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Chemical dynamics simulations are performed to study the dissociation of excited benzene-hexafluorobenzene (Bz-HFB) complex in N2 bath and the results are compared with the gas phase dynamics. Two N2 bath densities 20 and 750 kg/m3 are considered. Bz-HFB is excited with respect to the temperatures of 1000, 1500, and 2000 K at each bath density. The nature of the Bz-HFB* dissociation dynamics at the bath density of 20 kg/m3 is quite similar to gas phase one, but the same is drastically different at high bath density where energy transfer pathway dominates over dissociation and negligible direct dissociation of Bz-HFB* is reported.

We present a brief discussion of the phase-coherent dynamics of discrete breathers (intrinsic localized modes) in a system of two weakly coupled nonlinear chains and its comparison with periodic tunneling of quantum particles in a double-well potential and with macroscopic quantum tunneling of two weakly linked Bose–Einstein condensates. We consider the dynamics of relative phase of classically-tunneling discrete breathers in two weakly coupled nonlinear chains and show that the dynamics of the relative phase in the π/2 tunneling mode coincides with the experimentally observed dynamics of the relative phase of quantum particles, periodically tunneling in a double-well potential, both for noninteracting and strongly repulsively interacting particles. The observed coincidence demonstrates the correspondence between the dynamics of classical localized excitations in two weakly coupled nonlinear chains and tunneling dynamics of quantum object in the double-well potential. We show that in both π/2 and winding tunneling modes the relative phase experiences periodic jumps by π in the instants of complete depopulation of one of the weakly coupled chains or potential wells. The connection of the observed phase dynamics with the non-quantum uncertainty principle is discussed.

International audience; Protonated intermediates are postulated to be involved in the rate determining step of many sugar reactions. This paper presents a study of protonated sugar species, isolated in the gas phase, using a combination of infrared multiple photon dissociation (IRMPD) spectroscopy, classical ab initio molecular dynamics (AIMD) and quantum mechanical vibrational self-consistent field (VSCF) calculations. It provides a likely identification of the reactive intermediate oxocarbenium ion structure in a D-galactosyl system as well as the saccharide pyrolysis product anhydrogalactose (that suggests oxocarbenium ion stabilization), along with the spectrum of the protonated parent species: methyl D-galactopyranoside-H +. Its vibrational fingerprint indicates intramolecular proton sharing. Classical AIMD simulations for galactosyl oxocarbenium ions, conducted in the temperature range ~300-350 K (using B3LYP potentials on-the-fly) reveal efficient transitions on the picosecond timescale. Multiple conformers are likely to exist under the experimental conditions and along with static VSCF calculations, they have facilitated the identification of the individual structural motifs of the galactosyl oxocarbenium ion and protonated anhydrogalactose ion conformers that contribute to the observed experimental spectra. These results demonstrate the power of experimental IRMPD spectroscopy combined with dynamics simulations and with computational spectroscopy at the anharmonic level to unravel conformer structures of protonated saccharides, and to provide information on their lifetimes.

Transient phase dynamics, synchronization and desynchronization which are stimulus-locked (i.e. tightly time-locked to a repetitively administered stimulus) are studied in two coupled phase oscillators in the presence of noise. The presented method makes it possible to detect such processes in numerical and experimental signals. The time resolution is enormous, since it is only restricted by the sampling rate. Stochastic stimulus locking of the phases or the n:m phase difference at a particular time t relative to stimulus onset is defined by the presence of one or more prominent peaks in the cross-trial distribution of the phases or the n:m phase difference at time t relative to stimulus onset in an ensemble of post-stimulus responses. Unlike the presented approach, both triggered averaging (where an ensemble of post-stimulus responses is simply averaged) and cross-trial cross correlation (CTCC) lead to severe misinterpretations: The oscillators' coupling may cause a transient anti-phase clustering of the post-stimulus responses. Triggered averaging cannot distinguish such a response decorrelation from a mean amplitude decrease of the single responses. CTCC not only depends on the oscillators' phase difference but also on their phases and, thus, inevitably displays "artificial" oscillations that are not related to synchronization or desynchronization.

The conventional view of conversion reaction is based on the reversibility, returning to an initial material structure through reverse reaction at each cycle in cycle life, which impedes the complete understanding on a working mechanism upon a progression of cycles in conversion-reaction-based battery electrodes. Herein, a series of tin-doped ferrites (Fe3- xSn xO4, x = 0-0.36) are prepared and applied to a lithium-ion battery anode. By achieving the ideal reoxidation into SnO2, the Fe2.76Sn0.24O4 composite anchored on reduced graphene oxide shows a high reversible capacity of 1428 mAh g-1 at 200 mA g-1 after 100 cycles, which is the best performance of Sn-based anode materials so far. Significantly, a newly formed γ-FeOOH phase after 100 cycles is identified from topological features through synchrotron X-ray absorption spectroscopy with electronic and atomic structural information, suggesting the phase transformation from magnetite to lepidocrocite upon cycling. Contrary to the conventional view, our work suggests a variable working mechanism in an iron-based composite with the dynamic phases from iron oxide to iron oxyhydroxide in the battery cycle life, based on the reactivity of metal nanoparticles formed during reaction toward the solid electrolyte interface layer.

We report measurements on the phase dynamics of a detuned single mode laser which has in the past shown correspondence to the complex Lorenz equation. The corresponding ranges of periodic pulsing, of detuned chaos and of windows within the chaotic domain are investigated.

Physico-chemical systems driven away from thermal equilibrium usually undergo various types of instabilities leading to the formation of spatio-temporal patterns on macroscopic time and space scales. In two-dimensional geometries, patterns of different symmetries may be simultaneously stable. We study here the phase stability of hexagonal planforms in the framework of amplitude equations and reduced dynamical models close to the instability points.

Chemical vapour deposition on a Cu substrate is becoming a very important approach to obtain high quality graphene samples. Previous studies of graphene growth on Cu mainly focus on surface processes. However, recent experiments suggest that gas-phase dynamics also plays an important role in graphene growth. In this article, gas-phase processes are systematically studied using computational fluid dynamics. Our simulations clearly show that graphene growth is limited by mass transport under ambient pressures while it is limited by surface reactions under low pressures. The carbon deposition rate at different positions in the tube furnace and the concentration of different gas phase species are calculated. Our results confirm that the previously realized graphene thickness control by changing the position of the Cu foil is a result of gas-phase methane decomposition reactions.

Despite its simple mathematical structure, the Sprott E flow displays a chaotic dynamics whose complexity increases with the bifurcation parameter. This complexity shows up in the phase dynamics, which becomes highly incoherent. Such behavior is interpreted as the superposition of the dynamics of several different embedded standard maps.

We investigate the quantum-phase dynamics of a dissipative molecular system interacting with a single-mode amplitude-squeezed field (with a sub-Poissonian photon-number distribution) using the Monte Carlo wave-function method. As quantum dissipation, we consider molecular coherent (phase) and population relaxations, which are caused by nuclear vibration, and cavity relaxation (the dissipation of an internal single mode to outer mode). In this study, we elucidate the effects of these dissipations on the unique quantum dynamical behaviors of this coupled system, e.g., collapse-revival behavior of Rabi oscillations, using the quasiprobability (Q function) distribution of a single-mode field and the off-diagonal molecular density matrix. It is found that although the amplitude-squeezed field exhibits a distinct revival with larger amplitudes of molecular population in the presence of the molecular phase and population relaxations as compared to the coherent field, a very slight cavity relaxation suppresses the revival of molecular population and the increase in the magnitude of off-diagonal molecular density matrices during the quiescent region in the amplitude-squeezed field case more significantly than in the coherent field case. These features are shown to be closely related to the difference in the dynamics of Q function distributions between amplitude-squeezed and coherent fields.

We investigate the dynamics of a three-state atomic/molecular model system interacting with a two-mode squeezed vacuum field in view of the correlation between the atomic/molecular density matrix and photon-phase distribution. It is found that two-mode squeezed vacuum field realizes the anomalous situation that the coherency between the atomic/molecular states concerning the two-photon process is preserved well during the dynamics though the coherency between other states completely vanish. This implies that the quantum and thermal features can coexist in the atomic/molecular system in the presence of two-mode squeezed vacuum field. Such phenomenon is found to originate in the feature of its initial photon-phase correlation of a two-mode squeezed vacuum. We also discuss how the present attractive features in off-diagonal density matrices affect the molecular non-linear polarization.

We investigate the intermolecular-interaction (dipole–dipole interaction) effects on the quantum dynamics of dimer density matrices and photon-phase distributions using several dimer models with different intermolecular distances in the presence of a two-mode squeezed vacuum field. In this photon field, each mode is initially correlated and the reduced one-mode photon distribution is equivalent with that of a thermal field. For comparison, we perform parallel studies, in which the initial fields are two types of noncorrelated two-mode fields, i.e., a two-mode coherent field and a two-mode thermal field. It is found that although the two-mode squeezed vacuum field causes the random oscillations of dimer populations in the noninteracting dimer, the periodic oscillations like the collapse–revival behavior emerge as the intermolecular distance decreases (the intermolecular interaction increases). Similar and dissimilar features among quantum dynamics caused by these three types of fields are investigated by a...

It is well-known that the interaction among atoms/molecules and quantized electromagnetic fields with a small number of photons provides a peculiar quantum nature, i.e., collapses and revivals in the Rabi oscillations. In this study, we investigate the intermolecular interaction (dipole–dipole interaction) effect on the collapse-revival behavior using several dimer models (composed of two kinds of two-state monomers with slightly different excitation energies) with different intermolecular distances in the presence of a two-mode squeezed coherent field, in which each mode is initially correlated. It is found that although the collapse-revival behavior is fairly overlapped and indistinct in the case of a noninteracting dimer under the present two-mode squeezed coherent field, the decrease in the intermolecular distance (the increase in the intermolecular interaction) resurrects relatively distinct collapse-revival behavior with longer collapse and revival times. By analyzing the quantum behavior from the v...

We investigate the Poincare transformation dynamics describing the stochastic motion of a relativistic electron in the regular electrostatic field of a wave packet. The conditions of local instability of the phase trajectories are determined: it is shown that the system is a structurally stable Y system with an attracting set of the hyperbolic type. The relationship between the dynamics at the strange attractor characterized by Lyapunov indices and its statistical structure described by the Kolmogorov entropy is discussed. The fractal dimension of the phase space of the system is determined. The results of a numerical simulation of the effect are presented and discussed.

Analytical and numerical methods were used to study the dynamics of the mapping that describes a determinate dynamic system consisting of a relativistic electron and a wave packet of potential waves. The mapping dynamics is shown to depend essentially on a parameter that characterizes the wave-packet intensity. The system behaves in different ways, depending on that parameter: it executes ergodic motion with displacement or motion with simultaneous regular and irregular trajectories. This mapping is shown to be typical and structurally stable.

A single-layer graphene has been uniformly grown on a Cu surface at elevated temperatures by thermal processing of a poly(methyl methacrylate) (PMMA) film in a rapid thermal annealing (RTA) system under vacuum. The detailed chemistry of the transition from solid-state carbon to graphene on the catalytic Cu surface was investigated by performing in situ residual gas analysis while PMMA/Cu-foil samples were being heated, in conjunction with interrupted growth studies to reconstruct ex situ the heating process. The data clearly show that the formation of graphene occurs by vaporizing hydrocarbon molecules from PMMA, such as methane and/or methyl radicals, which act as precursors, rather than by the direct graphitization of solid-state carbon. We also found that the temperature for vaporizing hydrocarbon molecules from PMMA and the length of time the gaseous hydrocarbon atmosphere is maintained, which are dependent on both the heating temperature profile and the amount of a solid carbon feedstock, are the dominant factors that determine the crystalline quality of the resulting graphene film. Under optimal growth conditions, the PMMA-derived graphene was found to have a carrier (hole) mobility as high as ∼2700 cm(2) V(-1) s(-1) at room temperature, which is superior to common graphene converted from solid carbon.

Synaptically coupled neurons show in-phase or antiphase synchrony depending on the chemical and dynamical nature of the synapse. Deterministic theory helps predict the phase differences between two phase-locked oscillators when the coupling is weak. In the presence of noise, however, deterministic theory faces difficulty when the coexistence of multiple stable oscillatory solutions occurs. We analyze the solution structure of two coupled neuronal oscillators for parameter values between a subcritical Hopf bifurcation point and a saddle node point of the periodic branch that bifurcates from the Hopf point, where a rich variety of coexisting solutions including asymmetric localized oscillations occurs. We construct these solutions via a multiscale analysis and explore the general bifurcation scenario using the lambda-omega model. We show for both excitatory and inhibitory synapses that noise causes important changes in the phase and amplitude dynamics of such coupled neuronal oscillators when multiple oscillatory solutions coexist. Mixed-mode oscillations occur when distinct bistable solutions are randomly visited. The phase difference between the coupled oscillators in the localized solution, coexisting with in-phase or antiphase solutions, is clearly represented in the stochastic phase dynamics.

We review chimera patterns, which consist of coexisting spatial domains of coherent (synchronized) and incoherent (desynchronized) dynamics in networks of identical oscillators. We focus on chimera states involving amplitude as well as phase dynamics, complex topologies like small-world or hierarchical (fractal), noise, and delay. We show that a plethora of novel chimera patterns arise if one goes beyond the Kuramoto phase oscillator model. For the FitzHugh-Nagumo system, the Van der Pol oscillator, and the Stuart-Landau oscillator with symmetry-breaking coupling various multi-chimera patterns including amplitude chimeras and chimera death occur. To test the robustness of chimera patterns with respect to changes in the structure of the network, regular rings with coupling range R, small-world, and fractal topologies are studied. We also address the robustness of amplitude chimera states in the presence of noise. If delay is added, the lifetime of transient chimeras can be drastically increased.

New types of stable discrete solitons are discovered. They represent the first example of asymmetric dark solitons and shock waves with a nonzero background. Both types of solutions exhibit a strong intrinsic phase dynamics. Their domains of existence and criteria of stability are identified. Numerical experiments support the analytical findings.

A recent quantum computing paper (G. S. Uhrig, Phys. Rev. Lett. 98, 100504 (2007)) analytically derived optimal pulse spacings for a multiple spin echo sequence designed to remove decoherence in a two-level system coupled to a bath. The spacings in what has been called a "Uhrig dynamic decoupling (UDD) sequence" differ dramatically from the conventional, equal pulse spacing of a Carr-Purcell-Meiboom-Gill (CPMG) multiple spin echo sequence. The UDD sequence was derived for a model that is unrelated to magnetic resonance, but was recently shown theoretically to be more general. Here we show that the UDD sequence has theoretical advantages for magnetic resonance imaging of structured materials such as tissue, where diffusion in compartmentalized and microstructured environments leads to fluctuating fields on a range of different time scales. We also show experimentally, both in excised tissue and in a live mouse tumor model, that optimal UDD sequences produce different T(2)-weighted contrast than do CPMG sequences with the same number of pulses and total delay, with substantial enhancements in most regions. This permits improved characterization of low-frequency spectral density functions in a wide range of applications.

Hydrogen cyanide polymerizes readily under a variety of conditions and significant prebiotic roles have been suggested for these polymers due to the abundance of HCN in universe. However, the structures of HCN polymers have been more speculative than grounded in experimental data. Here we show that (13)C and (15)N solid state NMR spectra of polymers formed in neat HCN are inconsistent with the previously proposed structures and suggest instead that the polymers are formed by simple monomer addition, first in head-to-tail fashion to form linear, conjugated chains, and then laterally to form saturated two-dimensional networks. This interpretation of the NMR spectra finds support in other information about the polymerization of neat HCN, including the presence of free radicals. As expected from the literature, formation of the HCN tetramer, diaminomaleonitrile, is also observed, but only when the reaction is catalyzed exclusively by base and then in crystalline form.

We consider the phase dynamics of an ensemble of Kuramoto oscillators whose eigenfrequencies are perturbed to model the openness of living systems, and we show that it exhibits time-localized epochs of synchrony. A new quantitative measure is used to show that the model compares well with electroencephalography data recorded from a healthy awake human.

To reveal the dynamic mechanism underlying Parkinsonian resting tremor, we applied a phase dynamics modelling technique to local field potentials and accelerometer signals recorded in three Parkinsonian patients with implanted depth electrodes. We detect a bidirectional coupling between the subcortical oscillation and the tremor. The tremor → brain driving is a linear effect with a small delay corresponding to the neural transmission time. In contrast, the brain → tremor driving is a nonlinear effect with a long delay in the order of 1–2 mean tremor periods. Our results are well reproduced for an ensemble of 41 tremor epochs in three Parkinsonian patients and confirmed by surrogate data tests and model simulations. The uncovered mechanism of tremor generation suggests to specifically counteract tremor by desynchronizing the subcortical oscillatory neural activity.

Quantum-mechanical evolution of systems with periodic time-modulated Hamiltonians is often described by effective interactions. Such average Hamiltonians, calculated as few terms of an expansion in powers of the interaction, are sometimes difficult to relate to experimental observations. We propose a frequency-domain approach to this problem, which offers certain advantages and produces an approximate solution for the density matrix, better linked to measurable quantities. The formalism is suitable for calculating the intensities of narrowed spectral peaks. Fast magic-angle-spinning NMR spectra of solids are used to experimentally illustrate the method.

Longitudinal spin relaxation due to modulation of dipolar interactions often limits the development of hyperpolarized magnetic tracers. Recently, it has been demonstrated that transferring spin order to a singlet state significantly increases the polarization lifetimes in systems where nitrous oxide is dissolved in a liquid solvent. Additionally, previous studies have suggested that the longitudinal relaxation of nitrous oxide is largely dominated by the spin-rotation interaction. Models of spin-relaxation under Brownian motion naïvely predict the angular momentum reorienting correlation time of the spin rotation interaction to be inversely proportional to the viscosity of the solution. This dependence implies the singlet lifetime can be lengthened by increasing the dissolving solvent's viscosity-an extension which is not observed. Our work formulates a model which describes the relaxation of nitrous oxide dissolved in various solvents. We investigate the effect of altering the temperature of the solvent, as well as the effect of varying solute-solvent interactions on the singlet state as well as the longitudinal polarization lifetime. We predict the singlet lifetime for nitrous oxide dissolved in several solvents by fitting rotational and angular momentum correlation times measured at high magnetic field, and relate singlet relaxation to translational diffusion constants.

In-depth knowledge of water-water potential is important for devising and evaluating simple water models if they are to accurately describe water properties and reflect various solvation phenomena. Water-water potential depends upon inter-molecular distance, relative orientation of water molecules, and also local environment. When placed at a favorable distance in a favorable orientation, water molecules exhibit a particularly strong attractive interaction called hydrogen bond. Although hydrogen bond is very important for its effects on the elements of life, industrial applications, and bulk water properties, there is no scientific consensus on its true nature and origin. Using quantum-mechanical methods, hydrogen bond strength was calculated in different local environments. A simple empirical linear relationship was discovered between maximum hydrogen bond strength and the number of water molecules in the local environment. The local environment effect was shown to be considerable even on the second coordination shell. Additionally, a negative linear correlation was found between maximum hydrogen bond strength and the distance, at which it was observed. These results provide novel insights into the nature of hydrogen bonding.

Aqueous solutions of acetonitrile (MeCN) have been studied with oxygen K-edge x-ray Raman scattering (XRS) which is found to be sensitive to the interaction between water and MeCN. The changes in the XRS spectra can be attributed to water directly interacting with MeCN and are reproduced by density functional theory calculations on small clusters of water and MeCN. The dominant structural arrangement features dipole interaction instead of H-bonds between the two species as revealed by the XRS spectra combined with spectrum calculations. Small-angle x-ray scattering shows the largest heterogeneity for a MeCN to water ratio of 0.4 in agreement with earlier small-angle neutron scattering data.

In a previous report, we calculated the infrared absorption spectrum and both the isotropic and anisotropic pump-probe signals for the OD stretch of isotopically dilute water in dilauroylphosphatidylcholine (DLPC) multi-bilayers as a function of the lipid hydration level. These results were then compared to recent experimental measurements and are in generally good agreement. In this paper, we will further investigate the structure and dynamics of hydration water using molecular dynamics simulations and calculations of the two-dimensional infrared and vibrational echo peak shift observables for hydration water in DLPC membranes. These observables have not yet been measured experimentally, but future comparisons may provide insight into spectral diffusion processes and hydration water heterogeneity. We find that at low hydration levels the motion of water molecules inside the lipid membrane is significantly arrested, resulting in very slow spectral diffusion. At higher hydration levels, spectral diffusion is more rapid, but still slower than in bulk water. We also investigate the effects of several common approximations on the calculation of spectroscopic observables by computing these observables within multiple levels of theory. The impact of these approximations on the resulting spectra affects our interpretation of these measurements and reveals that, for example, the cumulant approximation, which may be valid for certain systems, is not a good approximation for a highly heterogeneous environment such as hydration water in lipid multi-bilayers.

We report the photoelectron spectrum of anionic N-acetylproline, (N-AcPro)(-), measured with 3.49 eV photons. This spectrum, which consists of a band centered at an electron binding energy of 1.4 eV and a higher energy spectral tail, confirms that N-acetylproline forms a valence anion in the gas phase. The neutrals and anions of N-AcPro were also studied computationally at the B3LYP∕6-31++G(d,p) level. Based on the calculations, we conclude that the photoelectron spectrum is due to anions which originated from proton transfer induced by electron attachment to the π* orbital localized at the acetyl group of N-AcPro. We also characterized the energetics of reaction paths leading to pyrrolidine ring opening in the anionic N-AcPro. These data suggest that electron induced decomposition of peptides/proteins comprising proline strongly depends on the presence of proton donors in the close vicinity to the proline residue.

An extension of the traditional Kirkwood-Buff (KB) theory of solutions is outlined which provides additional fluctuating quantities that can be used to characterize and probe the behavior of solution mixtures. Particle-energy and energy-energy fluctuations for local regions of any multicomponent solution are expressed in terms of experimentally obtainable quantities, thereby supplementing the usual particle-particle fluctuations provided by the established KB inversion approach. The expressions are then used to analyze experimental data for pure water over a range of temperatures and pressures, a variety of pure liquids, and three binary solution mixtures – methanol and water, benzene and methanol, and aqueous sodium chloride. In addition to providing information on local properties of solutions it is argued that the particle-energy and energy-energy fluctuations can also be used to test and refine solute and solvent force fields for use in computer simulation studies.

The theoretical basis of two-frequency saturation is given here in the framework of Provotorov theory. The parameters influencing the saturation efficiency are discussed and studied experimentally using a liquid-crystalline test system. It is shown that double-frequency irradiation can be extremely efficient when the irradiation frequencies are placed at opposite sides of the characteristic frequency of the spin system, and that the frequency separation in the double-frequency irradiation can be varied over a large range. Provotorov theory is also shown to provide good insights into the experimental findings, which would otherwise be difficult to obtain from simulations.

X-ray absorption spectroscopy (XAS) and small angle x-ray scattering (SAXS) were utilized to study the effect of fluoride (F(-)) anion in aqueous solutions. XAS spectra show that F(-) increases the number of strong H-bonds, likely between F(-) and water in the first hydration shell. SAXS data show a low-Q scattering intensity increase similar to the effect of a temperature decrease, suggesting an enhanced anomalous scattering behavior in F(-) solutions. Quantitative analysis revealed that fluoride solutions have larger correlation lengths than chloride solutions with the same cations but shorter compared to pure water. This is interpreted as an increased fraction of tetrahedral low-density structures in the solutions due to the presence of the F(-) ions, which act as nucleation centers replacing water in the H-bonding network and forming stronger H-bonds, but the presence of the cations restricts the extension of strong H-bonds.

All the channels of the reaction dynamics of gas-phase H (or D) atoms with D (or H) atoms adsorbed onto a Cu(111) surface have been studied by quasiclassical constant energy molecular dynamics simulations. The surface is flexible and is prepared at different temperature values, such as 30 K, 94 K, and 160 K. The adsorbates were distributed randomly on the surface to create 0.18 ML, 0.28 ML, and 0.50 ML of coverages. The multi-layer slab is mimicked by a many-body embedded-atom potential energy function. The slab atoms can move according to the exerted external forces. Treating the slab atoms non-rigid has an important effect on the dynamics of the projectile atom and adsorbates. Significant energy transfer from the projectile atom to the surface lattice atoms takes place especially during the first impact that modifies significantly the details of the dynamics of the collisions. Effects of the different temperatures of the slab are investigated in this study. Interaction between the surface atoms and the adsorbates is modeled by a modified London–Eyring–Polanyi–Sato (LEPS) function. The LEPS parameters are determined by using the total energy values which were calculated by a density functional theory and a generalized gradient approximation for an exchange-correlation energy for many different orientations, and locations of one- and two-hydrogen atoms on the Cu(111) surface. The rms value of the fitting procedure is about 0.16 eV. Many different channels of the processes on the surface have been examined, such as inelastic reflection of the incident hydrogen, subsurface penetration of the incident projectile and adsorbates, sticking of the incident atom on the surface. In addition, hot-atom and Eley-Rideal direct processes are investigated. The hot-atom process is found to be more significant than the Eley-Rideal process. Furthermore, the rate of subsurface penetration is larger than the sticking rate on the surface. In addition, these results are compared and analyzed as a function of the surface temperatures.

The technologically important properties of room temperature ionic liquids (RTILs) are fundamentally linked to the ion-ion interactions present among the constituent ions. These ion-ion interactions in one RTIL (1-ethyl-3-methylimidazolium trifluoromethanesulfonate, [C(2)mim]CF(3)SO(3)) are characterized with transmission FTIR spectroscopy and polarized attenuated total reflection (ATR) FTIR spectroscopy. A quasilattice model is determined to be the best framework for understanding the ionic interactions. A novel spectroscopic approach is proposed to characterize the degree of order that is present in the quasilattice by comparing the dipole moment derivative calculated from two independent spectroscopic measurements: (1) the TO-LO splitting of a vibrational mode using dipolar coupling theory and (2) the optical constants of the material derived from polarized ATR experiments. In principle, dipole moment derivatives calculated from dipolar coupling theory should be similar to those calculated from the optical constants if the quasilattice of the RTIL is highly structured. However, a significant disparity for the two calculations is noted for [C(2)mim]CF(3)SO(3), indicating that the quasilattice of [C(2)mim]CF(3)SO(3) is somewhat disorganized. The potential ability to spectroscopically characterize the structure of the quasilattice, which governs the long-range ion-ion interactions in a RTIL, is a major step forward in understanding the interrelationship between the molecular-level interactions among the constituent ions of an ionic liquid and the important physical properties of the RTIL.

Many quantum mechanical calculations indicate water molecules in the gas and liquid phase have much larger quadrupole moments than any of the common site models of water for computer simulations. Here, comparisons of multipoles from quantum mechanical∕molecular mechanical (QM∕MM) calculations at the MP2∕aug-cc-pVQZ level on a B3LYP∕aug-cc-pVQZ level geometry of a waterlike cluster and from various site models show that the increased square planar quadrupole can be attributed to the p-orbital character perpendicular to the molecular plane of the highest occupied molecular orbital as well as a slight shift of negative charge toward the hydrogens. The common site models do not account for the p-orbital type electron density and fitting partial charges of TIP4P- or TIP5P-type models to the QM∕MM dipole and quadrupole give unreasonable higher moments. Furthermore, six partial charge sites are necessary to account reasonably for the large quadrupole, and polarizable site models will not remedy the problem unless they account for the p-orbital in the gas phase since the QM calculations show it is present there too. On the other hand, multipole models by definition can use the correct multipoles and the electrostatic potential from the QM∕MM multipoles is much closer than that from the site models to the potential from the QM∕MM electron density. Finally, Monte Carlo simulations show that increasing the quadrupole in the soft-sticky dipole-quadrupole-octupole multipole model gives radial distribution functions that are in good agreement with experiment.

Solute-cluster aggregation and particle fusion have recently been suggested as alternative routes to the classical mechanism of nucleation from solution. The role of both processes in the crystallization of an aqueous electrolyte under controlled salt addition is here elucidated by molecular dynamics simulation. The time scale of the simulation allows direct observation of the entire crystallization pathway, from early events in the prenucleation stage to the formation of a nanocrystal in equilibrium with concentrated solution. The precursor originates in a small amorphous aggregate stabilized by hydration forces. The core of the nucleus becomes crystalline over time and grows by coalescence of the amorphous phase deposited at the surface. Imperfections of ion packing during coalescence promote growth of two conjoint crystallites. A parameter of order and calculated cohesive energies reflect the increasing crystalline order and stress relief at the grain boundary. Cluster aggregation plays a major role both in the formation of the nucleus and in the early stages of postnucleation growth. The mechanism identified shares common features with nucleation of solids from the melt and of liquid droplets from the vapor.

X-ray Raman scattering (XRS) spectroscopy and small angle x-ray scattering (SAXS) are used to study water in aqueous solutions of NaCl, MgCl(2), and AlCl(3) with the particular aim to provide information about the structure of the hydration shells of the cations. The XRS spectra show that Na(+) weakens the hydrogen bonds of water molecules in its vicinity, similar to the effect of increased temperature and pressure. Mg(2+) and Al(3+), on the other hand, cause the formation of short and strong hydrogen bonds between the surrounding water molecules. The SAXS data show that Mg(2+) and Al(3+) form tightly bound hydration shells that give a large density contrast in the scattering data. From the form factors extracted from the SAXS data, we found that Mg(2+) and Al(3+) have, respectively, an equivalent of one and one and a half stable hydration shells that appear as a density contrast. In addition, we estimated that the density of water in the hydration shells of Mg(2+) and Al(3+) is, respectively, ∼61% and ∼71% higher than in bulk water.

Water dynamics as reflected by the spectral diffusion of the water hydroxyl stretch were measured in w(0) = 2 (1.7 nm diameter) Aerosol-OT (AOT)/water reverse micelles in carbon tetrachloride and in isooctane solvents using ultrafast 2D IR vibrational echo spectroscopy. Orientational relaxation and population relaxation are observed for w(0) = 2, 4, and 7.5 in both solvents using IR pump-probe measurements. It is found that the pump-probe observables are sensitive to w(0), but not to the solvent. However, initial analysis of the vibrational echo data from the water nanopool in the reverse micelles in the isooctane solvent seems to yield different dynamics than the CCl(4) system in spite of the fact that the spectra, vibrational lifetimes, and orientational relaxation are the same in the two systems. It is found that there are beat patterns in the interferograms with isooctane as the solvent. The beats are observed from a signal generated by the AOT/isooctane system even when there is no water in the system. A beat subtraction data processing procedure does a reasonable job of removing the distortions in the isooctane data, showing that the reverse micelle dynamics are the same within experimental error regardless of whether isooctane or carbon tetrachloride is used as the organic phase. Two time scales are observed in the vibrational echo data, ~1 and ~10 ps. The slower component contains a significant amount of the total inhomogeneous broadening. Physical arguments indicate that there is a much slower component of spectral diffusion that is too slow to observe within the experimental window, which is limited by the OD stretch vibrational lifetime.

The "Swedish slow motion theory" [Nilsson and Kowalewski, J. Magn. Reson. 146, 345 (2000)] applied so far to Nuclear Magnetic Relaxation Dispersion (NMRD) profiles for solutions of transition metal ion complexes has been extended to ESR spectral analysis, including in addition g-tensor anisotropy effects. The extended theory has been applied to interpret in a consistent way (within one set of parameters) NMRD profiles and ESR spectra at 95 and 237 GHz for two Gd(III) complexes denoted as P760 and P792 (hydrophilic derivatives of DOTA-Gd, with molecular masses of 5.6 and 6.5 kDa, respectively). The goal is to verify the applicability of the commonly used pseudorotational model of the transient zero field splitting (ZFS). According to this model the transient ZFS is described by a tensor of a constant amplitude, defined in its own principal axes system, which changes its orientation with respect to the laboratory frame according to the isotropic diffusion equation with a characteristic time constant (correlation time) reflecting the time scale of the distortional motion. This unified interpretation of the ESR and NMRD leads to reasonable agreement with the experimental data, indicating that the pseudorotational model indeed captures the essential features of the electron spin dynamics.

We develop a statistical mechanical model for the thermal and volumetric properties of waterlike fluids. Each water molecule is a two-dimensional disk with three hydrogen-bonding arms. Each water interacts with neighboring waters through a van der Waals interaction and an orientation-dependent hydrogen-bonding interaction. This model, which is largely analytical, is a variant of the Truskett and Dill (TD) treatment of the "Mercedes-Benz" (MB) model. The present model gives better predictions than TD for hydrogen-bond populations in liquid water by distinguishing strong cooperative hydrogen bonds from weaker ones. We explore properties versus temperature T and pressure p. We find that the volumetric and thermal properties follow the same trends with T as real water and are in good general agreement with Monte Carlo simulations of MB water, including the density anomaly, the minimum in the isothermal compressibility, and the decreased number of hydrogen bonds for increasing temperature. The model reproduces that pressure squeezes out water's heat capacity and leads to a negative thermal expansion coefficient at low temperatures. In terms of water structuring, the variance in hydrogen-bonding angles increases with both T and p, while the variance in water density increases with T but decreases with p. Hydrogen bonding is an energy storage mechanism that leads to water's large heat capacity (for its size) and to the fragility in its cagelike structures, which are easily melted by temperature and pressure to a more van der Waals-like liquid state.

Fatty acids constitute one of the main components of the lipid lamellae in the top layer of the skin, known as the stratum corneum, which acts as a barrier to foreign substances entering the body and to water leaving the body. To better understand the mechanics of the skin, a molecular-level understanding of the structure of the lamellae needs to be investigated. As a first step toward this goal, the current work involves the development of a coarse-grained model for fatty acids in an amorphous and a crystalline state. In order to retain the structural details of the atomistic molecules, radial distribution functions have been used to provide target data against which the coarse-grained force field is optimized. The optimization was achieved using the method developed by Reith, Pütz, and Müller-Plathe with a damping factor introduced into the updating scheme to facilitate the convergence against the crystalline radial distribution functions. Using this approach, a transferable force field has been developed for both crystalline and amorphous systems that can be used to describe fatty acids of different chain lengths. We are unaware of any other coarse-grained model in the literature that has been developed to study solid phases. Additionally, the amorphous force field has been shown to accurately model mixtures of different free fatty acids based on the potentials derived from pure lipid systems.

A simple robust method to study resonance gas-phase reactions between neutral peptides of low volatility and free electrons has been designed and implemented. Resonance electron capture (REC) experiments were performed by several neutral model peptides and two naturally occurring peptides. The assignment of negative ions (NIs) formed in these gas-phase reactions was based on high mass-resolving power experiments. From these accurate mass measurements, it was concluded that fragment NIs formed by low (1-2 eV) energy REC are of the same types as those observed in electron capture/transfer dissociation, where the positive charge is a factor. The main feature resulting from these REC experiments by peptides is the occurrence of z(n)-1 ions, which are invariably of the highest abundances in the negative ion mass spectra of larger peptides. [M-H](-) NIs presumably the carboxylate anion structure dominate the REC spectra of smaller peptides. There was no evidence for the occurrence of the complementary reaction, i.e., the formations of c(n)+1 ions. Instead, c(n) ions arose without hydrogen/proton transfer albeit with lower abundances than that observed for z(n)-1 ions. Only the amide forms of small peptides showed more abundant ion peaks for the c(n) ions than for the z(n)-1 ions. The mechanisms for the N-C(alpha) bond cleavage are discussed.

The (13)C NMR signal of acetic acid 1-(13)C-AcH is enhanced by polarization transfer from hyperpolarized (129)Xe using a thermal mixing procedure. 1-(13)C-AcH acid and hyperpolarized (129)Xe are mixed as gases to disperse (129)Xe in the acetic acid. The mixture is frozen with liquid N(2) at 0.5 T. The magnetic field is then momentarily dropped to allow for exchange of spin polarization between (13)C and (129)Xe. After polarization exchange the magnetic field is raised to its original value and the mixture is thawed, resulting in a solution of polarization enhanced 1-(13)C-AcH. A (13)C nuclear spin polarization enhancement of 10 is observed compared to its thermal polarization at 4.7 T. This polarization enhancement is approximately three orders of magnitude lower than that predicted by theory. The discrepancy is attributed to the formation of either an inhomogeneous solid matrix and/or spin dynamics during polarization transfer. Despite the low polarization enhancement, this is the first report of polarization transfer from (129)Xe to (13)C nuclear spins achieved by thermal mixing for a proton-containing molecule of biomedical importance. If future work can increase the enhancement, this method will be useful in hyperpolarizing a wide range of (13)C enriched compounds important in biomedical and biophysical research.

The method developed in a previous paper [R. Mazo, J. Chem. Phys. 129, 154101 (2008)] for extracting information on the size of relative fluctuations in multicomponent systems is tested on ten binary systems and one ternary system. For the binary systems, it is found that the approximation works well for mole fractions in the range of 0.15-0.85 in most cases. For the ternary case, the method inherently yields less information and is valid only over a more restricted range for the case studied (chloroform-methanol-acetone). It is found that the predicted ratio of number fluctuations is approximately equal to the ratio of molar volumes of the components.

Recent experimental observations of time-resolved multidimensional signals in the light-harvesting antennae Fenna–Mathews–Olson [G. S. Engel et al., Nature (London) 446, 782 (2007)] show large oscillations of exciton populations coupled to the long-lived coherences. These effects may not be reproduced by the standard Redfield theory which assumes weak coupling to a bath. A more general relaxation superoperator which holds for all system-bath coupling parameter regimes is constructed by taking into account the statistics (covariances) of Lindblad equation parameters. Simulations for a model dimer reproduce all observed strong coupling effects.

The HCN tetramer, diaminomaleonitrile, crystallizes in sheets with amine and nitrile groups of neighboring molecules in close proximity. This suggests the possibility of relatively facile acid-base addition to form a protopeptide polymer. We find that moderate heating under argon indeed results in an unmistakable reaction, with the abrupt transformation of pale crystallites to shrunken dark particles that become electrically conductive upon doping with iodine. Since nearly a quarter of the mass is lost in the process and the released gas condenses, polymerizes, and reacts with aqueous AgNO(3) like HCN, it seems likely that the dark solid is a polymer of HCN trimer. (13)C and (15)N solid state NMR spectra show the formation of new N-C bonds, and entirely different functional groups from those observed in polymers formed by liquid HCN. These include three different types of nitrogen functionalities and an absence of saturated carbon or nitrile. The observed chemical shifts, optical properties, and electrical conductivity are consistent with polymers of HCN trimer that have undergone cyclization to form poly-[aminoimidazole].

The two-dimensional vibrational response of the disordered strongly fluctuating OH exciton band in liquid water is investigated using a new simulation protocol. The direct nonlinear exciton propagation generalizes the nonlinear exciton equations to include nonadiabatic time dependent Hamiltonian and transition dipole fluctuations. The excitonic picture is retained and the large cancellation between Liouville pathways is built-in from the outset. The sensitivity of the photon echo and double-quantum-coherence techniques to frequency fluctuations, molecular reorientation, intermolecular coupling, and the two-exciton coherence is investigated. The photon echo is particularly sensitive to the frequency fluctuations and molecular reorientation, whereas the double-quantum coherence provides a unique probe for intermolecular couplings and two-exciton coherence.

Due to the limited sensitivity of many nuclear magnetic resonance (NMR) applications, careful consideration must be given to the effect of NMR data processing on spectral noise. This work presents analytical relationships as well as simulated and experimental results characterizing the propagation of noise by unsymmetric covariance NMR processing, which concatenates two NMR spectra along a common dimension, resulting in a new spectrum showing spin correlations as cross peaks that are not directly measured in either of the two input spectra. It is shown how the unsymmetric covariance spectrum possesses an inhomogeneous noise distribution across the spectrum with the least amount of noise in regions whose rows and columns do not contain any cross or diagonal peaks and with the largest amount of noise on top of signal peaks. Therefore, methods of noise estimation commonly used in Fourier transform spectroscopy underestimate the amount of uncertainty in unsymmetric covariance spectra. Different data processing procedures, including the Z-matrix formalism, thresholding, and maxima ratio scaling, are described to assess noise contributions and to reduce noise inhomogeneity. In particular, determination of a Z score, which measures the difference in standard deviations of a statistic from its mean, for each spectral point yields a Z matrix, which indicates whether a given peak intensity above a threshold arises from the covariance of signals in the input spectra or whether it is likely to be caused by noise. Application to an unsymmetric covariance spectrum, obtained by concatenating two 2D (13)C-(1)H heteronuclear, single quantum coherence (HSQC) and (13)C-(1)H heteronuclear, multiple bond correlation (HMBC) spectra of a metabolite mixture along their common proton dimension, reveals that for sufficiently sensitive input spectra the reduction in sensitivity due to covariance processing is modest.

This report introduces a new approach that enhances nonlinear solution magnetic resonance signals from intermolecular dipolar interactions. The resulting signals can theoretically be as large as the full equilibrium magnetization. Simple, readily implemented pulse sequences using square-wave magnetization modulation simultaneously refocus all even order intermolecular multiple quantum coherences, leading to a substantial net signal enhancement, complex nonlinear dynamics, and improved structural sensitivity under realistic conditions.

Explicit expressions are developed for the chemical potential derivatives, partial molar volumes, and isothermal compressibility of solution mixtures involving four components at finite concentrations using the Kirkwood-Buff theory of solutions. In addition, a general recursion relationship is provided which can be used to generate the chemical potential derivatives for higher component solutions.