Study of the Crystal Structure and Hydrogen Bonding during Cold Crystallization of Poly(trimethylene 2,5-furandicarboxylate).

Here, we present a detailed description of the in situ isothermal crystallization of poly(trimethylene 2,5-furandicarboxylate)(PTF) as revealed by real-time Fourier transform infrared spectroscopy (FTIR) and grazing incidence wide-angle X-ray scattering (GIWAXS). From FTIR experiments, the evolution of hydrogen bonding with crystallization time can be monitored in real time, while from GIWAXS, crystal formation can be followed. Density functional theory (DFT) calculations have been used to simulate FTIR spectra for different theoretical structures, enabling a precise band assignment. In addition, based on DFT ab initio calculations, the influence of hydrogen bonding on the evolution with crystallization time can be understood. Moreover, from DFT calculations and comparison with both FTIR and GIWAXS experiments, a crystalline structure of poly(trimethylene 2,5-furandicarboxylate) is proposed. Our results demonstrate that hydrogen bonding is present in both the crystalline and the amorphous phases and its rearrangement can be considered as a significant driving force for crystallization of poly(alkylene 2,5-furanoate)s.

Estimation of diffusion coefficients during carrots cooking in arsenious solution at different temperatures.

This study is based on an investigation of the transport phenomenon, specifically the quantification of arsenic diffusion in carrots within a temperature range of 89 °C-99 °C using a thin plate model. Studying the diffusion of arsenic in carrots is important due to its toxicity, as it can concentrate during cooking. The World Health Organization considers arsenic as one of the ten chemical substances of public health concern. In this study, biennial hybrid carrots of the Nantesa variety were cooked whole with their epidermis in an aqueous solution containing diarsenic trioxide with an As concentration of 5 mgL-1 at 89 °C, 94 °C, and 99 °C. The cooking times of the carrots at different temperatures were based on a specific degree of tenderness, with a value of ≤3 kg m-2. The evaluated data showed consistency with increasing temperature. The calculated effective diffusion coefficients at temperatures of 89 °C, 94 °C, and 99 °C were 5.84E-09 m2s-1, 1.08E-08 m2s-1, and 2.51E-08 m2s-1 for the flesh (DL), and 1.601E-11 m2s-1, 2.15E-11 m2s-1, and 4.39E-11 m2s-1 for the epidermis (DE), respectively. The activation energy for diffusion was determined to be 159.54 kJmol-1 for the and 110.68 kJmol-1 for the epidermis. Similar behaviours were observed in different radial positions of the carrot, where the arsenic content decreased from the periphery to the centre, consistent with studies on diffusion phenomena with other solutes in food. The novelty was the detailed quantification of arsenic diffusion in the Nantes-type hybrid carrot matrix. This study is limited to a specific concentration of 5 mgL-1 of arsenic solution. The findings of this study may have significant implications for public health and food safety.

Effects of confinement and vaccination on an epidemic outburst: A statistical mechanics approach.

This work describes a simple agent model for the spread of an epidemic outburst, with special emphasis on mobility and geographical considerations, which we characterize via statistical mechanics and numerical simulations. As the mobility is decreased, a percolation phase transition is found separating a free-propagation phase in which the outburst spreads without finding spatial barriers and a localized phase in which the outburst dies off. Interestingly, the number of infected agents is subject to maximal fluctuations at the transition point, building upon the unpredictability of the evolution of an epidemic outburst. Our model also lends itself to testing vaccination schedules. Indeed, it has been suggested that if a vaccine is available but scarce it is convenient to carefully select the vaccination program to maximize the chances of halting the outburst. We discuss and evaluate several schemes, with special interest on how the percolation transition point can be shifted, allowing for higher mobility without epidemiological impact.

Energetics and structures of the tilted phases of fatty acid Langmuir monolayers.

Langmuir monolayers are monomolecular deep films composed of amphiphilic molecules which are typically confined to a water/air interface in a bi-dimensional structure. Due to the important applications in many research areas, they have been studied for many years. Their phase diagrams present several condensed phases, showing untilted or tilted structures at low values of surface pressure. In this paper, we present a novel density functional study on tilted phases of different fatty acid Langmuir monolayers. By means of this study, a further understanding of the physical chemistry properties and the nature of the formation of tilted monolayers can be achieved. Our calculations reveal that, regardless of the number of carbon atoms which form the apolar chain, the transversal (or conventional in the case of untilted phases) unit cell shows similar dimensions, ca. 4.9 × 6.8 Å, which is in fair agreement with the range of the observed data. The energy variation of the unit cell as a function of the inclination of the molecules, reveals an abrupt increase in values larger than 45° and 36° for NN- and NNN-tilt, respectively, in fair agreement with the experimental observation of L2h (NN) and L2' (NNN) phases of fatty acids. All of the fatty acids explored (from 10 to 19 carbon atoms) yield similar results. Finally, the energetics and structural changes of the monolayer along the variation of the area per molecule, obtained by enlarging in a-, b- or both axes of the untilted unit cell, have been explored. This study reveals that the untilted phases are energetically more stable at low values of area per molecule (high surface concentration), as it is expected. When the area per molecule values are increased, tilted phases (along NN or NNN-direction) with b/a ratio typical of herringbone (HB) or pseudo-herringbone (PHB) structures are found in the lowest energy configurations, which depend on how the distortion of the untilted unit cell is performed. For example, HB structures are the most stable when the molecules tilt along the enlarged axis of the untilted unit cell (a or b), meanwhile unit cell structures characteristic of PHB configurations occur in the opposite cases and at larger values of the area per molecule (low surface concentrations). All these predictions are in good agreement with the GIXD observations of the different phases of the phase diagram of fatty acid Langmuir monolayers.

Iodide conversion to iodate in aqueous and solid aerosols exposed to ozone.

The aqueous-phase and surface reactions of ozone (O3) with iodide (I-) in/on seawater have been recently found to be a strong atmospheric source of iodine. In addition, ozone also reacts with I- in solid and aqueous sea-salt aerosol. However, the primary products of the heterogeneous reactions of ozone with I- have not been clarified. In this paper, solid and aqueous KI aerosols have been exposed to ozone in an aerosol flow tube system and I- and iodate (IO3-) concentrations have been measured by UV-Vis spectroscopy. The results of these experiments have been combined with a kinetic model to elucidate the primary products of the aqueous and surface reactions. The reaction of ozone with aqueous iodide has been inferred to originate different products depending on whether it occurs at the surface via O3 adsorption (product I2-) or in the aqueous phase via O3 solvation (product IO-). The surface reaction of ozone with solid KI in the presence of water vapor forms KIO3, and other species, which are likely to be gaseous. Although the reactions have been studied in aerosols, the results can be extrapolated to aqueous solutions as well.

Energetics and structure of Langmuir monolayers of palmitic acid: a DFT study.

Langmuir monolayers are monomolecular wide films composed of amphiphilic molecules with a bi-dimensional structure typically formed at the air-water interface. They have been studied for many years because these monolayers have important applications in many research fields. Their phase diagrams present several condensed phases whose atomic structure is not yet completely known. We present a novel density functional study on palmitic acid dimers and monolayers. Our results reveal that dihydrogen contacts established among alkyl chains play a leading role in the final structure, regarding both dimers and for the arrangement of molecules in the monolayer. In addition, our calculations show that tilted phases at approx. 30° can be formed without significant loss of structure stability, a result that is in agreement with the experimental findings. Different structures for the high pressure phases, S and CS, are proposed here for the first time, being in good agreement with the diffraction data available. Furthermore, linear compressibility values also in accordance with previous experimental studies are presented for several structures.

A revisit of the interaction of gaseous ozone with aqueous iodide. Estimating the contributions of the surface and bulk reactions.

The main source of atmospheric iodine is the heterogeneous reaction of aqueous iodide (I-) with ozone (O3), which takes place in surface seawater and probably in sea-salt aerosols. However, there are seemingly contradictory conclusions about whether this heterogeneous reaction occurs in the bulk of the aqueous phase, via O3 dissolution, or at the aqueous surface, via O3 adsorption. In this work, the ozone uptake coefficient has been calculated as a function of the concentration of aqueous iodide ([I-]aq) and gaseous ozone near the aqueous surface ([O3]gs) by estimating parameters of the resistor model using results of previous studies. The calculated uptake coefficients suggest that the aqueous-phase reaction dominates at low I- concentrations (about <10-4 mol L-1), regardless of [O3]gs, and also at sufficiently high [O3]gs (about >80 ppm), regardless of [I-]aq. In contrast, the surface reaction dominates at high [I-]aq (about >10-4 mol L-1) as long as [O3]gs is low enough (about <80 ppm). This trend is able to reconcile previous studies of this reaction, and is a consequence of several factors, including the high surface excess of both reactants ozone and iodide. Given the typical O3 concentrations in the troposphere and the possible I- concentrations and O3 solubilities in sea-salt aerosols, the surface reaction may compete with the aqueous-phase reaction in accumulation-mode aerosols, unlike in surface seawater, where the aqueous-phase reaction probably prevails. The rate constant of the surface reaction has been estimated as (3-40) × 10-13 cm2 molecule-1 s-1.

A theoretical study on the reaction of ozone with aqueous iodide.

Atmospheric iodine chemistry plays a key role in tropospheric ozone catalytic destruction, new particle formation, and as one of the possible sinks of gaseous polar elemental mercury. Moreover, it has been recently proposed that reaction of ozone with iodide on the sea surface could be the major contributor to the chemical loss of atmospheric ozone. However, the mechanism of the reaction between aqueous iodide and ozone is not well known. The aim of this paper is to improve the understanding of such a mechanism. In this paper, an ab initio study of the reaction of aqueous iodide and ozone is presented, evaluating thermodynamic data of the different reactions proposed in previous experimental studies. In addition, the structures, energetics and possible evolution of the key IOOO(-) intermediate are discussed for the first time.

Metastable Nitric Acid Trihydrate in Ice Clouds.

The composition of high-altitude ice clouds is still a matter of intense discussion. The constituents in question are ice and nitric acid hydrates, but the exact phase composition of clouds and its formation mechanisms are still unknown. In this work, conclusive evidence for a long-predicted phase, alpha-nitric acid trihydrate (alpha-NAT), is presented. This phase was characterized by a combination of X-ray and neutron diffraction experiments, allowing a convincing structure solution. Furthermore, vibrational spectra (infrared and inelastic neutron scattering) were recorded and compared with theoretical calculations. A strong interaction between water ice and alpha-NAT was found, which explains the experimental spectra and the phase-transition kinetics. On the basis of these results, we propose a new three-step mechanism for NAT formation in high-altitude ice clouds.

Theoretical model of the interaction of glycine with hydrogenated amorphous carbon (HAC).

A theoretical model of hydrogenated amorphous carbon (HAC) is developed and applied to study the interaction of glycine with HAC surfaces at astronomical temperatures. Two models with different H content are tried for the HAC surface. The theory is applied at the Density Functional Theory (DFT) level, including a semiempirical dispersion correlation potential, d-DFT or Grimme DFT-D2. The level of theory is tested on glycine adsorption on a Si(001) surface. Crystalline glycine is also studied in its two stable phases, α and ß, and the metastable γ phase. For the adsorption on Si or HAC surfaces, molecular glycine is introduced in the neutral and zwitterionic forms, and the most stable configurations are searched. All theoretical predictions are checked against experimental observations. HAC films are prepared by plasma enhanced vapor deposition at room temperature. Glycine is deposited at 20 K into a high vacuum, cold temperature chamber, to simulate astronomical conditions. Adsorption takes place through the acidic group COO(-) and when several glycine molecules are present, they form H-bond chains among them. Comparison between experiments and predictions suggests that a possible way to improve the theoretical model would require the introduction of aliphatic chains or a polycyclic aromatic core. The lack of previous models to study the interaction of amino-acids with HAC surfaces provides a motivation for this work.

The formation of carbamate ions in interstellar ice analogues.

Carbon dioxide and ammonia are two of the most abundant species in astrophysical media, where they can react in the solid phase under certain conditions. This contribution presents a study of this reaction both in the presence of water and for anhydrous samples. It is shown that after deposition at 15 K, the reaction can start by warming the deposit, and the process continues on up to a temperature of 220 K. Reaction products are studied using infrared spectroscopy and mass spectrometry. For anhydrous samples, a 2 : 1 stoichiometry mixture of NH3 : CO2 gives the highest yield of products. The reaction is favored when a small amount of water is present, which enables ammonia and carbon dioxide molecules to collide within the pores and channels of the amorphous water solid. Large concentration of water, on the other hand, hampers such collisions. The main reaction product is found to be ammonium carbamate, but also carbamic acid is formed, and, in the presence of water, ammonium bicarbonate is produced as well. Theoretical calculations are carried out to provide the basis for the assignment of the spectra. Some of the experiments presented in this contribution consist of the generation of a compact water ice matrix where the carbamate and ammonium ions are embedded. If such a system was found in astrophysical media, it is shown that the ammonium ion could not be detected, whereas two infrared features of the carbamate ion in the 1040 to 1115 cm(-1) (9 to 9.6 µm) region could enable the observation of this species.

An infrared study of solid glycine in environments of astrophysical relevance.

The conversion from neutral to zwitterionic glycine is studied using infrared spectroscopy from the point of view of the interactions of this molecule with polar (water) and non-polar (CO(2), CH(4)) surroundings. Such environments could be found on astronomical or astrophysical matter. The samples are prepared by vapour-deposition on a cold substrate (25 K), and then heated up to sublimation temperatures of the co-deposited species. At 25 K, the neutral species is favoured over the zwitterionic form in non-polar environments, whereas for pure glycine, or in glycine/water mixtures, the dominant species is the latter. The conversion is easily followed by the weakening of two infrared bands in the mid-IR region, associated to the neutral structure. Theoretical calculations are performed on crystalline glycine and on molecular glycine, both isolated and surrounded by water. Spectra predicted from these calculations are in reasonable agreement with the experimental spectra, and provide a basis to the assignments. Different spectral features are suggested as probes for the presence of glycine in astrophysical media, depending on its form (neutral or zwitterionic), their temperature and composition.

Ab initio study of hydroxyl torsional barriers and molecular properties of mono- and di-iodotyrosine.

Phenol rings with one or two iodine atoms bonded to ortho carbons are the essential organic source of iodine for living organisms. The salvage of this halogen fundamental for a variety of biological functions is accomplished through enzymatic processes that rely on recognition of mono- and di-iodotyrosine (MIT and DIT, respectively). Ab initio quantum calculations are used to investigate molecular properties of MIT and DIT associated with their recognition by cognate proteins. Energies, electron density properties, atomic charges, and electrostatic potentials are analyzed in relation with the presence of one or two iodine atoms and internal rotation of hydroxyl hydrogen. The formation of an intramolecular hydrogen bond at some conformations has little effect on the properties that might affect the recognition and further deiodination of MIT and DIT. Polarizability of iodine and the reactive nature of iodinated tyrosines as nucleophilic targets are the essential features revealed in this work.

Clusters of atmospheric relevance: H(2)O/HCl/HNO(3). Prediction of IR & MW spectra.

Theoretical calculations at the B3LYP/aug-cc-pVQZ level are performed on ternary clusters of water, hydrogen chloride and nitric acid to predict their IR and MW spectra. The main IR spectral features and their changes in a set of 15 selected clusters are analyzed in terms of the different hydrogen bonding characteristics of the aggregates. The formation of these clusters in laboratory experiments and their possible identification based on their infrared and microwave spectral properties are discussed. Based on a calculation of the Gibbs free-energy of formation of the clusters from their monomers, the population distribution of the molecules at atmospherically relevant temperatures is evaluated, and the IR spectra of the composed mixture are predicted. The variations of specific spectral features with temperature are assessed, and the possible observation of these features is proposed as a means to detect the existence of these clusters, as well as an indication of the temperature of the corresponding atmospheric sample.

Interaction of CH4 and H2O in ice mixtures.

Ice mixtures of methane and water are investigated by means of IR spectroscopy in the 14-60 K range. The spectroscopic research is focused on the symmetry-forbidden nu(1) band of CH(4) and the dangling bond bands of water. The nu(1) band is visible in the spectra of the mixtures, revealing a distorted methane structure which co-exists with the normal crystalline methane. The water dangling bond bands are found to increase their intensity and appear at red-shifted frequency when distorted methane is present. Methane adsorbed on water micropores or trapped inside the amorphous solid water structure is assumed to be responsible for these effects. CH(4) mobility in water ice depends on the deposition method used to prepare the samples and on the temperature. After warming the samples to 60 K, above the methane sublimation point, a fraction of CH(4) is retained in the water ice. An adsorption isotherm analysis is performed yielding the estimation of the desorption energy of CH(4) on H(2)O amorphous surfaces.

Active Site, Catalytic Cycle, and Iodination Reactions of Vanadium Iodoperoxidase: A Computational Study.

A combined computational study using molecular surfaces and Poisson-Boltzmann electrostatic potentials for proteins and quantum calculations on complexes representing the vanadate cofactor throughout the catalytic cycle is employed to study the activity of vanadium iodoperoxidase (VIPO) from alga Laminaria digitata . A model structure of VIPO is compared with available crystal structures of chloroperoxidases (VClPOs) and bromoperoxidases (VBrPOs) focusing on properties of the active site that concern halogen specificity. It is found that VIPO displays distinctive features regarding electrostatic potentials at the site cavity and the local topography of the cavity entrance. Quantum calculations on cofactor stages throughout the catalytic cycle reveal that, while steps involving binding of hydrogen peroxide and halide oxidization agree with available data on VBrPO, final formation and subsequent release of hypohalous acid could follow a different pathway consisting of His476-assisted protonation of bonded hypoiodite and further displacement by a water molecule. Ab initio free energies of reaction computed to explore iodination of organic substrates predict strongly exoergonic reactions with HOI, whereas other possible iodination reagents give thermodynamically disfavored reactions.

Characterization of two types of intermolecular interactions on halogen monoxide monohydrates.

Monohydrates of halogen monoxides ClO.H2O and BrO.H2O have been studied by means of DFT (B3LYP) and ab initio (MP2) correlated calculations with aug-cc-pVnZ basis sets ranging from triple- up to quintuple-zeta. These complexes might be formed in the troposphere and stratosphere and participate in chemical reactions involved in ozone depletion. Two stable structures are found that differ in the intermolecular interaction which takes place, namely: conventional XO...HOH hydrogen bond and OX...OH2 halogen bond. We demonstrate that both types of interactions participate in the formation of these complexes yet all the computational methods tested predict a slightly greater stability for the latter OX...O link. Both intermolecular interactions are characterized upon analyzing electron density distribution, charge transfer effects, and electron localization domains. These analyses reveal the central role played by electron redistribution. Because of this, the greater spatial extent of the electron density in Cl or Br as compared to H could be the main cause to yield a slightly greater stability for the O-X...O halogen bond with respect to the O...H-O hydrogen bond.

Phases of solid methanol.

The solid phases of methanol were investigated using IR spectroscopy and numerical calculations with the SIESTA method. Improved spectra are reported of amorphous methanol at 90 K, and in particular of the alpha and beta phases at 130 and 165 K, respectively, with assignments of bands not previously measured. The main features of the spectra of each phase are discussed and compared. A study of spectral changes with temperature leads to the conclusion that the metastable phase previously reported might be a mixture of the two known stable phases. Such a mixture could explain all spectral features observed in this investigation. The theoretical calculations provide reasonable agreement with the experimental data for most of the parameters, but predict H-bondings stronger than those observed. Differences between the spectra of the alpha and beta phases are predicted with similar characteristics to the experimental results.

Ices of CO2/H2O mixtures. Reflection-absorption IR spectroscopy and theoretical calculations.

Ice mixtures of CO2 and H2O are studied using Fourier transform reflection-absorption infrared (RAIR) spectroscopy. Mixtures are prepared by sequential deposition or co-deposition of the two components from the gas phase onto an Al plate kept at 87 K inside a low-pressure chamber. Two CO2 structures are found in most experiments: a crystalline form similar to pure CO2, which evaporates when warming at 105 K, and a noncrystalline species which remains embedded in amorphous water ice after warming. Significant spectral variations are found depending on the deposition method and the thickness of the solid. Features characteristic of the RAIR technique appear in the spectral regions of the normal modes of the bending and asymmetric stretching CO2 vibrations. Simulations using Fresnel theory and Mie scattering are carried out with acceptable agreement with the experimental spectra of solids of variable thickness, from approximately 1 microm to the limit of nanoparticles. Theoretical calculations of a pure CO2 crystal are performed. The relaxed geometry of the solid and its vibrational spectrum are determined and compared to the experimental results.