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Materials 10(2), 208 (2017). doi:10.18154/RWTH-2017-03760, Published by MDPI, Basel

The processes governing multilayer nucleation in the chemical vapour deposition (CVD) of graphene are important for obtaining high-quality monolayer sheets, but remain poorly understood. Here we show that higher-order carbon species in the gas-phase play a major role in multilayer nucleation, through the use of in-situ ultraviolet (UV) absorption spectroscopy. These species are the volatilized products of reactions between hydrogen and carbon contaminants that have backstreamed into the reaction chamber from downstream system components. Consequently, we observe a dramatic suppression of multilayer nucleation when backstreaming is suppressed. These results point to an important and previously undescribed mechanism for multilayer nucleation, wherein higher-order gas-phase carbon species play an integral role. Our work highlights the importance of gas-phase dynamics in understanding the overall mechanism of graphene growth.

Cell viability and cytotoxicity assays are highly important for drug screening and cytotoxicity tests of antineoplastic or other therapeutic drugs. Even though biochemical-based tests are very helpful to obtain preliminary preview, their results should be confirmed by methods based on direct cell death assessment. In this study, time-dependent changes in quantitative phase-based parameters during cell death were determined and methodology useable for rapid and label-free assessment of direct cell death was introduced. The goal of our study was distinction between apoptosis and primary lytic cell death based on morphologic features. We have distinguished the lytic and non-lytic type of cell death according to their end-point features (Dance of Death typical for apoptosis versus swelling and membrane rupture typical for all kinds of necrosis common for necroptosis, pyroptosis, ferroptosis and accidental cell death). Our method utilizes Quantitative Phase Imaging (QPI) which enables the time-lapse observation of subtle changes in cell mass distribution. According to our results, morphological and dynamical features extracted from QPI micrographs are suitable for cell death detection (76% accuracy in comparison with manual annotation). Furthermore, based on QPI data alone and machine learning, we were able to classify typical dynamical changes of cell morphology during both caspase 3,7-dependent and -independent cell death subroutines. The main parameters used for label-free detection of these cell death modalities were cell density (pg/pixel) and average intensity change of cell pixels further designated as Cell Dynamic Score (CDS). To the best of our knowledge, this is the first study introducing CDS and cell density as a parameter typical for individual cell death subroutines with prediction accuracy 75.4% for caspase 3,7-dependent and -independent cell death.

It has recently been shown that diluting a semiconducting polymer with an insulating or large band gap host material can lead to elimination of charge trapping in the former. In this work we systematically study the role of the phase thermodynamics of such blends via tuning the miscibility between the semiconductor (here: MEH-PPV) and host (here: polystyrene or polyvinyl carbazole), by varying the molecular weight of the latter. We show that calculation of the ternary phase diagram of semiconductor, insulator and solvent can predict whether charge transport in the dry blend film will be trap-free or not. Blending MEH-PPV with 35 kg mol−1 polystyrene does not lead to alleviation of the trap-limited nature of the electron current due to strong segregation of the polymers and the formation of pure coexisting phases. In contrast, the electron current in miscible (1 kg mol−1 polystyrene) or partially miscible (30 kg mol−1 polyvinyl carbazole) blends increases by up to four orders of magnitude compared to the pristine semiconductor, together with a doubling in luminous efficiency of the corresponding light-emitting diode.

We report on $\hbox{YBa}_{2}\hbox{Cu}_{3}\hbox{O}_{7-x} $ biepitaxial grain boundary Josephson junctions (JJs) demonstrating significant tunability of their circuital parameters. We show how the enhanced control of the junction properties, and particularly of the capacitance, leads to advances in the understanding of phase dynamics of high-critical-temperature superconductor JJs and potentially of their intrinsic dissipation mechanisms.

We investigate the competition between intersystem crossing (ISC) and internal conversion (IC) as nonradiative relaxation pathways in cyclic alpha,beta-unsaturated enones following excitation to their lowest lying (1)pi pi* state, by means of time-resolved photoelectron spectroscopy and ab initio computation. Upon excitation, the (1)pi pi* state of 2-cyclopentenone decays to the lowest lying (1)pi pi* state within 120 +/- 20 fs. Within 1.2 +/- 0.2 ps, the molecule subsequently decays to the triplet manifold and the singlet ground state, with quantum yields of 0.35 and 0.65, respectively. The corresponding dynamics in modified derivatives, obtained by selective methylation, show a decrease in both IC and ISC rates, with the quantum yields of ISC varying between 0.35 and 0.08. The rapid rates of ISC are explained by a large spin orbit coupling of 45-60 cm(-1) over an extended region of near degeneracy between the singlet and triplet state. Furthermore, the rate of IC is depressed by the existence of a well-defined minimum on the (1)n pi* potential energy surface. The nonadiabatic pathways evinced by the present results highlight the fact that these molecular systems conceptually represent "intermediate cases" between ultrafast dynamics mediated by vibrational motions at conical intersections versus those by statistical decay mechanisms.

This paper investigates the linear and non-linear instabilities during evaporation of liquid layers and droplets by means of two-phase 3D direct numerical simulations. The interface is open to the atmosphere under the consideration that vapour diffusion is the rate- limiting mechanism for evaporation. In both configurations, the vapour-liquid interface is prone to travelling thermal instabilities, i.e., hydrothermal waves (HTWs), due to the presence of temperature gradients along the interface. We have already shown in our recent work 7 that under saturated conditions (negligible evaporation) the HTWs additionally give rise to interface deformations of similar features, i.e., physical waves. We have also demonstrated 8 that phase change plays a dual role through its effect on these instabilities: the latent energy required during the evaporation process tends to inhibit the HTWs while the accompanying level reduction enhances the physical waves by minimizing the role of gravity. The dynamics of the gas phase are also discussed. We have also established that the HTW-induced convective patterns in the gas along with the travelling nature of the instabilities have a significant impact on the local evaporation flux and the vapour distribution above the interface. The Marangoni effect plays a major role in the vapour distribution generating a vacuum effect in the warm region and vapour accumulations at the cold boundary capable of inverting the phase change, i.e., the capillary flow can lead to local condensation. These results provide evidence of the inefficiencies of the traditional phase change models based on pure vapour diffusion to capture the dynamics of thermocapillary flows. To conclude, we also present results of a parallel investigation focusing on three-dimensional phenomena on evaporating sessile drops placed on heated substrates.

Incorporating quantum mechanics into an atomistic simulation necessarily involves solving the Schroedinger equation. Unfortunately, the computational expense associated with solving this equation scales miserably with the number of included quantum degrees of freedom (DOF). The situation is so dire, in fact, that a molecular dynamics (MD) simulation cannot include more than a small number of quantum DOFs before it becomes computationally intractable. Thus, if one were to simulate a relatively large system, such as one containing several hundred atoms or molecules, it would be unreasonable to attempt to include the effects of all of the electrons associated with all of the components of the system. The mixed quantum/classical (MQC) approach provides a way to circumvent this issue. It involves treating the vast majority of the system classically, which incurs minimal computational expense, and reserves the consideration of quantum mechanical effects for only the few degrees of freedom more directly involved in the chemical phenomenon being studied. For example, if one were to study the bonding of a single diatomic molecule in the gas phase, one could employ a MQC approach by treating the nuclei of the molecule's two atoms classically—including the deeply bound, low-energy electrons that change relatively little—and solving the Schroedinger equation only for the high energy electron(s) directly involved in the bonding of the classical cores. In such a way, one could study the bonding of this molecule in a rigorous fashion while treating only the directly related degrees of freedom quantum mechanically. Pseudopotentials are then responsible for dictating the interactions between the quantum and classical degrees of freedom. As these potentials are the sole link between the quantum and classical DOFs, their proper development is of the utmost importance. This Thesis is concerned primarily with my work on the development of novel, rigorous and dynamical pseudopotentials for use in mixed quantum/ classical simulations in the condensed phase. The pseudopotentials discussed within are constructed in an ab initio fashion, without the introduction of any empiricism, and are able to exactly reproduce the results of higher level, fully quantum mechanical Hartree-Fock calculations. A recurring theme in the following pages is overcoming the so-called frozen core approximation (FCA). This essentially comes down to creating pseudopotentials that are able to respond in some way to the local molecular environment in a rigorous fashion. The various methods and discussions that are part of this document are presented in the context of two particular systems. The first is the sodium dimer cation molecule, which serves as a proof of concept for the development of coordinate-dependent pseudopotentials and is the subject of Chapters 2 and 3. Next, the hydrated electron—the excess electron in liquid water—is tackled in an effort to address the recent controversy concerning its true structure and is the subject of Chapters 4 and 5. In essence, the work in this Dissertation is concerned with finding new ways to overcome the problem of a lack of infinite computer processing power.

Much of the chemistry that affects life on planet Earth occurs in the condensed phase. The TeraHertz (THz) or far-infrared (far-IR) region of the electromagnetic spectrum (from 0.1 THz to 10 THz, 3 cm-1 to 300 cm-1, or 3000 μm to 30 μm) has been shown to provide unique possibilities in the study of condensed-phase processes. The goal of this work is to expand the possibilities available in the THz region and undertake new investigations of fundamental interest to chemistry. Since we are fundamentally interested in condensed-phase processes, this thesis focuses on two areas where THz spectroscopy can provide new understanding: astrochemistry and solvation science. To advance these fields, we had to develop new instrumentation that would enable the experiments necessary to answer new questions in either astrochemistry or solvation science. We first developed a new experimental setup capable of studying astrochemical ice analogs in both the TeraHertz (THz), or far-Infrared (far-IR), region (0.3 - 7.5 THz; 10 - 250 cm-1) and the mid-IR (400 - 4000 cm-1). The importance of astrochemical ices lies in their key role in the formation of complex organic molecules, such as amino acids and sugars in space. Thus, the instruments are capable of performing variety of spectroscopic studies that can provide especially relevant laboratory data to support astronomical observations from telescopes such as the Herschel Space Telescope, the Stratospheric Observatory for Infrared Astronomy (SOFIA), and the Atacama Large Millimeter Array (ALMA). The experimental apparatus uses a THz time-domain spectrometer, with a 1750/875 nm plasma source and a GaP detector crystal, to cover the bandwidth mentioned above with ~10 GHz (~0.3 cm-1) resolution. Using the above instrumentation, experimental spectra of astrochemical ice analogs of water and carbon dioxide in pure, mixed, and layered ices were collected at different temperatures under high vacuum conditions with the goal of investigating the structure of the ice. We tentatively observe a new feature in both amorphous solid water and crystalline water at 33 cm-1 (1 THz). In addition, our studies of mixed and layered ices show how it is possible to identify the location of carbon dioxide as it segregates within the ice by observing its effect on the THz spectrum of water ice. The THz spectra of mixed and layered ices are further analyzed by fitting their spectra features to those of pure amorphous solid water and crystalline water ice to quantify the effects of temperature changes on structure. From the results of this work, it appears that THz spectroscopy is potentially well suited to study thermal transformations within the ice. To advance the study of liquids with THz spectroscopy, we developed a new ultrafast nonlinear THz spectroscopic technique: heterodyne-detected, ultrafast THz Kerr effect (TKE) spectroscopy. We implemented a heterodyne-detection scheme into a TKE spectrometer that uses a stilbazoiumbased THz emitter, 4-N,N-dimethylamino-4-N-methyl-stilbazolium 2,4,6-trimethylbenzenesulfonate (DSTMS), and high numerical aperture optics which generates THz electric field in excess of 300 kV/cm, in the sample. This allows us to report the first measurement of quantum beats at terahertz (THz) frequencies that result from vibrational coherences initiated by the nonlinear, dipolar interaction of a broadband, high-energy, (sub)picosecond THz pulse with the sample. Our instrument improves on both the frequency coverage, and sensitivity previously reported; it also ensures a backgroundless measurement of the THz Kerr effect in pure liquids. For liquid diiodomethane, we observe a quantum beat at 3.66 THz (122 cm-1), in exact agreement with the fundamental transition frequency of the υ4 vibration of the molecule. This result provides new insight into dipolar vs. Raman selection rules at terahertz frequencies. To conclude we discuss future directions for the nonlinear THz spectroscopy in the Blake lab. We report the first results from an experiment using a plasma-based THz source for nonlinear spectroscopy that has the potential to enable nonlinear THz spectra with a sub-100 fs temporal resolution, and how the optics involved in the plasma mechanism can enable THz pulse shaping. Finally, we discuss how a single-shot THz detection scheme could improve the acquisition of THz data and how such a scheme could be implemented in the Blake lab. The instruments developed herein will hopefully remain a part of the groups core competencies and serve as building blocks for the next generation of THz instrumentation that pushes the frontiers of both chemistry and the scientific enterprise as a whole.

Binary fluorescence time series obtained from single-molecule imaging experiments can be used to infer protein binding kinetics, in particular, association and dissociation rate constants from waiting time statistics of fluorescence intensity changes. In many cases, rate constants inferred from fluorescence time series exhibit nonintuitive dependence on ligand concentration. Here we examine several possible mechanistic and technical origins that may induce ligand dependence of rate constants. Using aggregated Markov models, we show under the condition of detailed balance that non-fluorescent bindings and missed events due to transient interactions, instead of conformation fluctuations, may underly the dependence of waiting times and thus apparent rate constants on ligand concentrations. In general, waiting times are rational functions of ligand concentration. The shape of concentration dependence is qualitatively affected by the number of binding sites in the single molecule and is quantitatively tuned by model parameters. We also show that ligand dependence can be caused by non-equilibrium conditions which result in violations of detailed balance and require an energy source. As to a different but significant mechanism, we examine the effect of ambient buffers that can substantially reduce the effective concentration of ligands that interact with the single molecules. To demonstrate the effects by these mechanisms, we applied our results to analyze the concentration dependence in a single-molecule experiment EGFR binding to fluorophore-labeled adaptor protein Grb2 by Morimatsu et al. (PNAS,104:18013,2007)., 11 pages, 4 figures; J. Chem. Phys., 137, 2012

Ultrafast vibrational spectra of the aqueous oxalate ion in the region of its carboxylate asymmetric stretch modes show novel relaxation processes. Two-dimensional infrared vibrational echo spectra and the vibrational dynamics obtained from them along with measurements of the anisotropy decay provide a picture in which the localization of the oxalate vibrational excitation onto the carboxylate groups occurs in ∼450 fs. Molecular dynamics simulations are used to characterize the vibrational dynamics in terms of dihedral angle motion between the two carboxylate planes and solvation dynamics. The localization of the oxalate vibrational excitation onto the carboxylates is induced by the fluctuations in the carboxylate vibrational frequencies which are shown by theory and experiment to have a similar correlation time as the anisotropy decay.

NMR anisotropic parameters such as dipolar couplings and chemical shifts are central to structure and orientation determination of aligned membrane proteins and liquid crystals. Among the separated local field experiments, the proton evolved local field (PELF) scheme is particularly suitable to measure dynamically averaged dipolar couplings and give information on local molecular motions. However, the PELF experiment requires the acquisition of several 2D datasets at different mixing times to optimize the sensitivity for the complete range of dipolar couplings of the resonances in the spectrum. Here, we propose a new PELF experiment that takes the advantage of the Hadamard encoding (HE) to obtain higher sensitivity for a broad range of dipolar couplings using a single 2D experiment. The HE scheme is obtained by selecting the spin operators with phase switching of hard pulses. This approach enables one to detect four spin operators, simultaneously, which can be processed into two 2D spectra covering a broader range of dipolar couplings. The advantages of the new approach are illustrated for a U-(15)N NAL single crystal and the U-(15)N labeled single-pass membrane protein sarcolipin reconstituted in oriented lipid bicelles. The HE-PELF scheme can be implemented in other multidimensional experiments to speed up the characterization of the structure and dynamics of oriented membrane proteins and liquid crystalline samples.

General expressions relating the effects of pressure, temperature, and composition on solute association and conformational equilibria using the fluctuation theory of solutions are provided. The expressions are exact and can be used to interpret experimental or computer simulation data for any multicomponent mixture involving molecules of any size and character at any composition. The relationships involve particle-particle, particle-energy, and energy-energy correlations within local regions in the vicinity of each species involved in the equilibrium. In particular, it is demonstrated that the results can be used to study peptide and protein association or aggregation, protein denaturation, and protein-ligand binding. Exactly how the relevant fluctuating properties may be obtained from experimental or computer simulation data are also outlined. It is shown that the enthalpy, heat capacity, and compressibility differences associated with the equilibrium process can, in principle, be obtained from a single simulation. Fluctuation based expressions for partial molar heat capacities, thermal expansions, and isothermal compressibilities are also provided.

A new high quality three-dimensional potential energy surface for the Ne-CO van der Waals complex is developed using the CCSD(T) method and avqz∕avqz+33221 basis set. The ab initio calculation is performed in a total of 1365 configurations with supermolecule method. There is a single global minimum located in a nearly T-shaped geometry. The global minimum energy is -49.4090 cm(-1) at R(e)=6.40a(0) and θ(e)=82.5(∘) for V(00). Using the three-dimensional potential energy surface, we have calculated bound rovibrational energy levels up to J = 10 including the Coriolis coupling terms. Compared with the experimental transition frequencies, the theoretical results are in good agreement with the experimental results.

Thirteen specific infrared bands in the 2350 cm -1 region are assigned to carbon dioxide clusters, (CO 2) N, with N = 6, 7, 9, 10, 11, 12 and 13. The spectra are observed in direct absorption using a tuneable infrared laser to probe a pulsed supersonic jet expansion of a dilute mixture of CO 2 in He carrier gas. Assignments are aided by cluster structure calculations made using two reliable CO 2 intermolecular potential functions. For (CO 2) 6, two highly symmetric isomers are observed, one with S 6 symmetry (probably the more stable form), and the other with S 4 symmetry. (CO 2) 13 is also symmetric (S 6), but the remaining clusters are asymmetric tops with no symmetry elements. The observed rotational constants tend to be slightly (≈2%) smaller than those from the predicted structures. The bands have increasing vibrational blueshifts with increasing cluster size, similar to those predicted by the resonant dipole-dipole interaction model but significantly larger in magnitude. © 2011 American Institute of Physics.

Using small angle x-ray scattering, we find that the correlation length of bulk liquid water shows a steep increase as temperature decreases at subzero temperatures (supercooling) and that it can, similar to the thermodynamic response functions, be fitted to a power law. This indicates that the anomalous properties of water are attributable to fluctuations between low- and high-density regions with rapidly growing average size upon supercooling. The substitution of H(2)O with D(2)O, as well as the addition of NaCl salt, leads to substantial changes of the power law behavior of the correlation length. Our results are consistent with the proposed existence of a liquid-liquid critical point in the deeply supercooled region but do not exclude a singularity-free model.

While the Stokes-Einstein (SE) equation predicts that the diffusion coefficient of a solute will be inversely proportional to the viscosity of the solvent, this relation is commonly known to fail for solutes, which are the same size or smaller than the solvent. Multiple researchers have reported that for small solutes, the diffusion coefficient is inversely proportional to the viscosity to a fractional power, and that solutes actually diffuse faster than SE predicts. For other solvent systems, attractive solute-solvent interactions, such as hydrogen bonding, are known to retard the diffusion of a solute. Some researchers have interpreted the slower diffusion due to hydrogen bonding as resulting from the effective diffusion of a larger complex of a solute and solvent molecules. We have developed and used a novel micropipette technique, which can form and hold a single microdroplet of water while it dissolves in a diffusion controlled environment into the solvent. This method has been used to examine the diffusion of water in both n-alkanes and n-alcohols. It was found that the polar solute water, diffusing in a solvent with which it cannot hydrogen bond, closely resembles small nonpolar solutes such as xenon and krypton diffusing in n-alkanes, with diffusion coefficients ranging from 12.5x10(-5) cm(2)/s for water in n-pentane to 1.15x10(-5) cm(2)/s for water in hexadecane. Diffusion coefficients were found to be inversely proportional to viscosity to a fractional power, and diffusion coefficients were faster than SE predicts. For water diffusing in a solvent (n-alcohols) with which it can hydrogen bond, diffusion coefficient values ranged from 1.75x10(-5) cm(2)/s in n-methanol to 0.364x10(-5) cm(2)/s in n-octanol, and diffusion was slower than an alkane of corresponding viscosity. We find no evidence for solute-solvent complex diffusion. Rather, it is possible that the small solute water may be retarded by relatively longer residence times (compared to non-H-bonding solvents) as it moves through the liquid.

Two-dimensional (2D) nuclear magnetic resonance correlation experiments have recently been proposed as a means for studying exchange in porous media. Most notable of these is the T(2)-T(2) relaxation exchange spectroscopy (REXSY) experiment. Unfortunately, quantifying exchange with this method requires a relatively long, three-dimensional acquisition. To reduce acquisition times, novel 2D methods for quantifying exchange were developed. For each method, model equations were derived (for an arbitrary N-pool system), tested via simulation studies, and validated via experimental studies in an aqueous urea model system. Results indicate that the novel methods outperform REXSY-in terms of uncertainty per unit time for the fitted exchange rate-for certain model systems. The relative merits of each method are discussed in the text.

We apply ab initio molecular dynamics (AIMD) methods in conjunction with the thermodynamic integration or "lambda-path" technique to compute the intrinsic hydration free energies of Li+, Cl-, and Ag+ ions. Using the Perdew-Burke-Ernzerhof functional, adapting methods developed for classical force field applications, and with consistent assumptions about surface potential (phi) contributions, we obtain absolute AIMD hydration free energies (Delta G(hyd)) within a few kcal/mol, or better than 4%, of Tissandier 's [J. Phys. Chem. A 102, 7787 (1998)] experimental values augmented with the SPC/E water model phi predictions. The sums of Li+/Cl- and Ag+/Cl- AIMD Delta G(hyd), which are not affected by surface potentials, are within 2.6% and 1.2 % of experimental values, respectively. We also report the free energy changes associated with the transition metal ion redox reaction Ag++Ni+-> Ag+Ni2+ in water. The predictions for this reaction suggest that existing estimates of Delta G(hyd) for unstable radiolysis intermediates such as Ni+ may need to be extensively revised., 18 pages, 8 figures. This version is essentially the one published in J. Chem. Phys

Pulse sequences for spin-1/2-spin-1 pair heteronuclear single quantum correlation (HSQC), heteronuclear double quantum correlation (HDQC), and coupled-HSQC, and coupled-HDQC NMR spectroscopies are outlined, and experimental realization for a (13)C-(2)H pair is demonstrated in solution state. In both the coupled versions, conditions for generation of in-phase and antiphase multiplets in either dimension are arrived at. The patterns and the intensity ratios are explained. The double quantum (2Q) experiments confirm doubling of both the shift frequency and the splitting due to coupling (to spin 1/2) of the 2Q coherence emanating from spin 1. The frequency doubling is equivalent to the corresponding single quantum (1Q) coherence at double the magnetic field strength. The coupling doubling, however, is independent of the magnetic field strength and a signature feature of the 2Q coherence. The ramification of the relative relaxation rates of 1Q and 2Q coherences is discussed.

According to gap-phase dynamics theory, forests can be divided into four distinct patch types: gap patch (G), building patch (B), mature patch (M), and degeneration patch (D). Varying light conditions across patch types are one of the most important factors affecting the coexistence of vegetation. Mechanisms of coexistence can be understood through detailed knowledge of ecophysiological responses of codominant tree seedlings to patch types. The following study was conducted to determine ecophysiological responses of Cyclobalanopsis glauca (an evergreen broad-leaved species) and Bothrocaryum controversum (a deciduous broad-leaved species) to four different patch types. During the gap-phase dynamics, light intensity and the magnitude of change in the four different patches followed the order of: G B D M. Both species had the greatest photosynthetic capacity in the G patch. Dry leaf mass per area (LMA), Chlorophyll a + b concentration (Chl), carotenoids (Car), and nitrogen content per area (N a ) all responded to changes in light across patch type, but B. controversum showed greater sensitivity and changes than C. glauca. From G to M patch, the maximal quantum efficiency of PSII (F v /F m ) had a larger variation magnitude for B. controversum than for C. glauca. From G to M patch, B. controversum showed significant changes in gas exchange, while C. glauca showed only small changes. Ecophysiological trait partitioning of response to light in different patches provides a possible explanation of a coexistence mechanism.

Multi-pulse heterodyne pump-probe measurements are used to investigate the reverse bias dynamics of InAs/GaAs quantum dots in a waveguide structure. Using a femtosecond pulse, we simultaneously populate high energy ground states and low energy excited states and measure the resulting gain and phase dynamics over the bandwidth of the pulse. We identify a ∼5 ps timescale in the phase dynamics which can be associated with low energy ground states outside the pulse bandwidth and may provide an explanation for the deterioration of monolithic mode locked laser performance at high reverse voltages. © 2011 American Institute of Physics., SCOPUS: ar.j, info:eu-repo/semantics/published

Nonlinear THz-THz-Raman (TTR) liquid spectroscopy offers new possibilities for studying and understanding condensed-phase chemical dynamics. Although TTR spectra carry rich information about the systems under study, the response is encoded in a three-point correlation function comprising of both dipole and polarizability elements. Theoretical methods are necessary for the interpretation of the experimental results. In this work, we study the liquid-phase dynamics of bromoform, a polarizable molecule with a strong TTR response. Previous work based on reduced density matrix (RDM) simulations suggests that unusually large multi-quanta dipole matrix elements are needed to understand the measured spectrum of bromoform. Here, we demonstrate that a self-consistent definition of the time coordinates with respect to the reference pulse leads to a simplified experimental spectrum. Furthermore, we analytically derive a parametrization for the RDM model by integrating the dipole and polarizability elements to the 4th order in the normal modes, and we enforce inversion symmetry in the calculations by numerically cancelling the components of the response that are even with respect to the field. The resulting analysis eliminates the need to invoke large multi-quanta dipole matrix elements to fit the experimental spectrum; instead, the experimental spectrum is recovered using RDM simulations with dipole matrix parameters that are in agreement with independent ab initio calculations. The fundamental interpretation of the TTR signatures in terms of coupled intramolecular vibrational modes remains unchanged from the previous work.

The base-catalyzed rearrangement of arylindenols is a rare example of a suprafacial [1,3]-hydrogen atom transfer. The mechanism has been proposed to proceed via sequential [1,5]-sigmatropic shifts, which occur in a selective sense and avoid an achiral intermediate. A computational analysis using quantum chemistry casts serious doubt on these suggestions: These pathways have enormous activation barriers, and in constrast to what is observed experimentally, they overwhelmingly favor a racemic product. Instead we propose that a suprafacial [1,3]-prototopic shift occurs in a two-step deprotonation/reprotonation sequence. This mechanism is favored by 15 kcal mol–1 over that previously proposed. Most importantly, this is also consistent with stereospecificity since reprotonation occurs rapidly on the same π-face. We have used explicitly solvated molecular dynamics studies to study the persistence and condensed-phase dynamics of the intermediate ion-pair formed in this reaction. Chirality transfer is the result of a particularly resilient contact ion-pair, held together by electrostatic attraction and a critical NH···π interaction which ensures that this species has an appreciable lifetime even in polar solvents such as DMSO and MeOH.

International audience; Phase separation of thermo-responsive polymers in solution is a complex process, whose understanding is essential to screen and design materials with diverse technological applications. Here we report on a method based on dynamic light scattering (DLS) experiments to investigate the phase separation of thermo-responsive polymer solutions and precisely define the transition temperature (T$_{PS}$). Our results are applied on hydroxypropylcellulose (HPC) solutions as an important biosourced green water-soluble polymer. As determined by DLS, the amplitudes of the fast and slow modes of relaxation dynamics evolve as temperature gets closer to the phase transition point eventually leading to phase separation. The evolution of relaxation modes with temperature is markedly different for concentrations below the overlap concentration (c*) (dilute regime), above c* (semi-dilute regime) and above the entanglement concentration (c$_e$). In the three cases though, the fast and slow mode amplitudes undergo a sharp transition in a narrow temperature range, defining accurately the phase separation locus. The results agree with turbidimetric analysis for the phase transition determination but with a better precision. Our results also show that the one-phase dynamics and phase separation dynamics in the two-phase region are only in continuity for c 4 c e , revealing mechanistic details about the HPC phase separation process. Above T PS we identify a temperature range where the intensity autocorrelation function has a single-exponential shape. In the latter regime, we monitor the growth kinetics of polymer domains and provide clues to rationalize the stabilizing effects of the interfaces leading to the arrested-like phase separation behavior observed for HPC.

Summary: Decomposition of plant litter is a key process in the global carbon cycle, and its realistic representation is essential for accurate prediction of ecosystem carbon and nutrient dynamics. Traditionally, the exponential decay model, which assumes a constant relative decomposition rate through time, has been widely used for both the analysis of empirical data and large-scale modelling. While this model may be adequate in some contexts, there are also many empirical observations for which it does not fit the data well. Using a number of previously published leaf and wood decomposition data sets, comprising a diverse selection of litters, we compared the performance of five simple decay models varying in complexity and functional form. To accomplish this, we used a combination of model selection criteria and out-of-sample extrapolation analyses. Model selection criteria favoured an optimal balance between parsimony and flexibility, and a rarely used model built on the Weibull distribution proved to have sufficient flexibility to fit the full range of decomposition trajectories including litters that show an initial lag phase. Using the Weibull fits, we further showed that the litter N content affects the shape of the decomposition trajectory, a novel biological result. Out-of-sample extrapolation showed biased predictions for all models and estimates of steady-state stocks were often highly sensitive to model choice. As the field moves beyond the single-pool exponential framework, it is useful to confront alternate models with data from a wide array of litter types. This analysis demonstrates that model flexibility is important for representing the wide array of possible decomposition dynamics encountered in nature, with lag phase dynamics more widespread than previously thought. Out-of-sample extrapolation and derived parameters that rely on it remain problematic with all tested models. Progress in understanding the drivers and consequences of litter decomposition will come from combining empirical approaches with more focused process-based modelling that allow for the assessment of alternative model assumptions. © 2013 British Ecological Society.

Magnetic resonance (MR) imaging techniques have been used to study gas phase dynamics during co-current up-flow in a column of inner diameter 43 mm, packed with spherical non-porous elements of diameters of 1.8, 3 and 5 mm. MR measurements of gas hold-up, bubble-size distribution, and bubble-rise velocities were made as a function of flow rate and packing size. Gas and liquid flow rates were studied in the range of 20–250 cm3 s−1 and 0–200 cm3 min−1, respectively. The gas hold-up within the beds was found to increase with gas flow rate, while decreasing with increasing packing size and to a lesser extent with increasing liquid flow rate. The gas hold-up can be separated into a dynamic gas hold-up, only weakly dependent on packing size and associated with bubbles rising up the bed, and a ‘static’ hold-up which refers to locations within the bed associated with temporally-invariant gas hold-up, over the measurement times of 512 s, associated either with gas trapped within the void structure of the bed or with gas channels within the bed. This ‘static’ gas hold-up is strongly dependent on packing size, showing an increase with decreasing packing size. The dynamic gas hold-up is comprised of small bubbles – of order of the packing size – which have rise velocities of 10–40 mm s−1 and which move between the packing elements within the bed, along with much larger bubbles, or agglomerates of bubbles, which move with higher rise velocities (100–300 mm s−1). These ‘larger’ bubbles, which may exist as streams of smaller bubbles or ‘amoeboid’ bubbles, behave as a single large bubble in terms of the observed high rise velocity. Elongation of the bubbles in the direction of flow was observed for all packings.

The photochemical reaction dynamics of a light-oxygen-voltage (LOV) domain from the blue light sensor protein, FKF1 (flavin-binding Kelch repeat F-box) was studied by means of the pulsed laser-induced transient grating method. The observed absorption spectral changes upon photoexcitation were similar to the spectral changes observed for typical LOV domain proteins (e.g., phototropins). The adduct formation took place with a time constant of 6 μs. After this reaction, a significant conformational change with a time constant of 6 ms was observed as a change in the diffusion coefficient. An FKF1-LOV mutant without the conserved loop connecting helices E and F, which is present only in the FKF1/LOV Kelch protein 2/ZEITLUPE family, did not show these slow phase dynamics. This result indicates that the conformational change in the loop region represents a major change in the FKF1-LOV photoreaction.

A nonlinear initial boundary value problem for the lithium ion concentration, the electric potential and the electrode-electrolyte interface currents is introduced on the microscale. The model enables the resolution of porous electrode microstructures. Different exchange current densities for Butler–Volmer interface conditions are evaluated. The Cahn–Hilliard equation is used to describe the phase transition from solid-solution diffusion to two-phase dynamics. The resulting phase-field model is then discretized on a regular mesh. A first-order finite-volume scheme with an adaptive time integration method is applied. The parameters and their effects in the non-convex Helmholtz energy are investigated and explained. Furthermore, the numerical convergence of the scheme is examined. In order to illustrate the method, the charging process of several single-particles and a complex structure is numerically simulated.

Although important to heterogeneous catalysis, the ability to accurately model reactions of polyatomic molecules with metal surfaces has not kept pace with developments in gas phase dynamics. Partnering the specific reaction parameter (SRP) approach to density functional theory with ab initio molecular dynamics (AIMD) extends our ability to model reactions with metals with quantitative accuracy from only the lightest reactant, H2, to essentially all molecules. This is demonstrated with AIMD calculations on CHD3 + Ni(111) in which the SRP functional is fitted to supersonic beam experiments, and validated by showing that AIMD with the resulting functional reproduces initial-state selected sticking measurements with chemical accuracy (4.2 kJ/mol ≈ 1 kcal/mol). The need for only semilocal exchange makes our scheme computationally tractable for dissociation on transition metals.

Deuterium fluoride gets born shivering Modern spectroscopic techniques can analyze collisions between gas phase molecules in exquisite detail, highlighting exactly which vibrations and rotations come into play. However, much chemistry of interest takes place in solution, where it's harder to tease out what happens. Dunning et al. applied infrared spectroscopy to study solution-phase formation of deuterium fluoride (DF) from F atoms, a longstanding test bed of gas phase dynamics. The DF product vibrated for a surprisingly long time before dissipating its energy to the surrounding solvent molecules. Science , this issue p. 530

Bimolecular reactions in the gas phase exhibit rich and varied dynamical behaviour, but whether a profound knowledge of the mechanisms of isolated reactive collisions can usefully inform our understanding of reactions in liquid solutions remains an open question. The fluctuating environment in a liquid may significantly alter the motions of the reacting particles and the flow of energy into the reaction products after a transition state has been crossed. Recent experimental and computational studies of exothermic reactions of CN radicals with organic molecules indicate that many features of the gas-phase dynamics are retained in solution. However, observed differences may also provide information on the ways in which a solvent modifies fundamental chemical mechanisms. This perspective examines progress in the use of time-resolved infra-red spectroscopy to study reaction dynamics in liquids, discusses how existing theories can guide the interpretation of experimental data, and suggests future challenges for this field of research. (C) 2014 AIP Publishing LLC.

We previously identified the heterogeneous ribonucleoprotein SAF-A/hnRNP U as a substrate for DNA-PK, a protein kinase involved in DNA damage response (DDR). Using laser micro-irradiation in human cells, we report here that SAF-A exhibits a two-phase dynamics at sites of DNA damage, with a rapid and transient recruitment followed by a prolonged exclusion. SAF-A recruitment corresponds to its binding to Poly(ADP-ribose) while its exclusion is dependent on the activity of ATM, ATR and DNA-PK and reflects the dissociation from chromatin of SAF-A associated with ongoing transcription. Having established that SAF-A RNA-binding domain recapitulates SAF-A dynamics, we show that this domain is part of a complex comprising several mRNA biogenesis proteins of which at least two, FUS/TLS and TAFII68/TAF15, exhibit similar biphasic dynamics at sites of damage. Using an original reporter for live imaging of DNA:RNA hybrids (R-loops), we show a transient transcription-dependent accumulation of R-loops at sites of DNA damage that is prolonged upon inhibition of RNA biogenesis factors exclusion. We propose that a new component of the DDR is an active anti-R-loop mechanism operating at damaged transcribed sites which includes the exclusion of mRNA biogenesis factors such as SAF-A, FUS and TAF15.

Silicon (Si) nanoparticles were coated inflight with silver (Ag) atoms using a novel method to prepare multicomponent heterostructured metal-semiconductor nanoparticles. Molecular dynamics (MD) computer simulations were employed, supported by high-resolution bright field (BF) transmission electron microscopy (HRTEM) and aberration-corrected scanning transmission electron microscopy (STEM) with a resolution ≤0.1 nm in high angle annular dark field (HAADF) mode. These studies revealed that the alloying behavior and phase dynamics during the coating process are more complex than when attaching hetero-atoms to preformed nanoparticles. According to the MD simulations, Ag atoms condense, nucleate and diffuse into the liquid Si nanoparticles in a process that we term “inoculation”, and a phase transition begins. Subsequent solidification involves an intermediate alloying stage that enabled us to control the microstructure and crystallinity of the solidified hybrid heterostructured nanoparticles.

A laboratory-scale atomic layer deposition (ALD) reactor system model is derived for alumina deposition using trimethylaluminum and water as precursors. Model components describing the precursor thermophysical properties, reactor-scale gas-phase dynamics and surface reaction kinetics derived from absolute reaction rate theory are integrated to simulate the complete reactor system. Limit-cycle solutions defining continuous cyclic ALD reactor operation are computed with a fixed point algorithm based on collocation discretization in time, resulting in an unambiguous definition of film growth-per-cycle (gpc). A key finding of this study is that unintended chemical vapor deposition conditions can mask regions of operation that would otherwise correspond to ideal saturating ALD operation. The use of the simulator for assisting in process design decisions is presented.

Effects of stereoregularity and crystallization mode on the amorphous phase dynamics are investigated for poly(lactic acid) PLA. An isothermal crystallization from the melt and a cold crystallization are imposed. For each PLA, the cold crystallization leads to the appearance of a less perfect crystalline phase and to an important rigid amorphous fraction RAF content (35%), although only 10% of RAF is generated after crystallization from the melt. Temperature Modulated Differential Scanning Calorimetry is used to determine the Cooperative Rearranging Regions (CRR) size at the glass transition temperature in the mobile amorphous phase MAP. It is shown that the CRR size in the MAP is not modified by the appearance and the spherulite growth. For the intra-spherulite MAP, a confining effect is evidenced, causing an amorphous phase thickness decrease during crystallization, and inducing a drastic CRR size reduction.

The thermal behaviour, the physical ageing and the amorphous phase dynamics of polysulfone (PSU) and sulfonated polysulfone (SPSU) are characterized by thermogravimetric analysis and temperature modulated differential scanning calorimetry. The sulfonic group introduction (the sulfonation degree is 70%) in the polymer implies a drastic decrease of the thermal decomposition temperature (220 and 517 °C for SPSU and PSU respectively) and a modification of calorimetric parameters (for SPSU, the heat capacity in the glassy state is lower and the glass transition temperature Tg is higher than for PSU). In terms of molecular dynamics, the amorphous phase heterogeneities are greater and the cooperative rearranging region size at the glass transition temperature is smaller for SPSU than for PSU. Moreover, after a physical ageing process, the enthalpy recovery kinetic has slowed down by sulfonation. These results can be explained from the existence of sulfonic domains confining the amorphous phase domains.