmonic materials on the ultrafast time scale decisively proves that most plasmonic photocatalysis is not primarily thermally driven.

Coupling Protein Dynamics with Proton Transport in Human Carbonic Anhydrase II.

The role of protein dynamics in enzyme catalysis is one of the most highly debated topics in enzymology. The main controversy centers around what may be defined as functionally significant conformational fluctuations and how, if at all, these fluctuations couple to enzyme catalyzed events. To shed light on this debate, the conformational dynamics along the transition path surmounting the highest free energy barrier have been herein investigated for the rate limiting proton transport event in human carbonic anhydrase (HCA) II. Special attention has been placed on whether the motion of an excess proton is correlated with fluctuations in the surrounding protein and solvent matrix, which may be rare on the picosecond and subpicosecond time scales of molecular motions. It is found that several active site residues, which do not directly participate in the proton transport event, have a significant impact on the dynamics of the excess proton. These secondary participants are shown to strongly influence the active site environment, resulting in the creation of water clusters that are conducive to fast, moderately slow, or slow proton transport events. The identification and characterization of these secondary participants illuminates the role of protein dynamics in the catalytic efficiency of HCA II.

Probing the two-stage transition upon crossing the glass transition of polystyrene by solid-state NMR

A two-stage transition upon crossing the glass transition of polystyrene with increasing temperature was precisely determined and interpreted by using solid-state nuclear magnetic resonance (SSNMR), 1H-1H dipolar couplings based double quantum-filtered (DQF) and dipolar filter (DF) experiments and 13C chemical shift anisotropy (CSA) based centerband-only detection of exchange (CODEX) experiment are used to fully characterize the time scale of molecular motions during the glass transition. While differential scanning calorimetry (DSC) and CODEX experiment predicted the first stage of glass transiton, DQF and DF experiments provided the evidence for the second stage transition during which the time scale of molecular motions changed from very slow (t > ms) to very fast (t < µs). The first stage of glass transition begins with the occurrence of remarkable slow re-orientation motions of the polymer backbone segments and ends when the degree of slow motion reaches maximum. The onset and endpoint of the conventional calorimetric glass transition of polystyrene can be quantitatively determined at the molecular level by SSNMR. In the second stage, a subsequent dramatic transition associated with the melting of the glassy components was observed. In this stage liquid-like NMR signals appeared and rapidly increased in intensity after a characteristic temperature T f (~1.1T g). The signals associated with the glassy components completely disappeared at another characteristic temperature T c (~1.2T g).

Femtosecond spin-state photo-switching dynamics in an FeIII spin crossover solid accompanied by coherent structural vibrations

Femtosecond optical spectroscopy reveals coherent structural trapping accompanying spin-state photoswitching in a FeIII spin-crossover material.

Structural Dynamics of Hydrated Phospholipid Surfaces Probed by Ultrafast 2D Spectroscopy of Phosphate Vibrations.

The properties of biomembranes depend in a decisive way on interactions of phospholipids with hydrating water molecules. To map structural dynamics of a phospholipid-water interface on the length and time scale of molecular motions, we introduce the phospholipid symmetric and asymmetric phosphate stretch vibrations as probes of interfacial hydrogen bonds and electrostatic interactions. The first two-dimensional infrared spectra of such modes and a line shape analysis by density matrix theory reveal two distinct structural dynamics components; the first 300 fs contribution is related to spatial fluctuations of charged phospholipid head groups with additional water contributions at high hydration levels; the second accounts for water-phosphate hydrogen bonds persisting longer than 10 ps. Our results reveal a relatively rigid hydration shell around phosphate groups, a behavior relevant for numerous biomolecular systems.

Molecular dynamics and crystallization phenomenon of supercooled and glassy DNA and RNA nucleosides:β-adenosine,β-thymidine, andβ-uridine

Nucleosides are chemical compounds that have an extremely important biological role; they can be found in all types of living organisms. They are crucial components from which DNA and RNA acids are built. In addition, nucleosides are key regulators of many physiological processes. In this paper, the molecular dynamics in the liquid and glassy state of three selected nucleosides, β-adenosine, β-thymidine, and β-uridine, was investigated by means of dielectric spectroscopy. Our results revealed multiple relaxation processes associated with different types of molecular motions. Besides the primary α relaxation, two secondary modes in the glassy states of examined compounds were identified. Crystallization progress monitored by dielectric spectroscopy and x-ray diffraction technique at isostructural relaxation conditions revealed that the examined nucleosides possess completely different tendencies to recrystallize from the liquid as well as the glassy state. We have also made an attempt to predict the time scale of molecular motion below the glass transition temperatures of the respective nucleosides to discuss their potential stability at room temperature over prolonged storage time. Finally, combination of molecular mobility studies with evaluation of thermodynamic parameters from calorimetric measurements allowed us to discuss the fundamental roles of both kinetic and thermodynamic factors in governing the physical stability of the glassy state.

Sucrose in aqueous solution revisited, Part 2: Adaptively biased molecular dynamics simulations and computational analysis of NMR relaxation

We report 100 ns molecular dynamics simulations, at various temperatures, of sucrose in water (with concentrations of sucrose ranging from 0.02 to 4M), and in a 7:3 water-DMSO mixture. Convergence of the resulting conformational ensembles was checked using adaptive-biased simulations along the glycosidic Φ and ψ torsion angles. NMR relaxation parameters, including longitudinal (R₁) and transverse (R₂) relaxation rates, nuclear Overhauser enhancements (NOE), and generalized order parameter (S²) were computed from the resulting time-correlation functions. The amplitude and time scales of molecular motions change with temperature and concentration in ways that track closely with experimental results, and are consistent with a model in which sucrose conformational fluctuations are limited (with 80-90% of the conformations having ϕ-ψ values within 20° of an average conformation), but with some important differences in conformation between pure water and DMSO-water mixtures.

Lipid aggregate formation at an oscillating bubble surface: A simulation study

We perform a molecular dynamics simulation study of the behavior of a lipid coating layer on an oscillating bubble surface. Micrometer sized bubbles, stabilized with a lipid monolayer coating, are used in acoustic imaging as a contrast agent. The coating layer is expected to be strongly influenced by the oscillation of the bubble in the high frequency sound field, with a period of a microsecond. The typical time scale of molecular motion, however, is of the order of femtoseconds. One of the challenges is to bridge this nine decade gap in time scales. To this end we have developed a model that is highly coarse grained, but still features the essential mechanisms determining lipid dynamics, with time scales of picoseconds. This approach allows us to severely restrict the computing times, although we make use of very modest computing equipment. We show in our simulation that the amphiphilic monolayer folds upon contraction of the bubble, and forms micellar aggregates at the air-water interface. Some micellar structures survive consecutive re-expansion and indeed remain persistent over several cycles. These structures may add to the anisotropic behavior of the bubbles under oscillating conditions. We also investigated temperature and frequency dependence.

Surface-Enhanced Femtosecond Stimulated Raman Spectroscopy.

Surface-enhanced Raman spectroscopy (SERS) and femtosecond stimulated Raman spectroscopy (FSRS) have revolutionized the Raman spectroscopy field. SERS provides spectroscopic detection of single molecules, and FSRS enables the acquisition of Raman spectra on the ultrafast time scale of molecular motion. Here, we present the first successful combination of these two techniques, demonstrating surface-enhanced femtosecond stimulated Raman spectroscopy (SE-FSRS) using gold nanoantennas with embedded reporter molecules. Using a picosecond Raman and femtosecond probe pulse, the time- and ensemble-averaged enhancement factor is estimated to be in the range of 10(4)-10(6). We report the line shapes, power dependence, and magnitude of the SE-FSRS signal and discuss contributions to sample degradation on the minute time scale. With these first successful proof-of-principle experiments, time-resolved SE-FSRS techniques can now be rationally attempted with the goals of investigating the dynamics of plasmonic materials as well as examining the contributions of environmental heterogeneities by probing more homogeneous molecular subsets.

Molecular mobility in liquid and glassy states of Telmisartan (TEL) studied by Broadband Dielectric Spectroscopy

The molecular relaxation in liquid and glassy states of Telmisartan (TEL) has been studied by Broadband Dielectric Spectroscopy (BDS) covering wide temperature and frequency range. Multiple relaxation processes were observed. Besides the primary α-relaxation, two secondary relaxations β and γ (labelled in order of decreasing time scale) have been reported. Well-separated β-process observed above and below glass transition temperature T g , has activation energy E β = 81.8 kJ/mol and was identified as intermolecular Johari–Goldstein (JG) process. The γ-relaxation visible in dielectric loss spectra at very low temperatures is most likely non-JG relaxation. The temperature dependence of the relaxation times of α-process, measured over 11 orders of magnitude, cannot be described by a single Vogel–Fulcher–Tamman–Hesse (VFTH) equation. At temperature T B = 475.8 K the change in relaxation dynamics occurred, consequently a new set of VFTH parameters was required. From low temperature VFTH fits the glass transition temperature T g was estimated as T g = 400.3 K and fragility index m = 87 was calculated. Of particular interest was the time scale of molecular motion below the glass transition temperature. Our observation clearly indicates that the α-relaxation times at room temperature most probably would exceed 3 years and amorphous TEL should maintain physically and chemically stable over prolonged storage time.

Dynamics of the biopolymers in articular cartilage studied by magic angle spinning NMR

To understand the viscoelastic properties of cartilage tissue and for the development of tissue-engineered cartilage, we have studied the physicochemical properties of bovine nasal and pig articular cartilage by13C nuclear magnetic resonance (NMR) methods. The major macromolecular components of cartilage can be investigated individually by applying13C high-resolution (HR) NMR with scalar decoupling (for the polysaccharide component) and solid-state NMR with dipolar decoupling (for the collagen component). Partially resolved NMR spectra of the cartilage polysaccharides can be obtained by HR13C NMR indicating that these polysaccharides are highly mobile. Resonance lines have been assigned to chondroitin sulfate, the most mobile component of cartilage. To characterize time scales of molecular motions, we have measuredT 1 andT 2 relaxation times as a function of temperature and analyzed these data by means of a broad distribution of molecular correlation times. Typical correlation times for the large amplitude motions of chondroitin sulfate are of the order of 0.1–10 ns. For the detection and dynamical characterization of the cartilage collagen cross-polarization magic angle spinning (CP MAS) and high-power decoupling are indispensable.13C CP MAS spectra of cartilage are dominated by resonances from rigid collagen, while only low-intensity signals from the polysaccharides are observed. The good sensitivity at a magnetic field strength of 17.6 T allows the site-specific investigation of cartilage collagen dynamics by two-dimensional NMR methods. The cartilage collagen is essentially rigid with low-amplitude segmental motions on the fast time scale. Considering the high water content of cartilage and the almost isotropic mobility of the chondroitin sulfate molecules it is remarkable how little this affects the collagen dynamics. The dynamics of cartilage macromolecules is broadly distributed from almost completely rigid to highly mobile, which lends cartilage its mechanical strength and shock-absorbing properties.

Measurement of heat capacity to gain information about time scales of molecular motion from pico to megaseconds

Molecular motion has primarily a time scale of picoseconds. Quantum mechanical models of small-amplitude vibrations and local, large-amplitude motions can be fitted quantitatively to equilibrium heat capacities. Macroscopic calorimetry, thus yields indirectly the characteristic frequencies of molecular motion in the range of 10 11–10 13 Hz. At lower temperature, much of the large-amplitude molecular motion is restricted to cooperative movements and slows to macroscopic times so that calorimetry can directly measure the kinetics of these changes which may extend the time scales to megaseconds and beyond. In this light, instrumentation and interpretation of differential scanning temperature-modulated calorimetry (DSTMC) are discussed. Six basic thermal effects govern the thermal analysis of linear macromolecules: (1) the vibrational heat capacity; (2) heat capacities arising from large amplitude molecular motion; (3) reversible transitions; (4) annealing; (5) secondary crystallization and (6) primary crystallization. Of these only (1)–(3) are reversible. To these six thermal effects that do not change the molecular integrity, chemical reactions, evaporation, and condensation have to be added for a full thermal analysis. The latter effects have not been treated in this paper.

Recent advances in prethermal chemistry: real-time probing of elementary electron transfer reactions

In liquids and electrolyte solutions, elementary radical reactions may be investigated on the time scale of molecular motions by femtosecond visible-IR absorption spectroscopy. Some studies devoted to the microscopic understanding of sub-picosecond prehydration electron transfer between an aqueous halide ion (Cl-) and ionic acceptors (Cd++, H+) are presented. Within an electron hydration regime, the one-electron reduction of a metallic ion or a hydrated proton (hydronium or dihydronium ion) is totally achieved in less than 2 × 10-12 s at 294 K. The consequences of an early partition between reactive and nonreactive IR electronic pathways on the electron hydration process are discussed.

Characterization of the Time Scales of Molecular Motion in Pharmaceutically Important Glasses

Increased interest in molecular time scales below the glass transition temperature, Tg, has arisen from the desire to identify the conditions (e.g., temperature) where the molecular processes which lead to unwanted changes in amorphous systems (e.g., chemical reactivity, crystallization, structural collapse) are improbable. The purpose of this study was to characterize the molecular mobility of selected amorphous systems (i.e., indomethacin, sorbitol, sucrose, and trehalose) below Tg using a combined experimental and theoretical approach. Of particular interest was the temperature where the time scales for molecular motion (i.e., relaxation time) exceed expected lifetimes or storage times. As a first approximation of this temperature, the temperature where the thermodynamic properties of the crystal and the equilibrium supercooled liquid converge (i.e., the Kauzmann temperature, TK) was determined. TK values derived from heat capacity and enthalpy of fusion data ranged from 40 to 190 K below the calorimet...

Neutron transmission and quasi‐elastic neutron scattering in polymer hydrogels

AbstractInvestigations of hydrogels with high water contents have recently acquired special significance. Hydrogels are crosslinked three‐dimensional networks of water‐soluble macromolecules saturated by water or water solutions of different substances. The interest in examination the fundamental physical properties for such systems is related to their numerious applications. Using neutron transmission and quasi‐elastic neutron scattering (QENS), the mass transfer and self‐diffusion processes of water and water solutions in gelatin and poly(acrylamide) hydrogels were studied. It was shown that the macroscopic liquid flow through network of quasi‐porous polymer gels at relatively low pressure gradients as well as self‐diffusion of water and water solutions in the above systems are adequately described by “effective medium” approach. QENS data were also interpreted using an approach that accounts for the hierarchy of time scales of molecular motions: slow collective motions of liquid molecules contained in Lagrange's clusters and rapid single‐particle motions. The friction and self‐diffusion coefficient data were used to estimate the effective pore sizes of gels at different polymer concentrations as well as the mean Lagrange's cluster sizes.

Liquid Interfaces Probed by Second-Harmonic and Sum-Frequency Spectroscopy.

A powerful approach to the study of interfaces has been developing rapidly in the past decade. It is based on the spectroscopic methods of second-harmonic (SHG) and sum-frequency generation (SFG). These nonlinear optical techniques, being spectroscopic, provide information at the most fundamental level. A microscopic description of equilibrium and dynamic interface processes requires knowledge of the molecules at the interface, their orientational structure, the energetics that drive chemical and physical processes, and the time scale of molecular motions and relaxation processes. The techniques of second-harmonic and sum-frequency generation have made it possible to selectively probe the chemistry, physics, and biology of gas/liquid, liquid/liquid, liquid/solid, gas/solid, and solid/solid interfaces at the molecular level. In this abbreviated article only liquid interfaces will be considered; gas/solid and solid/solid interfaces are not included. This restriction is necessary because of the enormous increase in SH and SF studies in recent years, which makes it extremely difficult to properly discuss the range of work being carried out around the world. Unfortunately not all of the fine work even in the area of liquid interfaces has been included because of both space and time limitations. A number of review articles are referred to which cover some ofmore » the research material not covered in this article. 99 refs.« less

Solid-state NMR study of protein/polypeptide backbone fluctuations interpreted by multiple trapping diffusion of dilating defects

Diverse proteins and polypeptides have been studied by proton field-cycling relaxation spectroscopy and-after deuterium exchange-by solid-state deuteron NMR. These techniques cover very different and partially complementary time scales of molecular motions spread over many orders of magnitude. On the other hand, deuteron NMR is predominantly sensitive to rotational fluctuations, while proton NMR can be affected by translational displacements in addition. The latter type of motion is considered to be connected with the multiple trapping diffusion mechanism of dilating defects in the protein structure. In particular the mean-square displacement of the diffusing defects is expected to obey a nonlinear time dependence (“anomalous diffusion”). This concept enables us to explain simultaneously (a) the small amplitudes of rotational backbone fluctuations as far as can be judged by the diverse deuteron experiments, (b) the existence of translational backbone fluctuations concluded from the proton TI dispersion measurements, and (c) the peculiar v3I4 frequency dependence evident for the proton spin-lattice relaxation time in the vicinity of room temperature. In the limit far below room temperature, indications of a crossover to a fractal time process appear.

Paramagnetic nuclear relaxation study of the structure and dynamics of lyotropic lamellar phases

Abstract Lamellar phases of double tailed sodium alkyl-phosphates/water systems have been investigated by 31 P and 13 C relaxations enhanced by paramagnetic divalent ions exchanging rapidly among the polar heads of the surfactant molecules. In order to extract both structural and dynamic information from these experiments, the paramagnetic probes have been chosen such that their electron spin-lattice relaxation times are significantly larger (Mn2+, VO2+) or smaller (Ni2+) than the time scales of molecular motions generally found in the 0.1-2.0 ns range. The paramagnetic relaxation of surfactant nuclei results from intra- and intermolecular contributions, the latter corresponding to dipolar interactions in a two dimensional lattice. The sum of these contributions has been computed as an average over all accessible conformers resulting from the trans-gauche isomerizations of alkyl chains and fitted to the experimental relaxation rates at several magnetic field strengths. This procedure allows the determination of the populations of the main conformers, of the reorientational correlation times and of the lateral diffusion coefficient of the surfactant, which are sometimes difficult to obtain by other N.M.R. methods.