Efficient methods to study phase equilibria in multinary aqueous systems

We report the results of developing efficient universal isothermal methods for the determination of compositions of all phases (several solid phases and a liquid) involved in invariant equilibria in multicomponent aqueous systems using chemical analysis (a combination method) or not (an optimized sections method) to determine the composition of an equilibrium liquid phase.     

Crystal structure prediction using ab initio evolutionary techniques: principles and applications

We have developed an efficient and reliable methodology for crystal structure prediction, merging ab initio total-energy calculations and a specifically devised evolutionary algorithm. This method allows one to predict the most stable crystal structure and a number of low-energy metastable structures for a given compound at any P-T conditions without requiring any experimental input. Extremely high (nearly 100%) success rate has been observed in a few tens of tests done so far, including ionic, covalent, metallic, and molecular structures with up to 40 atoms in the unit cell. We have been able to resolve some important problems in high-pressure crystallography and report a number of new high-pressure crystal structures (stable phases: epsilon-oxygen, new phase of sulphur, new metastable phases of carbon, sulphur and nitrogen, stable and metastable phases of CaCO3). Physical reasons for the success of this methodology are discussed.     

Quantitative modal determination of geological samples based on X-ray multielemental map acquisition.

Multielemental X-ray maps collected by a remote scanning system of the electron beam are processed by a dedicated software program performing accurate modal determination of geological samples. The classification of different mineral phases is based on elemental concentrations. The software program Petromod loads the maps into a database and computes a matrix consisting of numerical values proportional to the elemental concentrations. After an initial calibration, the program can perform the chemical composition calculated on the basis of a fixed number of oxygens for a selected area. In this way, it is possible to identify all the mineral phases occurring in the sample. Up to three elements can be selected to calculate the modal percentage of the identified mineral. An automated routine scans the whole set of maps and assigns each pixel that satisfies the imposed requirements to the selected phase. Repeating this procedure for every mineral phase occurring in the mapped area, a modal distribution of the rock-forming minerals can be performed. The final output consists of a digitized image, which can be further analyzed by common image analysis software, and a table containing the calculated modal percentages. The method is here applied to a volcanic and a metamorphic rock sample.     

Direct evaluation of multicomponent phase equilibria using flat-histogram methods

We present a method for directly locating density-driven phase transitions in multicomponent systems. Phase coexistence conditions are determined through manipulation of a total density probability distribution evaluated over a density range that includes both coexisting phases. Saturation quantities are determined through appropriate averaging of density-dependent mean values of a given property of interest. We discuss how to implement the method in both the grand-canonical and isothermal-isobaric semigrand ensembles. Calculations can be conducted using any of the recently introduced flat-histogram techniques. Here, we combine the general algorithm with a transition-matrix approach to produce an efficient self-adaptive technique for determining multicomponent phase equilibrium properties. To assess the performance of the new method, we generate phase diagrams for a number of binary and ternary Lennard-Jones mixtures.     

The Differential Relationships of Thermodynamic Variables for the Equilibrium of Heterogeneous Substances

For the system without adiabatic walls, rigid walls or semi-permeable walls and without chemical reactions or without other restrictions except restrictions of phase equilibrium conditions, if the number of components of the system is k and the number of phases is φ, the degree of freedom of the system at equilibrium is f=k-φ+2. Because the degree of freedom is incapable of being negative, f=k-φ+2≥0, viz.φ≤k+2. For the heterogeneous equilibrium, the number of phases is at least 2, so φ=k+2-f≥2, viz. f≤k. Hence the range of change of φ and f is 2≤φ≤k+2,0≤f≤k, respectitvely. If φ=k+2, there are no independent variables in the system at equilibrium. If φ=k+1, there is one independent variable; if the temperature is selected as the independent variable, the other dependent variables can be expressed as the function of the temperature. If φ=k, there are two independent variables; if the temperature and pressure are selected as the independent variables, the other dependent variables can be expressed as the function of the temperature and pressure. If 2≤φ≤k-1, there are more than two independent variables; if the temperature, pressure and some concentrations are selected as independent variables, the other dependent variables can be expressed as the function of the temperature, pressure and these concentrations. The differential relationships of dependent variables and independent variables are educed out according to the principle of phase equilibriums for 2≤φ≤k-1. In any phase the number of the variables is(k+1), viz. temperature T, pressure p and (k-1) mole fractions x1, x2,…, xk-1. The temperature and pressure are common variables of every phase. The number of independent variables is at best k for the heterogeneous equilibriums of k components. The temperature, pressure and (k-2) concentrations are selected as independent variables. The independent concentration variables are selected entirely from the first phase and the concentration variables of the other phases all act as dependent variables. There is at least one dependent concentration variable in the first phase.     

Thermodynamic Studies as Predictive Tools of the Behavior of Electroceramics Under Different Hydrothermal Environments

Thermodynamic simulations are performed in all areas of materials processing because of the advances that have taken place in computer software for complex non-ideal calculations, together with the increasing availability of evaluated data for different phases. In the present work, a thermodynamic model of electrolytic solutions was applied to determine the reaction conditions favoring the hydrothermal synthesis of the following electroceramics: zinc ferrites, sodium niobates, and lead zirconates. Stability and yield diagrams were constructed relating the equilibrium concentration of all of the aqueous and solid species as functions of temperature, pressure, pH, and input reagent concentrations. The theoretical predictions avoided the empirical trial-and-error method of synthesis and were corroborated by experiments. The results demonstrate the important role that such thermodynamic simulations can play in significantly reducing the time and costs associated with hydrothermal processing.     

Diffusion relaxation times of nonequilibrium isolated small bodies and their solid phase ensembles to equilibrium states

The possibility of obtaining analytical estimates in a diffusion approximation of the times needed by nonequilibrium small bodies to relax to their equilibrium states based on knowledge of the mass transfer coefficient is considered. This coefficient is expressed as the product of the self-diffusion coefficient and the thermodynamic factor. A set of equations for the diffusion transport of mixture components is formulated, characteristic scales of the size of microheterogeneous phases are identified, and effective mass transfer coefficients are constructed for them. Allowing for the developed interface of coexisting and immiscible phases along with the porosity of solid phases is discussed. This approach can be applied to the diffusion equalization of concentrations of solid mixture components in many physicochemical systems: the mutual diffusion of components in multicomponent systems (alloys, semiconductors, solid mixtures of inert gases) and the mass transfer of an absorbed mobile component in the voids of a matrix consisting of slow components or a mixed composition of mobile and slow components (e.g., hydrogen in metals, oxygen in oxides, and the transfer of molecules through membranes of different natures, including polymeric).     

A general approach to calculating isotopic distributions for mass spectrometry

Fundamental principles for obtaining mass spectral isotopic distributions are applied to a general computer program that can be used to calculate and present in tabular and graphic form the isotopic contributions for any molecular formula. A unique feature is the retention of the isotopic distribution, exact mass, and absolute abundance for all individual peaks at each mass. Special considerations have been made for the large number of isotopic combinations that occur for many higher mass compounds. The computer program accepts the input of a molecular formula followed by interactive input of a number of parameters that affect the final presentation of the theoretical distribution profile.     

Solventless polymerization: spatial migration of a catalyst to form polymeric thin films in microchannels

This paper reports a simple, additive process to generate patterned polymer films without using any solvent. This process involves a highly efficient catalyst, a Grubbs's catalyst, and a volatile monomer, norbornene. The catalyst and monomers have higher local concentrations inside the microchannels, formed by contacting poly(dimethylsiloxane) stamps to a solid surface, and allow the polymeric thin films to be defined by the microchannels. The patterned thin film serves as an excellent resistant to reactive ion etching, which promises that this process is a complementary, useful alternative to spin-coating and plasma polymerization in microfabrication.     

Solid phase thermodynamic perturbation theory: test and application to multiple solid phases

A simple procedure for the determination of hard sphere (HS) solid phase radial distribution function (rdf) is proposed, which, thanks to its physical foundation, allows for extension to other crystal structures besides the fcc structure. The validity of the procedure is confirmed by comparing (1) the predicted HS solid phase rdf's with corresponding simulation data and (2) the predicted non-HS solid phase Helmholtz free energy by the present solid phase first-order thermodynamic perturbation theory (TPT) whose numerical implementation depends on the HS solid phase rdf's as input, with the corresponding predictions also by the first-order TPT but the required HS solid phase rdf is given by an "exact" empirical simulation-fitted formula. The present solid phase first-order TPT predicts isostructural fcc-fcc transition of a hard core attractive Yukawa fluid, in very satisfactory agreement with the corresponding simulation data and is far more accurate than a recent thermodynamically consistent density functional perturbation theory. The present solid phase first-order TPT is employed to investigate multiple solid phases. It is found that a short-ranged potential, even if it is continuous and differentiable or is superimposed over a long-ranged potential, is sufficient to induce the multiple solid phases. When the potential range is short enough, not only isostructural fcc-fcc transition but also isostructural bcc-bcc transition, simple cubic (sc)-sc transition, or even fcc-bcc, fcc-sc, and bcc-sc transitions can be induced. Even triple point involving three solid phases becomes possible. The multiple solid phases can be stable or metastable depending on the potential parameters.     

Computer generation of the characteristic polynomials of chemical graphs

A computer program based on the Frame method for the characteristic polynomials of graphs is developed. This program makes use of an efficient polynomial algorithm of Frame for generating the coefficients in the characteristic polynomials of graphs. This program requires as input only the set of vertices that are neighbors of a given vertex and with labels smaller than the label of that vertex. The program generates and stores only the lower triangle of the adjacency matrix in canonical ordering in a one-dimensional array. The program is written in integer arithmetic, and it can be easily modified to real arithmetic. The coefficients in the characteristic polynomials of several graphs were generated in less than a few seconds, thus solving the difficult problem of generating characteristic polynomials of graphs. The characteristic polynomials of a number of very complicated graphs are obtained including for the first time the characteristic polynomial of an honeycomb lattice graph containing 54 vertices.     

Simulation of the rheological properties of liquid media containing solid anisometric particles

Theoretical simulation of the rheological properties of liquid media containing solid anisometric particles is performed. Procedures for the calculation of the degree of ordering in the nematic systems under equilibrium conditions and their rheological characteristics are proposed. Earlier developed notions of the calculation procedures for the properties of systems considered are analyzed and corrections to the theory are substantiated. Based on developed model notions, equilibrium and transport equations are derived and a program for their numerical solution is proposed. Model calculations of the lines of phase transition and the ordering of systems containing isotropic and nematic phases, as well as anisotropic (in orienting field) and effective dynamic viscosities under the conditions of free flow of such systems, are carried out at various concentrations and geometry of anisometric particles. A comparison of calculated and experimental data for the solutions of polymer-salt compositions with induced chain rigidity demonstrates the adequacy of the model proposed.     

SENECA: A platform-independent, distributed, and parallel system for computer-assisted structure elucidation in organic chemistry.

The program package SENECA for Computer-Assisted Structure Elucidation (CASE) of organic molecules is described. SENECA is written completely in the programming language Java and divided into a server, a client, and a gatekeeper part. While the client allows for input of spectroscopic information, the server part performs the actual structure elucidation by stochastically walking through constitution space while optimizing the molecule toward agreement with given spectral properties. The convergence is guided by simulated annealing. The gatekeeper administers a list of server processes, which can be retrieved by the client. The package is completely platform-independent and its server part can be distributed over the Internet or an intranet using a heterogeneous network of almost any number and type of computers, thus allowing for parallel CASE computations on ordinary networks, present in almost any institution.     

Analytical energy gradients for local second-order Møller-Plesset perturbation theory using density fitting approximations

An efficient method to compute analytical energy derivatives for local second-order M?ller-Plesset perturbation energy is presented. Density fitting approximations are employed for all 4-index integrals and their derivatives. Using local fitting approximations, quadratic scaling with molecular size and cubic scaling with basis set size for a given molecule is achieved. The density fitting approximations have a negligible effect on the accuracy of optimized equilibrium structures or computed energy differences. The method can be applied to much larger molecules and basis sets than any previous second-order M?ller-Plesset gradient program. The efficiency and accuracy of the method is demonstrated for a number of organic molecules as well as for molecular clusters. Examples of geometry optimizations for molecules with 100 atoms and over 2000 basis functions without symmetry are presented.     

Direct calculation of solid-vapor coexistence points by thermodynamic integration: application to single component and binary systems

We present a new thermodynamic integration method that directly connects the vapor and solid phases by a reversible path. The thermodynamic integration in the isothermal-isobaric ensemble yields the Gibbs free energy difference between the two phases, from which the sublimation temperature can be easily calculated. The method extends to the binary mixture without any modification to the integration path simply by employing the isothermal-isobaric semigrand ensemble. The thermodynamic integration, in this case, yields the chemical potential difference between the solid and vapor phases for one of the components, from which the binary sublimation temperature can be calculated. The coexistence temperatures predicted by our method agree well with those in the literature for single component and binary Lennard-Jones systems.     

Determination of catecholamines in urine using hydrophilic interaction chromatography with electrochemical detection

The determination of catecholamines in urine was investigated using hydrophilic interaction chromatography (HILIC) as an alternative to the commonly used reversed-phase (RP) method. A number of different approaches were explored, including per-aqueous liquid chromatography (PALC), and HILIC using bare silica, bonded amide and zwitterionic phases. The bonded phases gave superior results in terms of both peak shape and selectivity. The mechanism of the HILIC separation was investigated particularly with respect to the contribution of ion exchange to retention. The electrochemical detection of catecholamines was studied and optimised in typical HILIC mobile phases that contain high concentrations of acetonitrile. HILIC offered a number of advantages over the conventional RP approach, giving good retention of the solutes without use of ion pair reagents, the absence of which also would facilitate detection by mass spectrometry. HILIC used in conjunction with solid phase extraction based on RP also gives orthogonal separation mechanisms in the cleanup and analysis steps. Furthermore, good recoveries from the cleanup stage were obtained, as high concentrations of acetonitrile can be used as eluting solvent that are fully compatible with HILIC, and lipophilic impurities are eluted close to the void volume of the HILIC column.     

COMPLX: a computer algorithm for the detection of protein-ligand and other macromolecular complexes in mass spectra

A new algorithm has been designed and tested to identify protein, or any other macromolecular, complexes that have been widely reported in mass spectral data. The program takes advantage of the appearance of multiply charged ions that are common to both electrospray ionization and, to a lesser extent, matrix-assisted laser desorption/ionization (MALDI) mass spectra. The algorithm, known as COMPLX for the COMposition of Protein-Ligand compleXes, is capable of identifying complexes for any protein or macromolecule with a binding partner of molecular mass up to 100 000 Da. It does so by identifying ion pairs present in a mass spectrum that, when they share a common charge, have an m/z value difference that is an integer fraction of a ligand or binding partner molecular mass. Several additional criteria must be met in order for the result to be ranked in the output file including that all m/z values for ions of the protein or complex have progressively lower values as their assigned charge increases, the difference between the m/z values for adjacent charge states (z, z + 1) decrease as the assigned charge state increases, and the ratio of any two m/z values assigned to a protein or complex is equal to the inverse ratio of their charge. The entries that satisfy these criteria are then ranked according to the appearance of ions in the mass spectrum associated with the binding partner, the length of a continuous series of charges across any set of ions for a protein and complex and the lowest error recorded for the molecular mass of the ligand or binding partner. A diverse range of hypothetical and experimental mass spectral data were used to implement and test the program, including those recorded for antibody-peptide, protein-peptide and protein-heme complexes. Spectra of increasing complexity, in terms of the number of ions input, were also successfully analysed in which the number of input m/z values far exceeds the few associated with a macromolecular complex. Thus the program will be of value in a future goal of proteomics, where mass spectrometry already plays a central role, for the direct analysis of protein and other associations within biological extracts.     

Predicting equilibrium structures in freezing processes

We propose genetic algorithms as a new tool that is able to predict all possible solid candidate structures into which a simple fluid can freeze. In contrast to the conventional approach where the equilibrium structures of the solid phases are chosen from a preselected set of candidates, genetic algorithms perform a parameter-free, unbiased, and unrestricted search in the entire search space, i.e., among all possible candidate structures. We apply the algorithm to recalculate the zero-temperature phase diagrams of neutral star polymers and of charged microgels over a large density range. The power of genetic algorithms and their advantages over conventional approaches is demonstrated by the fact that new and unexpected equilibrium structures for the solid phases are discovered. Improvements of the algorithm that lead to a more rapid convergence are proposed and the role of various parameters of the method is critically assessed.     

A Numerical Approach for Multicomponent Vapor Solid Equilibrium Calculations in Gas Hydrate Formation

A new numerical approach has been developed for vapor solid equilibrium calculations and for predicting vapor solid equilibrium constant and composition of vapor and solid phases in gas hydrate formation. Equation of state methods generally do a good job of determining vapor phase properties, but for solid phase it is much more difficult and inaccurate. This proposed new model calculates vapor solid equilibrium constant and vapor and solid phase composition as a function of temperature and partial pressure. The results of this proposed numerical approach, for vapor solid equilibrium, have a good agreement with the available reported data. This new numerical model also has an advantage to tune coefficients, to cover different sets of experimental data accurately.