Progress toward chemical accuracy in the computer simulation of condensed phase reactions.

We describe a procedure for the generation of chemically accurate computer-simulation models to study chemical reactions in the condensed phase. The process involves (i) the use of a coupled semiempirical quantum and classical molecular mechanics method to represent solutes and solvent, respectively; (ii) the optimization of semiempirical quantum mechanics (QM) parameters to produce a computationally efficient and chemically accurate QM model; (iii) the calibration of a quantum/classical microsolvation model using ab initio quantum theory; and (iv) the use of statistical mechanical principles and methods to simulate, on massively parallel computers, the thermodynamic properties of chemical reactions in aqueous solution. The utility of this process is demonstrated by the calculation of the enthalpy of reaction in vacuum and free energy change in aqueous solution for a proton transfer involving methanol, methoxide, imidazole, and imidazolium, which are functional groups involved with proton transfers in many biochemical systems. An optimized semiempirical QM model is produced, which results in the calculation of heats of formation of the above chemical species to within 1.0 kcal/mol (1 kcal = 4.18 kJ) of experimental values. The use of the calibrated QM and microsolvation QM/MM (molecular mechanics) models for the simulation of a proton transfer in aqueous solution gives a calculated free energy that is within 1.0 kcal/mol (12.2 calculated vs. 12.8 experimental) of a value estimated from experimental pKa values of the reacting species.

GE models and algorithms for condensed phase equilibrium data regression in ternary systems: limitations and proposals

Phase equilibrium data regression is an unavoidable task necessary to obtain the appropriate values for any model to be used in separation equipment design for chemical process simulation and optimization. The accuracy of this process depends on different factors such as the experimental data quality, the selected model and the calculation algorithm. The present paper summarizes the results and conclusions achieved in our research on the capabilities and limitations of the existing GE models and about strategies that can be included in the correlation algorithms to improve the convergence and avoid inconsistencies. The NRTL model has been selected as a representative local composition model. New capabilities of this model, but also several relevant limitations, have been identified and some examples of the application of a modified NRTL equation have been discussed. Furthermore, a regression algorithm has been developed that allows for the advisable simultaneous regression of all the condensed phase equilibrium regions that are present in ternary systems at constant T and P. It includes specific strategies designed to avoid some of the pitfalls frequently found in commercial regression tools for phase equilibrium calculations. Most of the proposed strategies are based on the geometrical interpretation of the lowest common tangent plane equilibrium criterion, which allows an unambiguous comprehension of the behavior of the mixtures. The paper aims to show all the work as a whole in order to reveal the necessary efforts that must be devoted to overcome the difficulties that still exist in the phase equilibrium data regression problem.

Condensed-phase optical refrigeration

We review progress on laser cooling of solids. The general process that enables cooling to occur is based on anti-Stokes fluorescence. Candidate materials for laser cooling are discussed, including gases, dyes, crystals, semiconductors, and ionically doped glasses. Cooling processes and necessary conditions for cooling are outlined, and general thermodynamic limitations are discussed. This is followed by a more detailed discussion of one specific material, ytterbium-doped ZBLAN, with consideration given to optimization of the laser cooling process and applications. (C) 2003 Optical Society of America.

DEVELOPMENT OF A CONDENSED PHASE VELOCITY MAP IMAGING APPARATUS: DISSOCIATION PHOTODYNAMICS OF NITROGEN DIOXIDE AT 355 NM

The photochemistry of the polar regions of Earth, as well as the interstellar medium, is driven by the effect of ultraviolet radiation on ice surfaces and on the materials trapped within them. While the area of ice photochemistry is vast and much research has been completed, it has only recently been possible to study the dynamics of these processes on a microscopic level. One of the leading techniques for studying photoreaction dynamics is Velocity Map Imaging (VMI). This technique has been used extensively to study several types of reaction dynamics processes. Although the majority of these studies have utilized molecular beams as the main medium for reactants, new studies showed the versatility of the technique when applied to molecular dynamics of molecules adsorbed on metal surfaces. Herein the development of a velocity map imaging apparatus capable of studying the photochemistry of condensed phase materials is described. The apparatus is used to study of the photo-reactivity of NO2 condensed within argon matrices to illustrate its capabilities. A doped ice surface is formed by condensing Ar and NO2 gas onto a sapphire rod which is cooled using a helium compressor to 20 K. The matrix is irradiated using an Nd:YAG laser at 355 nm, and the resulting NO fragment is state-selectively ionized using an excimer-pumped dye laser. In all, we are able to detect transient photochemically generated species and can collect information on their quantum state and kinetic energy distribution. It is found that the REMPI spectra changes as different sections of the dissociating cloud are probed. The rotational and translational energy populations are found to be bimodal with a low temperature component roughly at the temperature of the matrix, and a second component with much higher temperature, the rotational temperature showing a possible population inversion, and the translational temperature of 100-200 K. The low temperature translational component is found to dominate at long delay times between dissociation and ionization, while at short time delays the high temperature component plays a larger role. The velocity map imaging technique allows for the detection of both the axial and radial components of the translational energy. The distribution of excess energy over the rotational, electronic and translational states of the NO photofragments provides evidence for collisional quenching of the fragments in the Ar-matrix prior to their desorption.

Multifunctional acid formation from the gas-phase ozonolysis of beta-pinene

The gas-phase ozonolysis of beta-pinene was studied in static chamber experiments, using gas chromatography coupled to mass spectrometric and flame ionisation detection to separate and detect products. A range of multifunctional organic acids-including pinic acid, norpinic acid, pinalic-3- acid, pinalic-4-acid, norpinalic acid and OH-pinalic acid-were identified in the condensed phase after derivatisation. Formation yields for these products under systematically varying reaction conditions (by adding different OH radical scavengers and Criegee intermediate scavengers) were investigated and compared with those observed from alpha-pinene ozonolysis, allowing detailed information on product formation mechanisms to be elucidated. In addition, branching ratios for the initial steps of the reaction were inferred from quantitative measurements of primary carbonyl formation. Atmospheric implications of this work are discussed.

Formation of organic acids from the gas-phase ozonolysis of terpinolene

Gas-phase ozonolysis of terpinolene was studied in static chamber experiments using gas chromatography coupled to mass spectrometric and flame ionisation detection to separate and detect products. Two isomers of C-7-diacids and three isomers of C-7-aldehydic acids were identified in the condensed phase after derivatisation. Possible mechanisms of formation of these acids were investigated using different OH radical scavengers and relative humidities, and were compared to those reported earlier for the ozonolysis of beta-pinene. In addition, branching ratios for some of the individual reaction steps, e. g. the branching ratio between the two hydroperoxide channels of the C-7-CI, were deduced from the quantitative product yield data. Branching ratios for POZ decomposition and the stabilisation/decomposition of the C-7-CI were also obtained from measurements of the C-7 primary carbonyl product.

Mechanisms for the formation of organic acids in the gas-phase ozonolysis of 3-carene

This paper describes experimental studies aimed at elucidating mechanisms for the formation of low-volatility organic acids in the gas-phase ozonolysis of 3-carene. Experiments were carried out in a static chamber under 'OH-free' conditions. A range of multifunctional acids-which are analogous to those observed from alpha-pinene ozonolysis-were identified in the condensed phase using gas chromatography coupled to mass spectrometry after derivation. Product yields were determined as a function of different OH radical scavengers and relative humidities to give mechanistic information about their routes of formation. Furthermore, an enone and an enal derived from 3-carene were ozonised in order to probe the early mechanistic steps in the reaction and, in particular, which of the two initially formed Criegee intermediates gives rise to which products. Branching ratios for the formation of the two Criegee Intermediates are determined. Similarities and differences in product formation from 3-carene and alpha-pinene ozonolysis are discussed and possible mechanisms-supported by experimental evidence-are developed for all acids investigated.

Mechanisms for the formation of secondary organic aerosol components from the gas-phase ozonolysis of alpha-pinene

Gas-phase ozonolysis of alpha-pinene was studied in static chamber experiments under 'OH-free' conditions. A range of multifunctional products-in particular low-volatility carboxylic acids-were identified in the condensed phase using gas chromatography coupled to mass spectrometry after derivatisation. The dependence of product yields on reaction conditions (humidity, choice of OH radical scavengers, added Criegee intermediate scavengers, NO2 etc.) was investigated to probe the mechanisms of formation of these products; additional information was obtained by studying the ozonolysis of an enal and an enone derived from alpha-pinene. On the basis of experimental findings, previously suggested mechanisms were evaluated and detailed gas-phase mechanisms were developed to explain the observed product formation. Atmospheric implications of this work are discussed.

A stochastic principle behind polar properties of condensed molecular matter

A statistical mechanics view leads to the conclusion that polar molecules allowed to populate a degree of freedom for orientational disorder in a condensed phase thermalize into a bi-polar state featuring zero net polarity. In cases of orientational disorder polar order of condensed molecular matter can only exist in corresponding sectors of opposite average polarities. Channel type inclusion compounds, single component molecular crystals, solid solutions, optically anomalous crystals, inorganic ionic crystals, biomimetic crystals and biological tissues investigated by scanning pyroelectric and phase sensitive second harmonic generation microscopy all showed domains of opposite polarities in their final grown state. For reported polar molecular crystal structures it is assumed that kinetic hindrance along one direction of the polar axis is preventing the formation of a bi-polar state, thus allowing for a kinetically controlled mono-domain state. In this review we summarize theoretical and experimental findings leading to far reaching conclusions on the polar state of solid molecular matter. “… no stationary state … of a system has an electrical dipole moment.” P. W. Anderson, Science, 1972, 177, 393.

A microscopic view of substitution reactions solvated by ionic liquids

The solvation effect of the ionic liquid 1-N-butyl-3-methylimidazolium hexafluorophosphate on nucleophilic substitution reactions of halides toward the aliphatic carbon of methyl p-nitrobenzenesulfonate (pNBS) was investigated by computer simulations. The calculations were performed by using a hybrid quantum-mechanical/molecular-mechanical (QM/MM) methodology. A semiempirical Hamiltonian was first parametrized on the basis of comparison with ab initio calculations for Cl(-) and Br(-) reaction with pNBS at gas phase. In condensed phase, free energy profiles were obtained for both reactions. The calculated reaction barriers are in agreement with experiment. The structure of species solvated by the ionic liquid was followed along the reaction progress from the reagents, through the transition state, to the final products. The simulations indicate that this substitution reaction in the ionic liquid is slower than in nonpolar molecular solvents proper to significant stabilization of the halide anion by the ionic liquid in comparison with the transition state with delocalized charge. Solute-solvent interactions in the first solvation shell contain several hydrogen bonds that are formed or broken in response to charge density variation along the reaction coordinate. The detailed structural analysis can be used to rationalize the design of new ionic liquids with tailored solvation properties. (c) 2008 American Institute of Physics.

Rat osseous plate alkaline phosphatase as Langmuir monolayer - An infrared study at the air-water interface

A glycosylphosphatidylinositol (GPI)-anchored enzyme (rat osseous plate alkaline phosphatase-OAP) was studied as monolayer (pure and mixed with lipids) at the air-water interface. Surface pressure and surface potential-area isotherms showed that the enzyme forms a stable monolayer and exhibits a liquid-expanded state even at surface pressure as high as 30 mN m(-1). Isotherms for mixed dimyristoylphosphatidic acid (DMPA)-OAP monolayer showed the absence of a liquid-expanded/liquid-condensed phase transition as observed for pure DMPA monolayer. In both cases, pure or mixed monolayer, the enzyme preserves its native conformation under compression at the air-water interface as observed from in situ p-polarized light Fourier transform-infrared reflection-absorption spectroscopic (FT-IRRAS) measurements. Changes in orientation and conformation of the enzyme due to the presence or absence of DMPA, as well as due to the surface compression, are discussed. (C) 2008 Published by Elsevier Inc.

Dermaseptin 01 as antimicrobial peptide with rich biotechnological potential: study of peptide interaction with membranes containing Leishmania amazonensis lipid-rich extract and membrane models

This article addresses the interactions of the synthetic antimicrobial peptide dermaseptin 01 (GLWSTIKQKGKEAAIAAA-KAAGQAALGAL-NH(2), DS 01) with phospholipid (PL) monolayers comprising (i) a lipid-rich extract of Leishmania amazonensis (LRE-La), (ii) zwitterionic PL (dipalmitoylphosphatidylcholine, DPPC), and (iii) negatively charged PL (dipalmitoylphosphatidylglycerol, DPPG). The degree of interaction of DS 01 with the different biomembrane models was quantified from equilibrium and dynamic liquid-air interface parameters. At low peptide concentrations, interactions between DS 01 and zwitterionic PL, as well as with the LRE-La monolayers were very weak, whereas with negatively charged PLs the interactions were stronger. For peptide concentrations above 1 mu g/ml, a considerable expansion of negatively charged monolayers occurred. In the case of DPPC, it was possible to return to the original lipid area in the condensed phase, suggesting that the peptide was expelled from the monolayer. However, in the case of DPPG, the average area per lipid molecule in the presence of DS 01 was higher than pure PLs even at high surface pressures, suggesting that at least part of DS 01 remained incorporated in the monolayer. For the LRE-La monolayers, DS 01 also remained in the monolayer. This is the first report on the antiparasitic activity of AMPs using Langmuir monolayers of a natural lipid extract from L. amazonensis. Copyright (C) 2011 European Peptide Society and John Wiley & Sons, Ltd.

Laser cooling of a solid from ambient temperature

A 250 mum diameter fibre of ytterbium-doped ZBLAN was cooled by 13 K from room temperature. The cooling was performed in vacuum to limit the thermal load on the fibre. 0.85 W of laser light at 1015 nm was coupled into the fibre. The ytterbium ions absorbed this light, and the excited atoms thermalized phononically and on average emitted light at a wavelength of 996 nm. Since the quantum efficiency of the transition was high, this resulted in a net loss of energy from the glass, producing net bulk cooling.

A fast atom bombardment mass spectrometry study of tris (3, 6-dioxaheptyl) amine-alkali metal halide complexes and hydrogen bonded complexes

The objective of this thesis was to demonstrate the potential of fast atom bombardment mass spectrometry (FABMS) as a probe of condensed phase systems and its possible uses for the study of hydrogen bonding. FABMS was used to study three different systems. The first study was aimed at investigating the selectivity of the ligand tris(3,6-dioxaheptyl) amine (tdoha) for the alkali metal cations. FABMS results correlated well with infrared and nmr data. Systems where a crown ether competed with tdoha for a given alkali metal cation were also investigated by fast atom bombardment. The results were found to correlate with the cation affinity of tdoha and the ability of the crown ether to bind the cation. In the second and third studies, H-bonded systems were investigated. The imidazole-electron donor complexes were investigated and FABMS results showed the expected H-bond strength of the respective complexes. The effects of concentration, liquid matrix, water content, deuterium exchange, and pre-ionization of the complex were also investigated. In the third system investigated, the abundance of the diphenyl sulfone-ammonium salt complexes (presumably H-bonded) in the FABMS spectrum were found to correlate with qualitative considerations such as steric hindrance and strength of ion pairs.

Hydrolysis of N2O5 on sub-micron mineral salt aerosols

The kinetics of reactive uptake of gaseous N2O5 on sub-micron aerosol particles composed of aqueous ammonium sulfate, ammonium hydrogensulfate and sodium nitrate has been investigated. Uptake was measured in a laminar flow reactor, coupled with a differential mobility analyser (DMA) to obtain the aerosol size distribution, with N2O5 detection using NO chemiluminescence. FTIR spectroscopy was used to obtain information about the composition and water content of the aerosol particles under the conditions used in the kinetic measurements. The aerosols were generated by the nebulisation of aqueous salt solutions. The uptake coefficient on the sulfate salts was in the range [gamma]=0.0015 to 0.033 depending on temperature, humidity and phase of the aerosol. On sodium nitrate aerosols the values were much lower, [gamma]<0.001, confirming the inhibition of N2O5 hydrolysis by nitrate ions. At high humidity (>50% r.h.) the uptake coefficient on liquid sulfate aerosols is independent of water content, but at lower humidity, especially below the efflorescence point, the reactivity of the aerosol declines, correlating with the lower water content. The lower uptake rate on solid aerosols may be due to limitations imposed by the liquid volume in the particles. Uptake on sulfate aerosols showed a negative temperature dependence at T>290 K but no significant temperature dependence at lower temperatures. The results are generally consistent with previous models of N2O5 hydrolysis where the reactive intermediate is NO2+ produced by autoionisation of nitrogen pentoxide in the condensed phase.