Molecular dynamics simulations for CO2 spectra. II. The far infrared collision-induced absorption band

Classical molecular dynamics simulations have been carried out for gaseous CO(2) starting from various anisotropic intermolecular potential energy surfaces. Through calculations for a large number of molecules treated as rigid rotors, the time evolution of the interaction-induced electric dipole vector is obtained and the Laplace transform of its autocorrelation function gives the collision-induced absorption rototranslational spectrum. The results are successfully compared with those of previous similar calculations before studies of the influences of the intermolecular potential and induced-dipole components are made. The calculated spectra show a significant sensitivity to anisotropic forces consistently with previous analyses limited to the spectral moments. The present results also demonstrate the importance of vibrational and back-induction contributions to the induced dipole. Comparisons between measured far infrared (0-250 cm(-1)) spectra at different temperatures and results calculated without the use of any adjustable parameter are made. When the best and more complete input data are used, the quality of our predictions is similar to that obtained by Gruszka et al. [Mol. Phys. 93, 1007 (1998)] after the introduction of ad hoc short-range overlap contributions. Our results thus largely obviate the need for such contributions the magnitudes of which remain questioned. Nevertheless, problems remain since, whereas good agreements with measurements are obtained above 50 cm(-1), the calculations significantly underestimate the absorption below, a problem which is discussed in terms of various possible error sources.     

Molecular mechanisms of cryoprotection in aqueous proline: light scattering and molecular dynamics simulations

Free proline amino acid is a natural cryoprotectant expressed by numerous organisms under low-temperature stress. Previous reports have suggested that complex assemblies underlie its functional properties. We investigate here aqueous proline solutions as a function of temperature using combinations of Raman spectroscopy, Rayleigh-Brillouin light scattering, and molecular dynamics simulations with the view to revealing the molecular origins of the mixtures' functionality as a cryoprotectant. The evolution of the Brillouin frequency shifts and line widths with temperature shows that, above a critical proline concentration, the water-like dynamics is suppressed and viscoelastic behavior emerges: Here, the Landau-Placzek ratio also shows a temperature-independent maximum arising from concentration fluctuations. Molecular dynamics simulations reveal that the water-water correlations in the mixtures depend much more weakly on temperature than does bulk water. By contrast, the water OH Raman bands exhibit strong red-shifts on cooling similar to those seen in ices; however, no evidence of ice lattice phonons is observed in the low-frequency spectrum. We attribute this primarily to enhanced proline-water hydrogen bonding. In general, the picture that emerges is that aqueous proline is a heterogeneous mixture on molecular length scales (characterized by significant concentration fluctuations rather than well-defined aggregates). Simulations reveal that proline also appears to suppress the normal dependence of water structure on temperature and preserves the ambient-temperature correlations even in very cold solutions. The water structure in cold proline solutions therefore appears to be similar to that at a higher effective temperature. This, coupled with the emergence of glassy dynamics offers a molecular explanation for the functional properties of proline as a cryoprotectant without the need to invoke previously proposed complex aggregates.     

Molecular dynamics and X-ray scattering simulations of cyclic siloxane-based liquid crystal mesogens

Molecular dynamics simulations of cyclic siloxane-based liquid crystals offer new insights into the conformational flexibility of these materials. Interdigitation between the cholesteryl-4'-allyloxybenzoate and biphenyl-4'-allyloxybenzoate mesogens pendant on the cyclic siloxane ring is observed in the simulated structures. All molecular models considered viz. disc, cone, and cylinder, display a large conformational flexibility, which is important regarding the liquid crystalline phase behavior. The disc molecular model exhibits the largest flexibility as indicated by mean dihedral angles and their range for certain principal torsions, evaluated from the molecular dynamics simulations. Results from the dynamics simulations of cylinder molecular pairs indicate a significant amount of conformational flexibility in the siloxane rings. The degree of interdigitation between mesogens is dependent on the flexibility of the siloxane rings, as shown by calculations for a fixed ring system resulting in less interdigitation, also reflected in calculated X-ray scattering sections along the starting molecular direction. Weaker molecular transforms were observed for the non-fixed system due to a lack of boundary conditions. In general, the qualitative agreement of the starting structure's reflections and those shown by the experimental data is encouraging.     

Molecular dynamics simulations of matrix deposition. III. Site structure analysis for porphycene in argon and xenon

Porphycene (1) and porphyrin (2), two constitutional isomers, reveal completely different electronic spectral patterns in argon and xenon matrices. For the former the spectra recorded in the two solidified gases resemble each other, whereas for the latter they are completely different. This difference can be rationalized by molecular-dynamics simulations of the structure of the microenvironment carried out for the two chromophores embedded in argon and xenon hosts. For 1, the structure of the main substitutional site is the same for Ar and Xe and consists of a hexagonal cavity obtained by removing seven host atoms from the [111] crystallographic plane. An analogous structure is obtained for 2 in xenon. However, in argon the porphyrin chromophore environment is shared between several different sites, with the number of replaced host atoms ranging from seven to ten. These results demonstrate that a relatively minor structural alternation may lead to major changes in the spectral pattern of molecules embedded in rare-gas cryogenic matrices.     

A comparison of light scattering and far infrared absorption spectra of simple liquids

Light scattering and far infrared absorption spectra of CCl₄, C₂Cl₄, C₆H₁₂, CHCl₃, and CH₂Cl₂ in the liquid phase have been obtained in the range of 2 – 200 and 20 – 200 cm^?1 respectively. The energy absorption spectra obtained by the two techniques and the corresponding relaxation times were compared for each liquid. We observe systematic differences between the energy absorption profiles obtained from the light scattering spectra and the far infrared absorption spectras. We also find generally shorter relaxation times from the infrared absorption spectra. Despite the similarity of the physical processes leading to light scattering and to far infrared absorption some significant differences are observed (ref. 1,2).     

Molecular dynamics as studied by Fourier transforms of optical absorption spectra. Theoretical method and application to benzene

We have obtained the autocorrelation function of the transition dipole moment by a Fourier transform of the optical absorption spectrum of benzene in solution. From this, we have evaluated some parameters related to the molecular dynamics in the excited state, the Brownian motion of the solution and the HT and BO couplings.     

Examining the collision-induced decomposition spectra of ammoniated triglycerides. III. The linoleate and arachidonate series

A series of positionally pure triglycerides (TAGs) of the form LXL, YLY, AXA, and YAY was synthesized and analyzed by reversed-phase high-performance liquid chromatography/tandem mass spectrometry. L and A represent the linoleate and arachidate moieties, respectively, and X and Y represent large arrays of fatty acid moieties of various chain lengths, degree of unsaturations, double-bond positions, and cis/trans configurations. The abundances of the collision-induced decomposition (CID) products of ammoniated TAGs were examined as a function of these parameters. The major CID products, the diglyceride (DAG) product ions and the MH(+) ions, are plotted as functions of chain length for the saturated and monounsaturated series of X and Y. The following trends are observed in the data. TAGs with higher degrees of unsaturation tend to show greater relative abundances of MH(+) in the CID spectra of their ammoniated precursor ions. The position of the fatty acid constituents along the glycerol backbone also seems to influence the abundances of the MH(+) ion in the CID spectra of the ammoniated precursor ions. A fatty acid constituent with double bonds along the fatty acid chain positioned close to the carbonyl promotes the formation of the DAG product ion that corresponds to its loss upon CID of the ammoniated precursor ion. Linoleic acid substituents also seem to promote the formation of DAG product ions, but to a lesser extent. Data for the YAY TAGs are used to predict the abundances of the product ions in the CID spectra of ammoniated YAX TAGs. These data are discussed in context of a broader project to develop and validate software algorithims to support a platform for comprehensive analysis of complex mixtures of TAGs.     

Effects of nuclear dynamics in the low-kinetic-energy Auger spectra of CO and CO2

The CO and CO(2) carbon and oxygen Auger spectra have been measured by electron impact and compared with accurate theoretical calculations accounting for the effects of the dynamics of the nuclei on the energy and linewidth of the Auger bands. The calculations for CO were previously published [L. S. Cederbaum et al., J. Chem. Phys. 95, 6634 (1991)], while for CO(2) they are new and presented here for the first time. For both molecules, particular attention has been paid to the low-kinetic-energy region of the spectra, which corresponds to doubly charged ion states with the two holes mainly localized in the inner valence region. New bands have been observed. It is shown that a proper consideration of the vibrational broadening and shift of the bands due to the dynamics of the nuclei is needed to assign these features. For CO, very large energy shifts between corresponding features in the C 1s and O 1s spectra have been observed, confirming the theoretical predictions of 1991. The new computed spectra of CO(2) allow a very accurate analysis of the experiments over the whole energy range.     

Molecular dynamics simulations for water and ions in protein crystals

The spatial and temporal properties of water and ions in bionanoporous materials-protein crystals-have been investigated using molecular dynamics simulations. Three protein crystals are considered systematically with different morphologies and chemical topologies: tetragonal lysozyme, orthorhombic lysozyme, and tetragonal thermolysin. It is found that the thermal fluctuations of C(alpha) atoms in the secondary structures of protein molecules are relatively weak due to hydrogen bonding. The solvent-accessible surface area per residue is nearly identical in the three protein crystals; the hydrophobic and hydrophilic residues in each crystal possess approximately the same solvent-accessible surface area. Water distributes heterogeneously and has different local structures within the biological nanopores of the three protein crystals. The mobility of water and ions in the crystals is enhanced as the porosity increases and also by the fluctuations of protein atoms particularly in the two lysozyme crystals. Anisotropic diffusion is found preferentially along the pore axis, as experimentally observed. The anisotropy of the three crystals increases in the order: tetragonal thermolysin < tetragonal lysozyme < orthorhombic lysozyme.     

Molecular dynamics simulations for the growth of CH4-CO2 mixed hydrate

Molecular dynamics simulations are performed to study the growth mechanism of CH4-CO2 mixed hydrate in xco2 = 75%, xco2 = 50%, and zco2 = 25% systems at T = 250 K, 255 K and 260 K, respectively. Our simulation results show that the growth rate of CH4-CO2 mixed hydrate increases as the CO2 concentration in the initial solution phase increases and the temperature decreases. Via hydrate formation, the composition of CO2 in hydrate phase is higher than that in initial solution phase and the encaging capacity of CO2 in hydrates increases with the decrease in temperature. By analysis of the cage occupancy ratio of CH4 molecules and CO2 molecules in large cages to small cages, we find that CO2 molecules are preferably encaged into the large cages of the hydrate crystal as compared with CH4 molecules. Interestingly, CH4 molecules and CO2 molecules frequently replace with each other in some particular cage sites adjacent to hydrate/solution interface during the crystal growth process. These two species of guest molecules eventually act to stabilize the newly formed hydrates, with CO2 molecules occupying large cages and CH4 molecules occupying small cages in hydrate.     

Molecular dynamics simulations for the growth of CH_4-CO_2 mixed hydrate

Molecular dynamics simulations are performed to study the growth mechanism of CH4-CO2 mixed hydrate in xCO2= 75%, xCO2= 50%, and xCO2= 25% systems at T = 250 K, 255 K and 260 K, respectively. Our simulation results show that the growth rate of CH4-CO2 mixed hydrate increases as the CO2 concentration in the initial solution phase increases and the temperature decreases. Via hydrate formation, the composition of CO2 in hydrate phase is higher than that in initial solution phase and the encaging capacity of CO2 in hydrates increases with the decrease in temperature. By analysis of the cage occupancy ratio of CH4 molecules and CO2 molecules in large cages to small cages, we find that CO2 molecules are preferably encaged into the large cages of the hydrate crystal as compared with CH4 molecules. Interestingly, CH4 molecules and CO2 molecules frequently replace with each other in some particular cage sites adjacent to hydrate/solution interface during the crystal growth process. These two species of guest molecules eventually act to stabilize the newly formed hydrates, with CO2 molecules occupying large cages and CH4 molecules occupying small cages in hydrate.     

CO2 diffusivity in LiY and NaY faujasite systems: a combination of molecular dynamics simulations and quasi-elastic neutron scattering experiments

Quasi-elastic Neutron Scattering combined with Molecular Dynamics simulations have been carried out to gain further insight into the CO₂ dynamics in LiY and NaY Faujasites. In both materials, it was pointed out that the transport diffusivity (D_T) increases with the loading whereas the self diffusivity (D_S) decreases. In addition, it was shown that LiY exhibits a significant slower CO₂ self diffusivity process due to a strong interaction between the Li⁺ cation and the adsorbate molecules at the initial stage of diffusion. This result is consistent with higher simulated activation energy in this cation exchanged faujasite form. By contrast, the transport diffusivity is revealed to be slightly faster in LiY than in NaY.     

Phase behavior in model homopolymer/CO2 and surfactant/CO2 systems: discontinuous molecular dynamics simulations

Discontinuous molecular dynamics simulations are performed on surfactant (HmTn)/solvent systems modeled as a mixture of single-sphere solvent molecules and freely jointed surfactant chains composed of m slightly solvent-philic head spheres (H) and n solvent-philic tail spheres (T), all of the same size. We use a square-well potential to account for the head-head, head-solvent, tail-tail, and tail-solvent interactions and a hard-sphere potential for the head-tail and solvent-solvent interactions. We first simulate homopolymer/supercritical CO2 (scCO2) systems to establish the appropriate interaction parameters for a surfactant/scCO2 system. Next, we simulate surfactant/scCO2 systems and explore the effect of the surfactant volume fraction, packing fraction, and temperature on the phase behavior. The transition from the two-phase region to the one-phase region is located by monitoring the contrast structure factor of the equilibrated surfactant/scCO2 system, and the micelle to unimer transition is located by monitoring the aggregate size distribution of the equilibrated surfactant/scCO2 system. We find a two-phase region, a micelle phase, and a unimer phase with increasing packing fraction at fixed temperature or with increasing temperature at fixed packing fraction. The phase diagram for the surfactant/scCO2 system in the surfactant volume fraction-packing fraction plane and the density dependence of the critical micelle concentration are in qualitative agreement with experimental observations. The phase behavior of a surfactant/scCO2 system can be directly related to the solubilities of the corresponding homopolymers that serve as the head and tail blocks for the surfactant. The influence of surfactant structure (head and tail lengths) on the phase transitions is explored.     

Correlated angular and quantum state-resolved CO2 scattering dynamics at the gas-liquid interface

Molecular beam scattering dynamics at the gas-liquid interface are investigated for CO2 (E(inc) = 10.6(8) kcal/mol) impinging on liquid perfluoropolyether (PFPE), with quantum state (v, J) populations measured as a function of incident (theta(inc)) and final (theta(scat)) scattering angles. The internal state distributions are well-characterized for both normal and grazing incident angles by a two-component Boltzmann model for trapping desorption (TD) and impulsive scattering (IS) at rotational temperatures T(rot)(TD/IS), where the fractional TD probability for CO2 on the perfluorinated surface is denoted by TD and IS densities (rho) as alpha = rhoTD/(rhoTD + rhoIS). On the basis of an assumed cos(theta(scat)) scattering behavior for the TD flux component, the angular dependence of the IS flux at normal incidence (theta(inc) = 0 degrees) is surprisingly well-modeled by a simple cos(n)(theta(scat)) distribution with n = 1.0 +/- 0.2, while glancing incident angles (theta(inc) = 30 degrees, 45 degrees, and 60 degrees) result in lobular angular IS distributions scattered preferentially in the forward direction. This trend is also corroborated in the TD fraction alpha, which decreases rapidly under non-normal incident conditions as a function of backward versus forward scattering direction. Furthermore, the extent of rotational excitation in the IS channel increases dramatically with increasing angle of incidence, consistent with an increasing rotational torque due to surface roughness at the gas-liquid interface.