bluuebunny/crossref_metadata_2025_split huggingface dataset:
Ab initio QM/MM MD simulations of the hydrated Ca2+ ion
Authors: Schwenk C. F. , Rode B. M. 
Published: October 2007

Abstract
The comparison of two different combined quantum mechanical (QM)/molecular mechanical (MM) simulations treating the quantum mechanical region at Hartree-Fock (HF) and B3-LYP density functional theory (DFT) level allowed us to determine structural and dynamical properties of the hydrated calcium ion. The structure is discussed in terms of radial distribution functions, coordination number distributions, and various angular distributions and the dynamical properties, as librations and vibrations, reorientational times and mean residence times were evaluated by means of velocity autocorrelation functions. The QM/MM molecular dynamics (MD) simulation results prove an eightfold-coordinated complex to be the dominant species, yielding average coordination numbers of 7.9 in the HF and 8.0 in the DFT case. Structural and dynamical results show higher rigidity of the hydrate complex using DFT. The high instability of calcium ion's hydration shell allows the observation of water-exchange processes between first and second hydration shell and shows that the mean lifetimes of water molecules in this first shell (<100 ps) have been strongly overestimated by conclusions from experimental data.
Solid-state proton conduction: An ab initio molecular dynamics investigation of ammonium perchlorate doped with neutral ammonia
Authors: Rosso L. , Tuckerman M. E. 
Published: October 2007

Abstract
The charge-transport mechanism in solid ammonium perchlorate crystal exposed to an ammonia-rich environment is studied using ab initio molecular dynamics. Ammonium perchlorate is an ionic crystal composed of NH4
+ and ClO4
- ; units that possesses an orthorhombic phase at T < 513 K and a cubic phase at T > 513 K. Exposure to an ammonia-rich atmosphere allows ammonia molecules to be absorbed into the crystal at interstitial sites. It has been proposed that these neutral ammonias can form short-lived N2H7
+ complexes with the NH4
+ ions allowing proton transfer between them, thereby enhancing the conductivity considerably. To date, however, there has been no direct evidence of this proposed mechanism. In this paper, ab initio molecular dynamics techniques are employed to explore this mechanism. By comparing computed infrared spectra of the pure and ammonia-doped crystals, we observe a significant broadening of the NH stretch peak into a lower frequency region, indicating through an experimentally verifiable observable, the formation of hydrogen bonds between NH3 and NH4
+ units. This suggestion is confirmed by direct observation of N2H7
+ complexes from the trajectory. Comparison of the diffusion constants of NH4
+ in the pure and doped crystals yields a ratio that is comparable to the experimentally measured conductivity ratio and clearly shows an enhanced positive charge mobility. Finally, compelling evidence suggesting the possibility of an ammonia umbrella inversion following proton transfer from NH4
+ and NH3 is obtained.
Thermodynamical, structural, and dielectric properties of molecular liquids from integral equation theories and from simulations
Authors: Krienke H. 
Published: October 2007

Abstract
A survey is given on our attempts to calculate equilibrium properties of molecular liquids (pure solvents and electrolyte solutions) with the help of spatial pair correlation functions, starting from classical molecular pair interactions. The selection of potential models, especially the influence of molecular polarizability, is discussed as well as the limitations of the different methods of calculation of molecular pair correlation functions (e.g., from molecular and site-site Ornstein-Zernike theories, from MC and from MD simulations). We have performed simulations and integral equation calculations for spatial distribution functions in pure solvents with very low dielectric constants as dioxane and tetrahydrofurane, up to solvents with a very high dielectric constant like n-methylformamide. Ionic solvation is studied in pure solvent systems as well as in solvent mixtures. The general features of ion solvation and association, of the solvent structure around solutes, and their influence on solution properties, are discussed in the framework of the different theoretical approaches.
Polar solvation dynamics: A combination of the reference interaction-site model and mode-coupling theories
Authors: Nishiyama K. , Yamaguchi T. , Hirata Fumio , Okada T. 
Published: October 2007

Abstract
We employ the reference interaction-site model (RISM) theory for solvation dynamics of simple ions in acetonitrile. For the description of time evolution of solvent relaxation, we apply the mode-coupling theory recently developed by Yamaguchi and coworkers [Mol. Phys.
101, 1211 (2003)]. The combination of the RISM/mode-coupling theory is used for the calculation of the dynamic response function, SS(t), which measures the relaxation of average energy of the solute-solvent system. SS(t) decays with the Gaussian plus underdamped curves in the time duration of first 1 ps, followed by slow, long-tailed components down to tens of picoseconds. We show that the RISM/mode-coupling framework is applicable rather well for the detailed description of solvation dynamics at the molecular level.
Inelastic X-ray scattering and high-frequency dynamics of molecular liquids
Authors: Pontecorvo E. , Di Leonardo R. , Masciovecchio C. , Ruocco G. , Ruzicka B. , Scopigno T. , Sette F. 
Published: October 2007

Abstract
The recently developed inelastic X-ray scattering technique opens a new kinematic region at the observation of molecular liquids vibrational dynamics over the lengthscales of the interparticle separation. We illustrate the capabilities of this powerful technique through the results obtained from liquid glycerol. A detailed analysis of the high-frequency vibrational dynamics of this system at ambient temperature is reported. New results in the study of structural relaxational dynamics in the high-temperature range (up to T = 560 K) are also discussed.
Application of a compact synchrotron radiation facility to studies on the structure of solvated chloride and iodide ions in various solvents
Authors: Ozutsumi K. , Ohtaki H. 
Published: October 2007

Abstract
A beamline equipped on the compact superconductive synchrotron radiation (SR) facility at Ritsumeikan University was designed for performing extended X-ray absorption fine structure (EXAFS) analyses of solutions and solids. The introduction of three different crystals, Si(220), Ge(220), and InSb(111), as the monochromator of the EXAFS spectrometer covers the K-edge absorption energy range of elements with low atomic numbers from silicon (atomic number 14) through zinc (30). The LIII-edge of the iodide ion could be measured by Si(220) and Ge(220). It is, however, not possible to measure the absorption of the bromide ion with this equipment. Using this spectrometer, the solvation structure of Cl- and I- ions was investigated in water, methanol, and ethanol under atmospheric pressure.
Ultrasonically induced birefringence in polymer solutions
Authors: Nomura H. , Matsuoka Tatsuro , Koda Shinobu 
Published: October 2007

Abstract
For ultrasonically induced birefringence in polymer solutions, both the linear sinusoidal birefringence and the nonlinear stationary birefringence were observed. The sign and value of the stationary ultrasonically induced birefringence depended on the molecular structure of segment and its anisotropy in polarizability. Furthermore, no molecular weight dependence could be observed above the molecular weight 104. The theory based on the viscoelastic ones using the Rouse-Zimm model could not explain our experimental results as a whole. These results strongly suggest that the stationary ultrasonically induced birefringence should be caused by the local segmental motion of polymer chain in solution. For all polymer solutions investigated here, the stationary birefringence per ultrasonic intensity decreased with increasing frequency. This frequency dependence is not consistent with the present treatment for the ultrasonically induced birefringence.
External double reference method to study concentration and temperature dependences of chemical shifts determined on a unified scale
Authors: Mizuno K. , Tamiya Y. , Mekata Mamoru 
Published: October 2007

Abstract
We present the principle of an external reference method of NMR, named the external double reference method, to study concentration and temperature dependences of chemical shifts. By the method, we refer chemical shifts of various samples at different temperatures to the peak of a reference substance at a fixed referring temperature. Thus, we can determine the chemical shifts in a variety of sample conditions on a unified scale. Results of the application of the method to 1H- and 1
3C-chemical shifts of water and methanol are presented. We also report new data of volume magnetic susceptibilities for several deuterated solvents useful for the calibration in the method.
Dynamics and metastable surface structure of double atomic layer of water molecules and ions at the interface between KBr(c) and water
Authors: Ichikawa K. , Sato S. , Shimomura N. 
Published: October 2007

Abstract
The metastable surface structure and dynamics of water molecules, cations, and anions at the interface between KBr(001) and water have been demonstrated from the images in situ observed in atomic resolution using atomic force microscopy. The vertical motion of potassium ions, which means their own transfer from the equilibrium sites to the upper height right on the underlying bromide ions, has been observed at the interface. They are used to be located in some steady state stabilized by their interaction with water molecules in the double atomic layer at the interface. The observed water molecules bridge two bromide ions by hydrogen bond; the water molecules are sandwiched by the potassium ions and vice versa.
Dynamics and structure of an amphiphilic triblock copolymer of styrene and 5-(N,N-diethylamino) isoprene in selective solvents
Authors: Riegel I. C. , de Bittencourt F. M. , Terrau O. , Eisenberg A. , Petzhold C. L. , Samios D. 
Published: October 2007

Abstract
Solution properties of a highly asymmetric aminofunctionalized triblock copolymer of 5-(N,N-diethylamino)isoprene and styrene were investigated in dilute regime. Toluene, THF, 1,4-dioxane, or DMF were used to prepare the solutions. It was found that the solvent selectivity for one or both block affects the copolymer solution behavior as reflected by the calculated parameters through light-scattering techniques: weight-averaged, molecular-weight, radius of gyration, translational diffusion coefficient, and hydrodynamic radius. According to what was determined, the quality of the polymer-solvent interactions decreases in the order: toluene, THF, 1,4-dioxane, and DMF. After quaternization with dimethyl sulfate, the triblock copolymer consisted of a polystyrene (PS) block with short poly[5-(N,N,N-diethylmethylammonium)isoprene][methyl sulfate] block at both chain ends, shows a better solvation in polar solvents. Transmission electron microscopy (TEM) was used to characterize the crew-cut aggregates prepared from the quaternized copolymer.
Supercritical water: Local order and molecular dynamics
Authors: Tassaing T. , Danten Y. , Besnard M. 
Published: October 2007

Abstract
This paper is a study of the structure and dynamics of near-critical and supercritical water for thermodynamic states above the critical temperature in a wide range of density by infrared absorption and quasi-elastic neutron scattering. The evolution of the shape of the infrared profiles associated with the internal vibrational modes of water has been investigated. In supercritical water, at T = 380 °C and low pressure (density), in the range 25-50 bar (0.01-0.05 g·cm-3), only monomers are detected. A progressive increase of the pressure (density) from 50 to 250 bar (from 0.05 to 0.4 g·cm-3) leads to the appearance of dimers and trimers. In order to obtain information on the dynamics, we have performed incoherent quasi-elastic neutron-scattering experiments on light water for several thermodynamic states (200 < T < 400 °C and 184 < P < 400 bar) corresponding to densities ranging from 0.2 to 0.9 g·cm-3. The results have been analyzed using a jump diffusion model and the two parameters of this model, namely, τ0, the residence time and D, the translational diffusion coefficient, have been determined as a function of the density.
Local density inhomogeneities detected by Raman scattering in supercritical hexafluorobenzene
Authors: Cabaço M. I. , Besnard M. , Tassaing T. , Danten Y. 
Published: October 2007

Abstract
The influence of the local density inhomogeneities in supercritical hexafluorobenzene C6F6 has been assessed using Raman spectroscopy.
The polarized and depolarized profiles associated with the "breathing" mode of the molecule has been analyzed for the fluid in a wide density range, namely under isothermal conditions.
The evolution upon the density of the band center position of the isotropic profile along the near-critical isotherm showed an anomalous behavior, characterized by a plateau in the density range (0.6 < ρ* = ρ/ρC < 1.3), which is not observed along the isotherm T* ~ 1.11. It has been interpreted as due to the existence of local-density inhomogeneities and the density enhancement factor has been evaluated.
The rotational dynamics of the main symmetry axis of the molecule is governed by a diffusional process. The rotational correlation time τ2R exhibits an anomalous behavior (plateau regime) for both isotherms.
These findings put in evidence the existence of local density inhomogeneities in a pure fluid and show that Raman spectroscopy is well adapted to investigate these phenomena.
Critical Raman line shape behavior of fluid nitrogen
Authors: Musso M. , Matthai F. , Keutel D. , Oehme K.-L. 
Published: October 2007

Abstract
Isotropic Raman line shapes of simple molecular fluids exhibit critical line broadening near their respective liquid-gas critical points. In order to observe this phenomenon, it is essential that the band position of a given vibrational mode is density-dependent, and that vibrational depopulation processes negligibly contribute to line broadening. Special attention was given to the fact that the isotropic (i.e., nonrotationally broadened) line shape of liquid N2 is affected by resonant intermolecular vibrational interactions between identical oscillators. By means of the well-chosen isotopic mixture (14N2).975 - (14N15N).025, the temperature and density dependences of shift, width, and asymmetry of the resonantly coupled 14N2 and, depending on the S/N ratio available, of the resonantly uncoupled 14N15N were determined, with up to milli-Kelvin resolution, in the coexisting liquid and gas phases and along the critical isochore, using a highest-resolution double monochromator and modern charge-coupled device detection techniques. Clear evidence was found that vibrational resonance couplings are present in all dense phases studied.
Raman noncoincidence effect: A spectroscopic manifestation of the intermolecular vibrational coupling in dipolar molecular liquids
Authors: Giorgini M. G. 
Published: October 2007

Abstract
This lecture addresses the analysis of the noncoincidence effect (NCE), a spectroscopic manifestation of the intermolecular coupling in molecular liquids. The vibrational bandshapes of molecular groups like C=O (strongly active in the IR spectrum) in dipolar liquids exhibit this phenomenon at a rather large extent. It will be shown that the vibrational exciton approach, developed under the assumption of the transition dipole coupling (TDC) mechanism, predicts how the orientational structure of the molecular liquid determines the magnitude and sign of the NCE. Specifically, it predicts that in simple molecular liquids, solely structured by dipolar forces, the NCE is large and positive, whereas when liquid structures are dominated by non-dipolar forces (as those present in H-bonded liquids), this scenario dramatically changes and IR-active modes may give rise to negative NCEs.
This lecture is intended to offer a general overview of NCEs observed in dipolar (simple and structured) liquids in different thermodynamic conditions and of the theoretical and simulation results that assisted in their interpretation.
Spectroscopy of interparticle interactions in ionic and molecular liquids: Novel approaches
Authors: Kirillov S. A. 
Published: October 2007

Abstract
The paper deals with several novel approaches to the studies of interactions and dynamics in liquids. A new, flexible time-correlation function is introduced. It has an analytical counterpart in the frequency domain and enables one to fit even badly overlapped vibrational line profiles obtaining dynamical information at the same time. As examples, quantitative description of the interaction potential in molten salts containing halide complexes of zinc and manganese is presented, the dynamic criterion of complex entities in a melt is introduced, and the spectroscopic features of molten alkali and alkaline earth halides are explained in terms of short-lived collision complexes. Finally, the model treatment of "anomalous" noncoincidence effects in liquids is discussed, and the contribution of repulsion and attraction forces resulting in frequency non-coincidences is separated.
Peripheral substituent and solvent effects on the aggregation and photochemical properties of copper(II)phthalocyanine and copper(II)phthalocyanine-3,4',4'',4'''-tetrasulfonic anion
Authors: Szymczyk I. , Abramczyk H. 
Published: October 2007

Abstract
The role played by the peripheral substituent and the solvent on the aggregation and photochemical properties of copper(II) phthalocyanine and copper(II)phthalocyanine-3,4',4'',4'''-tetrasulfonic anion [Cu(tsPc)-4] in aqueous solution has been studied by resonance Raman spectroscopy (RRS). The vibrational mode ν4 (1530 cm-1) and the symmetric and antisymmetric stretching modes of water have been used as a probe of interactions and aggregation in resonance Raman measurements. It has been shown that the Cu(tsPc)-4 molecules have a tremendous influence on water properties in solutions. In contrast, the influence of water on the Cu(tsPc)-4 properties appears to be weak.
Derivation of a molecular mechanics force field for cholesterol
Authors: Cournia Zoe , Vaiana A. C. , Ullmann G. M. , Smith J. C. 
Published: October 2007

Abstract
As a necessary step toward realistic cholesterol:biomembrane simulations, we have derived CHARMM molecular mechanics force-field parameters for cholesterol. For the parametrization we use an automated method that involves fitting the molecular mechanics potential to both vibrational frequencies and eigenvector projections derived from quantum chemical calculations. Results for another polycyclic molecule, rhodamine 6G, are also given. The usefulness of the method is thus demonstrated by the use of reference data from two molecules at different levels of theory. The frequency-matching plots for both cholesterol and rhodamine 6G show overall agreement between the CHARMM and quantum chemical normal modes, with frequency matching for both molecules within the error range found in previous benchmark studies.
Structure of the porphyrazine monolayer at the air-water interface: Computer simulation
Authors: Borodin A. , Kiselev M. 
Published: October 2007

Abstract
Molecular dynamics simulations of porphyrazine monolayers at the air-water interface have been carried out. All possible molecular orientations found by analysis of the π-A isotherms are reproduced by computer simulations. The existence of "guest-water" molecules has been observed in the simulation; this confirms the assumptions of experimentalists concerning this phenomenon.
Translational and rotational dynamics in supercritical methanol from molecular dynamics simulation
Authors: Chalaris Michalis , Samios J. 
Published: October 2007

Abstract
The purpose of this paper is to review our latest molecular dynamics (MD) simulation studies on the temperature and density dependence of the translational and reorientational motion in supercritical (SC) methanol. In the present treatment, Jorgensen's [W. L. Jorgensen. J. Phys. Chem. A
102, 8641 (1998)] transferable potential model, tested in a recent MD study of hydrogen bonds in this fluid [M. Chalaris and J. Samios, J. Phys. Chem. B
103, 1161 (1999)], was employed to simulate the dynamics of the system. The simulations were performed in the canonical (NVT) ensemble along the isotherms 523, 623, and 723 K and densities corresponding to the pressures from 10 to 30 MPa. Several dynamical properties of the fluid have been obtained and analyzed in terms of appropriate time-correlation functions (CFs). With respect to the translational dynamics, the self-diffusion coefficients obtained have been used to test the applicability of the well-known Chapman-Enskog kinetic theory. We have found that the theoretical predictions for the self-diffusion coefficients are only in qualitative agreement with the MD results over the whole temperature and density range studied. Finally, the inspection of the reorientational CFs and their corresponding correlation times lead to the conclusion that the reorientational motion of the SC methanol molecules in the sample is anisotropic.
Origin of the enhanced structural and reorientational relaxation rates in the presence of relatively weak dc electric fields
Authors: Vegiri A. 
Published: October 2007

Abstract
The origin of the dramatic increase of the reorientational and structural relaxation rates of single water molecules in clusters of size N = 16, 32, and 64 at T = 200 K, under the influence of an external, relatively weak electric field (~0.5 107 V/cm) is examined through molecular dynamics simulations. The observed effect is attributed not to any profound structural changes, but to the increase of the size of the molecular cage. The response of water to an electric field in this range shows many similarities with the dynamics of water under low pressure. By referring to simulations and experiments from the literature, we show that in both cases the observed effects are dictated by a common mechanism.
Transport properties of diatomic ions in moderately dense gases in an electrostatic field
Authors: Koutselos A. D. , Samios J. 
Published: October 2007

Abstract
The motion of diatomic ions in moderately dense fluids under the action of an electrostatic field is studied through a nonequilibrium molecular dynamics simulation method. The method simulates the motion of the ions and the fluid molecules that constitute their immediate environment. Thus, effectively, the dissipation of the excess energy of the ions is reproduced leading to steady drift motion. Results revealed the effect of the fluid density on mobility, ion-effective temperatures and diffusion coefficients parallel and perpendicular to the field at various field strengths for a model diatomic ion in Ar. Extension of the method to dense fluids and to polyatomic ions and neutral molecules is discussed.