Gas-phase Properties Research Articles

Polarizable empirical force field for sulfur-containing compounds based on the classical Drude oscillator model.

Condensed-phase computational studies of molecules using molecular mechanics approaches require the use of force fields to describe the energetics of the systems as a function of structure. The advantage of polarizable force fields over nonpolarizable (or additive) models lies in their ability to vary their electronic distribution as a function of the environment. Toward development of a polarizable force field for biological molecules, parameters for a series of sulfur-containing molecules are presented. Parameter optimization was performed to reproduce quantum mechanical and experimental data for gas phase properties including geometries, conformational energies, vibrational spectra, and dipole moments as well as for condensed phase properties such as heats of vaporization, molecular volumes, and free energies of hydration. Compounds in the training set include methanethiol, ethanethiol, propanethiol, ethyl methyl sulfide, and dimethyl disulfide. The molecular volumes and heats of vaporization are in good accordance with experimental values, with the polarizable model performing better than the CHARMM22 nonpolarizable force field. Improvements with the polarizable model were also obtained for molecular dipole moments and in the treatment of intermolecular interactions as a function of orientation, in part due to the presence of lone pairs and anisotropic atomic polarizability on the sulfur atoms. Significant advantage of the polarizable model was reflected in calculation of the dielectric constants, a property that CHARMM22 systematically underestimates. The ability of this polarizable model to accurately describe a range of gas and condensed phase properties paves the way for more accurate simulation studies of sulfur-containing molecules including cysteine and methionine residues in proteins.

A systematic computational study on flavonoids.

17 selected flavones derivatives, flavonoids, were analyzed through a systematic B3LYP/6-311++G** computational study with the aim of understanding the molecular factors that determine their structural and energetic properties in gas phase. Flavonoids were selected in a systematic way to infer the effect of the number and relative positions of hydroxyl groups on molecular properties. Different conformers for each flavonoid were analyzed and the strength and topology of the intramolecular hydrogen bonds studied through the computation of the corresponding torsional profiles. Atoms in a Molecule, and Natural Bond Orbital methodology was applied to the analysis of charge distribution along the studied molecules, and the intramolecular hydrogen bonds. Molecular shapes were studied through full geometry optimization, and the position of the catechol ring analyzed through dihedral scans.

Studies of Ti 1.5Zr 5.5V 0.5(M xNi 1− x) 9.5 (M = Cr, Mn, Fe, Co, Cu, Al): Part 2. Hydrogen storage and electrochemical properties

In Part 2 of this two part series of papers, the gas phase and electrochemical properties of the quinary alloy Ti 1.5Zr 5.5V 0.5(M x Ni 1− x ) 9.5 with M = Cr, Mn, Fe, Co, Cu, or Al and x = 0.1 or 0.2 are studied and compared to the structural properties reported in Part 1. The electrochemical properties of the alloys are strongly related to the non-Laves phases. For example, the Zr 7Ni 10 phase provides a more catalytic surface and improves the high rate discharge capability of the alloy at the expense of discharge capacity due to the higher Ni to Zr ratio; the Zr 9Ni 11 phase, on the contrary, improves the discharge capacity but hinders the high rate discharge capability. In the Laves phases, C14 provides a stable hydride with lower equilibrium pressure, higher gas phase storage capacity and lower electrochemical rate capability. The C15 phase provides a less stable hydride with higher equilibrium pressure, lower gas phase storage capacity and higher electrochemical storage capacity. The main effect of each modifying element can be summarized as follows: Mn is the most beneficial substitution element found in this study. Mn increases both the gas phase and electrochemical capacities with good reversibility; it also improves the activation, hydrogen diffusion, surface reaction, and high rate discharge capability. Co increases the degree of disorder in the alloy, reduces both gas phase and electrochemical capacities, destabilizes the hydride, improves activation, and reduces surface reactivity. Fe decreases the gas phase capacity but improves the electrochemical discharge capacity. Fe facilities activation, but its surface reaction is the least active among the substituents used in this study. Al, Cr, and Cu are less desirable because they reduce: (1) the electrochemical and gas phase capacities, (2) the reversibility, and (3) the rate capability. They also slow activation.

Hydration of cyanin dyes

We investigated the hydration properties of the cyanin dye molecule in the ionic flavylium configuration, through massive classical (force field) and ab initio (Car-Parrinello) molecular dynamics simulations at room temperature. Classical and quantum mechanical results coherently describe the structure of the first solvation shell. We discuss the hydrophobicity/hydrophilicity of the molecule in terms of attractive lateral hydroxyl-water and repulsive carbon pi-water interactions. The analysis of the electronic structure shows a net polarization and a molecular orbital redistribution induced by the polar solvent on the intrinsic (gas phase) properties of the dye. Changing the properties of the molecule, the hydration effects should be carefully taken into account in the further interactions of cyanin with the external environment.

Structural discrimination of isomeric tetrahydrofuran lignan glucosides by tandem mass spectrometry

Due to the possible role in human health, the number of analytical studies on lignans aimed at their quali- and quantitative analysis in plant extracts, biological fluids and foods is continuously increasing. However, helpful systematic mass spectrometric investigations on these compounds are few and rather limited to specific lignan sub-classes. To increase the comprehension of the previously outlined picture of the gas-phase properties of furofuran lignans, we extended the study to tetrahydrofuran lignans and here we reported the collision-activated dissociation (CAD) fragmentation patterns of the alkali metal cation adducts, [M+Alk](+), and [M-H](-) ions of three isomeric tetrahydrofuran lignans, (+)-8'-hydroxylariciresinol 4'-O-beta-D-glucopyranoside (1), (+)-7'-hydroxylariciresinol 7'-O-beta-D-glucopyranoside (2) and 4-O-beta-D-glucopyranosyloxy-3,3'-dimethoxy-7,9'-epoxylignan-5',8',9-triol (3) investigated by electrospray ionization triple quadrupole mass spectrometry (ESI-TQMS). Hydrogen/deuterium (H/D) solution exchange experiments, allowing the selective H/D exchange of all the acidic hydrogen atoms, proved to be a very effective tool to obtain information on the nature of fragments generated during TQ/CAD processes. The [M+Na](+) CAD mass spectra of the three isomeric tetrahydrofurans revealed four different pathways involving the loss of the glucose moiety, which allowed the assignment of the glycosylation site. In the negative ion mode, the main fragmentation channel of the [M-H](-) ions of O-glucosylated lignans at the phenolic oxygen atoms is represented by the loss of 162 Da. When the sugar is bound to a benzylic OH group the loss of the sugar as a 180 Da unit occurs eventually following the loss of a water molecule involving both the C(9)H(2)OH chain and the sugar.

Gas-phase flame synthesis and properties of magnetic iron oxide nanoparticles with reduced oxidation state

Iron oxide nanoparticles of reduced oxidation state, mainly in the form of magnetite, have been synthesized utilizing a new continuous, gas-phase, nonpremixed flame method using hydrocarbon fuels. This method takes advantage of the characteristics of the inverse flame, which is produced by injection of oxidizer into a surrounding flow of fuel. Unlike traditional flame methods, this configuration allows for the iron particle formation to be maintained in a more reducing environment. The effects of flame temperature, oxygen-enrichment and fuel dilution (i.e. the stoichiometric mixture fraction), and fuel composition on particle size, Fe oxidation state, and magnetic properties are evaluated and discussed. The crystallite size, Fe(II) fraction, and saturation magnetization were all found to increase with flame temperature. Flames of methane and ethylene were used, and the use of ethylene resulted in particles containing metallic Fe(0), in addition to magnetite, while no Fe(0) was present in samples synthesized using methane.

The 1,4-phenylenediisocyanide dimer: gas-phase properties and insights into organic self-assembled monolayers

The 1,4-phenylenediisocyanide (PDI) dimer serves as an intriguing case of the substituted benzene dimer, as well as a prototype system for self-assembled monolayers of organic isocyanide complexes. Structures and binding energies are explored using recently developed dual-basis second-order Møller-Plesset perturbation theory energies and gradients. The structures are dictated by a combination of dispersion and electrostatics, a combination not properly treated with local or gradient-corrected density functionals. The PDI dimer binds more than twice as strongly as unsubstituted benzene dimers in several configurations, and greater directional specificity between parallel-displaced and T-shaped structures is observed. A rotated-parallel structure is the predicted lowest-energy, gas-phase configuration, in which the isocyanide ligands are staggered on the monomers. Relevant potential energy curves of the dimer are also presented, and insights into PDI monolayer formation on metal surfaces are explored via simple two-body models. Based on the adsorbate interaction alone, a high-coverage configuration and non-vertical tilt are predicted to be favorable, although the total binding for PDI in these configurations is still insufficient to form ordered monolayers, a result consistent with previous experimental findings. Additional phenyl rings (biphenyldiisocyanide, triphenyldiisocyanide) significantly stabilize the interaction and provide the additional dispersion necessary for an ordered monolayer.

Rhodamines in the gas phase: cations, neutrals, anions, and adducts with metal cations

Optical spectroscopy of biological molecules in the gas phase has recently gained considerable attention, being able to provide complementary structural information in the absence of native matrix. Biomolecules can change their properties when brought into the gas phase, and so can chromophores associated with them. Understanding the photophysics of chromophore labels is central for the correct interpretation of experimental data. In this report, the structure and the optical properties of Rhodamine 19 (R19) in the gas phase were examined by a combination of Fourier-transform ion cyclotron resonance mass spectrometry and visible-light laser spectroscopy. While R19 in solution is found either in neutral (R19(n)) or protonated (R19+H(+)) forms, other structures can be generated in the gas phase, such as anions (R19-H(-)) and adducts with metal cations (R19+M(+)). Experimental evidence for the lactone structure of neutral gas-phase R19 is presented for the first time. The different properties of gas-phase compared to solution-phase R19 are discussed in view of structural analysis of labeled gas-phase biological molecules by optical spectroscopy.

Theoretical study of the linear and nonlinear optical properties of the Photosensibilizer molecules: Photofrin and foscan in gas phase

A theoretical study on the static linear () and nonlinear ( and ) optical properties in gas phase of Photofrin and Foscan molecules is reported. These compounds are known as porphyrin derivatives w...

Theoretical study of the linear and nonlinear optical properties of the Photosensibilizer molecules: Photofrin and foscan in gas phase

A theoretical study on the static linear (α) and nonlinear (β and γ) optical properties in gas phase of Photofrin and Foscan molecules is reported. These compounds are known as porphyrin derivatives which act as photosensibilizers in photo dynamic therapy for cancer treatment. The geometric parameters of Photofrin and Foscan were fully optimized using ab initio and Density Functional Theory levels, at Hartree-Fock and B3LYP hybrid functional approach, respectively. The STO-3G, 3-21G* and the 3-21+G standard basis sets were employed for the calculations. The 3-21+G basis set is augmented with one s and three p diffuse functions for carbon, nitrogen, oxygen and sodium atoms. The bond distances and the bond angles of the two optimized molecules obtained with different method/basis set combinations show only minor variation. The Hartree-Fock and B3LYP methods provide a suitable evaluation of the geometrical and optical properties of Photofrin and Foscan molecules, since the calculated α$_{ave}$, β$_{v}$ and γ$_{ave}$ results are in good agreement with previous reports for similar porphyrin derivatives. The optical properties of Foscan and Photofrin molecules have the same tendencies: the α$_{ave}$ results have an almost linear relationship with the conjugated bond number, the β$_{v}$ results are mainly determined by the nature and symmetry of the susbstituent groups to the porphyrin centre and the γ$_{ave}$ results are extremely depending on the calculation strategies.

Modeling of subcontinuum thermal transport across semiconductor-gas interfaces

A physically rigorous computational algorithm is developed and applied to calculate subcontinuum thermal transport in structures containing semiconductor-gas interfaces. The solution is based on a finite volume discretization of the Boltzmann equation for gas molecules (in the gas phase) and phonons (in the semiconductor). A partial equilibrium is assumed between gas molecules and phonons at the interface of the two media, and the degree of this equilibrium is determined by the accommodation coefficients of gas molecules and phonons on either side of the interface. Energy balance is imposed to obtain a value of the interface temperature. The classic problem of temperature drop across a solid-gas interface is investigated with a simultaneous treatment of solid and gas phase properties for the first time. A range of transport regimes is studied, varying from ballistic phonon transport and free molecular flow to continuum heat transfer in both gas and solid. A reduced-order model is developed that captures the thermal resistance of the gas-solid interface. The formulation is then applied to the problem of combined gas-solid heat transfer in a two-dimensional nanoporous bed and the overall thermal resistance of the bed is characterized in terms of the governing parameters. These two examples exemplify the broad utility of the model in practical nanoscale heat transfer applications.

Particle deposition in human respiratory system: Deposition of concentrated hygroscopic aerosols

In the nearly saturated human respiratory tract, the presence of water-soluble substances in the inhaled aerosols can cause change in the size distribution of the particles. This consequently alters the lung deposition profiles of the inhaled airborne particles. Similarly, the presence of high concentration of hygroscopic aerosols also affects the water vapor and temperature profiles in the respiratory tract. A model is presented to analyze these effects in human respiratory system. The model solves simultaneously the heat and mass transfer equations to determine the size evolution of respirable particles and gas-phase properties within human respiratory tract. First, the model predictions for nonhygroscopic aerosols are compared with experimental results. The model results are compared with experimental results of sodium chloride particles. The model reproduces the major features of the experimental data. The water vapor profile is significantly modified only when a high concentration of particles is present. The model is used to study the effect of equilibrium assumptions on particle deposition. Simulations show that an infinite dilution solution assumption to calculate the saturation equilibrium over droplet could induce errors in estimating particle growth. This error is significant in the case of particles of size greater than 1 μm and at number concentrations higher than 105/cm3.

Laser Photolysis and Thermolysis of Organic Selenides and Tellurides for Chemical Gas-phase Deposition of Nanostructured Materials

Laser radiation-induced decomposition of gaseous organic selenides and tellurides resulting in chemical deposition of nanostructured materials on cold surfaces is reviewed with regard to the mechanism of the gas-phase decomposition and properties of the deposited materials. The laser photolysis and laser thermolysis of the Se and Te precursors leading to chalcogen deposition can also serve as a useful approach to nanostructured chalcogen composites and IVA group (Si, Ge, Sn) element chalcogenides provided that it is carried out simultaneously with laser photolysis or thermolysis of polymer and IVA group element precursor.

Investigation of gas properties, design, and operational parameters on hydrodynamic characteristics, mass transfer, and biomass production from natural gas in an external airlift loop bioreactor

An external airlift loop bioreactor (EALB) was used for production of biomass from natural gas. The effect of riser to downcomer cross sectional area ratio ( A r / A d ), volume of gas–liquid separator, superficial gas velocity ( U sgr ), and physical properties of gases and their mixtures [ υ g ( μ/ ρ) and D g ] were investigated on mixing time, gas hold-up, and volumetric gas liquid mass transfer coefficients ( k La ). It was found that A r / A d has remarkable effects on gas hold-up and k La due to its influence on mixing time. Kinematic viscosity ( υ g ) showed its significant role on mixing time, gas hold-up and k La when different gases used (mixing time changes directly whereas gas hold-up and k La change indirectly). Moreover, it was found that diffusion coefficient of gas in water ( D g ) has remarkable effect on k La . The volumetric mass transfer coefficients for methane and its mixtures with oxygen (three different mixtures) were determined at different geometrical and operational factors. In average, the rate of oxygen utilization is approximately 1.8 times higher than that of methane. A gas mixture of 25 vol% methane and 75 vol% oxygen was the best gas mixture for biomass production in the EALB. The correlations developed for predicting the mixing time, gas hold-up, and k La in terms of U sgr , A r / A d , volume of gas–liquid separator, and gas phase properties have been found to be encouraging.

CN Surface Interactions and Temperature-Dependent Film Growth During Plasma Deposition of Amorphous, Hydrogenated Carbon Nitride

The properties of amorphous hydrogenated carbon nitride (a-C:N:H) materials create the potential for a variety of commercial applications. Plasma-enhanced chemical vapor deposition (PECVD) provides a convenient means of creating thin a-C:N:H films, but the chemistry that dominates the deposition remains unclear. The CN radical likely plays a role in the process; here, CH3CN was used as a single-source precursor for the generation of CN radicals and the PECVD of a-C:N:H films. Several plasma diagnostic techniques were used in an effort to clarify important deposition mechanisms, with special attention given to the role of CN radicals in the deposition process. Gas phase characterization methods, including laser-induced fluorescence (LIF) and optical emission spectroscopy (OES), provide insight into the formation and gas phase properties of CN(g). In addition, the behavior of CN at the plasma-surface interface was probed using the imaging of radicals interacting with surfaces (IRIS) technique. Results sugge...

Incorporating Phase-Dependent Polarizability in Non-Additive Electrostatic Models for Molecular Dynamics Simulations of the Aqueous Liquid-Vapor Interface.

We discuss a new classical water force field that explicitly accounts for differences in polarizability between liquid and vapor phases. The TIP4P-QDP (4-point transferable intermolecular potential with charge dependent-polarizability) force field is a modification of the original TIP4P-FQ fluctuating charge water force field of Rick et al.(1) that self-consistently adjusts its atomic hardness parameters via a scaling function dependent on the M-site charge. The electronegativity (χ) parameters are also scaled in order to reproduce condensed-phase dipole moments of comparable magnitude to TIP4P-FQ. TIP4P-QDP is parameterized to reproduce experimental gas-phase and select condensed-phase properties. The TIP4P-QDP water model possesses a gas phase polarizability of 1.40 Å(3) and gas-phase dipole moment of 1.85 Debye, in excellent agreement with experiment and high-level ab initio predictions. The liquid density of TIP4P-QDP is 0.9954(±0.0002) g/cm(3) at 298 K and 1 atmosphere, and the enthalpy of vaporization is 10.55(±0.12) kcal/mol. Other condensed-phase properties such as the isobaric heat capacity, isothermal compressibility, and diffusion constant are also calculated within reasonable accuracy of experiment and consistent with predictions of other current state-of-the-art water force fields. The average molecular dipole moment of TIP4P-QDP in the condensed phase is 2.641(±0.001) Debye, approximately 0.02 Debye higher than TIP4P-FQ and within the range of values currently surmised for the bulk liquid. The dielectric constant, ε = 85.8 ± 1.0, is 10% higher than experiment. This is reasoned to be due to the increase in the condensed phase dipole moment over TIP4P-FQ, which estimates ε remarkably well. Radial distribution functions for TIP4P-QDP and TIP4P-FQ show similar features, with TIP4P-QDP showing slightly reduced peak heights and subtle shifts towards larger distance interactions. Since the greatest effects of the phase-dependent polarizability are anticipated in regions with both liquid and vapor character, interfacial simulations of TIP4P-QDP were performed and compared to TIP4P-FQ, a static polarizability analog. Despite similar features in density profiles such as the position of the GDS and interfacial width, enhanced dipole moments are observed for the TIP4P-QDP interface and onset of the vapor phase. Water orientational profiles show an increased preference (over TIP4P-FQ) in the orientation of the permanent dipole vector of the molecule within the interface; an enhanced z-induced dipole moment directly results from this preference. Hydrogen bond formation is lower, on average, in the bulk for TIP4P-QDP than TIP4P-FQ. However, the average number of hydrogen bonds formed by TIP4P-QDP in the interface exceeds that of TIP4P-FQ, and observed hydrogen bond networks extend further into the gaseous region. The TIP4P-QDP interfacial potential, calculated to be -11.98(±0.08) kcal/mol, is less favorable than that for TIP4P-FQ by approximately 2% as a result of a diminished quadrupole contribution. Surface tension is calculated within a 1.3% reduction from the experimental value. Results reported demonstrate TIP4P-QDP as a model comparable to the popular TIP4P-FQ while accounting for a physical effect previously neglected by other water models. Further refinements to this model, as well as future applications are discussed.

An embedded upward flame spread model using 2D direct numerical simulations

A fully coupled 2D fluid–solid direct numerical simulation (DNS) approach is used to simulate co-flow flame spread over poly(methyl methacrylate) (PMMA) at different angles of inclination. Comparison of simulations and experimental measurements are conducted over a range of flame spread rates. Results show that the heat flux to the preheating region varies considerably in time — contradicting often employed assumptions used in established flame spread theories. Accounting for the time dependent behavior is essential in accurate predictions of flame spread, however, a universal characterization in terms of easily defined parameters is not found. Alternatively, a reaction progress variable based embedded flame model is developed using mixture fraction, total enthalpy and surface temperature. State maps of the gas-phase properties and surface heat flux are constructed and stored in pre-computed lookup tables. The resulting model provides a computationally efficient and a local formulation to determine the flame heat flux to the surface resulting in excellent agreement to DNS and experiments for predictions of flame spread rate and position of the pyrolysis front.

Structure and dynamics of molecules of pharmaceutical interest in gas phase and in aqueous phase

Flexible structures of small isolated biomolecules of pharmaceutical interest can be investigated by means of infrared spectroscopy coupled to mass spectrometry, spectroscopy and quantum calculations. Gas-phase studies then offer the possibility of scrutinizing weak interactions established between molecular partners in the absence of any competition with a surrounding solvent. The introduction of pharmacophoric parameters makes it possible to connect structure and bioactivity. In order to come closer to realistic biological conditions, it is possible to link gas-phase properties to those in an aqueous environment at room temperature.

Synthesis, characterization, redox and photocatalytic properties of Ce1−xPdxVO4 (0 ≤ x ≤ 0.1)

Zircon-type CeVO4 and Ce1−xPdxVO4 (0.02≤x≤0.1) were synthesized by a single step solution combustion method. The materials were characterized by powder X-ray diffraction, magnetic measurement and temperature-programmed reduction (TPR) with H2. The redox properties of CeVO4 and Ce0.98Pd0.02VO4 have been investigated by temperature-programmed reduction. The gas-phase and liquid-phase catalytic properties of CeVO4 and Ce0.98Pd0.02VO4 were investigated. Ce0.98Pd0.02VO4 shows better catalytic activity than CeVO4 towards CO oxidation by O2, NO reduction by CO and the photocatalytic degradation of various dyes. This higher catalytic activity of Ce0.98Pd0.02VO4 can be attributed to the lattice labile oxygen and high surface area compared to that of CeVO4.

Additive empirical force field for hexopyranose monosaccharides.

We present an all-atom additive empirical force field for the hexopyranose monosaccharide form of glucose and its diastereomers allose, altrose, galactose, gulose, idose, mannose, and talose. The model is developed to be consistent with the CHARMM all-atom biomolecular force fields, and the same parameters are used for all diastereomers, including both the alpha- and beta-anomers of each monosaccharide. The force field is developed in a hierarchical manner and reproduces the gas-phase and condensed-phase properties of small-molecule model compounds corresponding to fragments of pyranose monosaccharides. The resultant parameters are transferred to the full pyranose monosaccharides, and additional parameter development is done to achieve a complete hexopyranose monosaccharide force field. Parametrization target data include vibrational frequencies, crystal geometries, solute-water interaction energies, molecular volumes, heats of vaporization, and conformational energies, including those for over 1800 monosaccharide conformations at the MP2/cc-pVTZ//MP2/6-31G(d) level of theory. Although not targeted during parametrization, free energies of aqueous solvation for the model compounds compare favorably with experimental values. Also well-reproduced are monosaccharide crystal unit cell dimensions and ring pucker, densities of concentrated aqueous glucose systems, and the thermodynamic and dynamic properties of the exocyclic torsion in dilute aqueous systems. The new parameter set expands the CHARMM additive force field to allow for simulation of heterogeneous systems that include hexopyranose monosaccharides in addition to proteins, nucleic acids, and lipids.