Computer-aided product design of alternative solvents based on phase equilibrium synergism in mixtures

A systematic methodology is proposed to find binary azeotropic mixtures as new alternative solvents for the extraction process of volatile aroma molecules widely used in perfume and cosmetic industries. We investigated the use of the reverse engineering approach with computer-aided product design (CAPD) instead of the traditional “trial and error” approach. First, the design problem is defined from the real functionalities of the classical solvents. The latter are translated into physicochemical properties and the corresponding boundary values for each property are defined. The reverse engineering method coupled with CAPD consists in using optimization techniques for building molecular structures that match as best as possible the complete set of target physicochemical properties, thus defining for each candidate a performance index. Property values are evaluated by using group contribution methods for each molecular structure generated by a CAPD tool or by using database values. Acknowledging the contradictory relationship between two selected physicochemical properties, that is, low boiling temperature and high flash point, which is rarely found in pure components, binary azeotropic mixtures were studied to enhance the global performance of solvent candidates. Dimethyl carbonate used as a solvent for the extraction of aroma molecules from plants exhibits between the boiling temperature and the flash point. It was selected as the key component for designing binary azeotropic mixtures. The global performance of the binary azeotropic mixtures was verified by means of calculations of the vapor–liquid and liquid–liquid equilibrium using modified universal functional activity coefficient (UNIFAC) method as a thermodynamic method.     

SDOCK: a global protein-protein docking program using stepwise force-field potentials

Fast Fourier transform (FFT) method limits the forms of scoring functions in global protein-protein docking. On the other hand, force field potentials can effectively describe the energy hyper surface of biological macromolecules. In this study, we developed a new protein-protein docking program, SDOCK, that incorporates van der Waals attractive potential, geometric collision, screened electrostatic potential, and Lazaridis-Karplus desolvation energy into the scoring function in the global searching process. Stepwise potentials were generated from the corresponding continuous forms to treat the structure flexibility. After optimization of the atom solvation parameters and the weights of different potential terms based on a new docking test set that contains 142 cases with small or moderate conformational changes upon binding, SDOCK slightly outperformed the well-known FFT based global docking program ZDOCK3.0. Among the 142 cases tested, 52.8% gave at least one near-native solutions in the top 100 solutions. SDOCK was also tested on six blind testing cases in Critical Assessment of Predicted Interactions rounds 13 to 18. In all six cases, the near-native solutions could be found within the top 350 solutions. Because the SDOCK approach performs global docking based on force-field potentials, one of its advantages is that it provides global binding free energy surface profiles for further analysis. The efficiency of the program is also comparable with that of other FFT based protein-protein docking programs. SDOCK is available for noncommercial applications at http://mdl.ipc.pku.edu.cn/cgi-bin/down.cgi.     

Global optimization of binary Lennard-Jones clusters using three perturbation operators

Global optimization of binary Lennard-Jones clusters is a challenging problem in computational chemistry. The difficulty lies in not only that there are enormous local minima on the potential energy surface but also that we must determine both the coordinate position and the atom type for each atom and thus have to deal with both continuous and combinatorial optimization. This paper presents a heuristic algorithm (denoted by 3OP) which makes extensive use of three perturbation operators. With these operators, the proposed 3OP algorithm can efficiently move from a poor local minimum to another better local minimum and detect the global minimum through a sequence of local minima with decreasing energy. The proposed 3OP algorithm has been evaluated on a set of 96 × 6 instances with up to 100 atoms. We have found most putative global minima listed in the Cambridge Cluster Database as well as discovering 12 new global minima missed in previous research.     

Fluid-phase diagrams of binary mixtures from constant pressure integral equations

A new algorithm for solving integral equations of the theory of liquids at fixed pressure is introduced. Combining this technique with the Lee's star function approximation for the chemical potentials, we obtain an efficient method to investigate fluid-phase diagrams of binary mixtures. We have tested the capabilities of such technique to study symmetric and asymmetric phase diagrams in nonadditive hard spheres and Lennard-Jones mixtures. We find that the integral equation theories, although approximate, can provide a flexible tool to determine the fluid-phase diagrams whose accuracy is critically dependent on the quality of the closure and of the resulting chemical potentials.     

On the use of big-bang method to generate low-energy structures of atomic clusters modeled with pair potentials of different ranges

The efficiency of the so-called big-bang method for the optimization of atomic clusters is analysed in detail for Morse pair potentials with different ranges; here, we have used Morse potentials with four different ranges, from long- ρ = 3) to short-ranged ρ = 14) interactions. Specifically, we study the efficacy of the method in discovering low-energy structures, including the putative global minimum, as a function of the potential range and the cluster size. A new global minimum structure for long-ranged ρ = 3) Morse potential at the cluster size of n= 240 is reported. The present results are useful to assess the maximum cluster size for each type of interaction where the global minimum can be discovered with a limited number of big-bang trials.     

First Step Towards Planning of Syntheses in Solid-State Chemistry: Determination of Promising Structure Candidates by Global Optimization

A method is presented here that allows, in principle, the prediction of the existence and structure of (meta)stable solid compounds. It is based on a set of adjustable modules that are applied to the study of the energy function of the chemical system of interest. The main elements are a set of routines for global optimization and local minimization, as well as algorithms for the investigation of the phase space structure near local minima of the potential energy, and the analysis and characterization of the structure candidates. The current implementation focuses on ionic compounds, for which empirical potentials are used for the evaluation of the energy function in the first stage, and a Hartree–Fock algorithm for refinements. The global optimization is performed with a stochastic simulated annealing algorithm, and the local minimization employs stochastic quenches and gradient methods. The neighborhoods of the local minima are studied with the threshold algorithm. The results of this approach are illustrated with a number of examples: compounds of binary noble gases, and binary and ternary ionic compounds. These include several substances that have not been synthesized yet, but should stand a fair chance of being kinetically stable, for example further alkali metal nitrides besides Li₃N, as well as Ca₃SiBr₂ or SrTi₂O₅.     

Global exploration of the energy landscape of solids on the ab initio level

Predicting which crystalline modifications can be present in a chemical system requires the global exploration of its energy landscape. Due to the large computational effort involved, in the past this search for sufficiently stable minima has been performed employing a variety of empirical potentials and cost functions followed by a local optimization on the ab initio level. However, this entails the risk of overlooking important modifications that are not modeled accurately using empirical potentials. In order to overcome this critical limitation, we develop an approach to employ ab initio energy functions during the global optimization phase of the structure prediction. As an example, we perform a global exploration of the landscape of LiF on the ab initio level and show that the relevant crystalline modifications are found during the search.     

Structure, phase behavior, and inhomogeneous fluid properties of binary dendrimer mixtures

The effective pair potentials between different kinds of dendrimers in solution can be well approximated by appropriate Gaussian functions. We find that in binary dendrimer mixtures the range and strength of the effective interactions depend strongly upon the specific dendrimer architecture. We consider two different types of dendrimer mixtures, employing the Gaussian effective pair potentials, to determine the bulk fluid structure and phase behavior. Using a simple mean field density functional theory (DFT) we find good agreement between theory and simulation results for the bulk fluid structure. Depending on the mixture, we find bulk fluid-fluid phase separation (macrophase separation) or microphase separation, i.e., a transition to a state characterized by undamped periodic concentration fluctuations. We also determine the inhomogeneous fluid structure for confinement in spherical cavities. Again, we find good agreement between the DFT and simulation results. For the dendrimer mixture exhibiting microphase separation, we observe a rather striking pattern formation under confinement.     

Structure,solvatochromism, and solvation of trans-[CoIII(cyclam)(NCS)2](NCS) and the structure of [CoII(Me4cyclam) (NCS)]2[Co(NCS)4]MeOH

The structures of trans-[CoIII(cyclam)(NCS)2](NCS) and of [CoII(Me4cyclam)(NCS)]2[Co(NCS)4]·MeOH have been established by X-ray diffraction methods. The solvatochromic behavior of the trans-[Co(cyclam)(NCS)2]+ cation in several binary aqueous solvent mixtures is reported. Transfer chemical potentials for this complex from H2O into MeOH-H2O mixtures have been established from solubility measurements on its thiocyanate salt. The solvatochromic behavior of this cation is discussed in the context of other solvatochromic inorganic complexes; its transfer chemical potentials are discussed in relation to those of other cobalt(III) complexes.     

On the stability of "non-magic" endohedrally doped Si clusters: a first-principles sampling study of MSi16(+) (M = Ti,V,Cr)

Density-functional theory is used to study the geometric and electronic structure of cationic Si(16)(+) clusters with a Ti, V, or Cr dopant atom. Through unbiased global geometry optimization based on the basin-hopping approach, we confirm that a Frank-Kasper polyhedron, with the metal atom at the center, represents the ground-state isomer for all three systems. The endohedral cage geometry is thus stabilized even though only VSi(16)(+) achieves electronic shell closure within the prevalent spherical potential model. Our analysis of the electronic structure traces this diminished role of shell closure for the stabilization back to the adaptive capability of the metal-Si bonding, which is more the result of a complex hybridization than the originally proposed mere formal charge transfer. The resulting flexibility of the metal-Si bond can also help to stabilize "non-magic" cage-dopant combinations, which suggests that a wider range of materials may eventually be cast into this useful geometry for cluster-assembled materials.     

锗分族元素二元团簇及其与Co形成的团簇离子

通过比较激光烧蚀E1/E2 (代表Ge/Sn， Ge/Pb和Sn/Pb) 和Co/E (E为Ge、Sn、Pb)混合样品形成的二元团簇负离子飞行时间质谱分布和谱峰的相对强度及形成的幻数团簇离子峰，发现E1/E2二元团簇离子中原子量大的锗分族元素在团簇离子中占主要组分，而原子量小的元素则少量掺杂，其组成和分布特点说明其结构和性质与纯E团簇离子相似，可能的结构为该类负离子团簇所有原子都在笼结构的骨架上；对于二元团簇离子GeSn9－、GePb9－和SnPb9－其结构可能是双帽反四棱柱构型，只是每个原子均为骨架的一部分.而对激光烧蚀过渡金属钴与锗分族元素的混合物的研究发现，反应形成了丰富的Co/E二元合金团簇负离子，分析发现该类簇离子为钴内包覆于E(锗分族元素)笼状结构.幻数离子CoGe10－、CoSn10－和CoPb10－可能具有双帽四角反棱柱结构，而CoPb12－可能具有二十面体构型，钴原子均为笼状结构的中心.     

Adsorption mechanism of substituted pyridines on silica suspensions: an NMR study

Adsorption isotherms of 2,5-dimethylpyridine (2,5-DMP) on Aerosil 200 silica from water-2,5-DMP binary mixtures are known to exhibit special features indicative of surface phase transitions in the adsorbed layer. We have made similar observations on another substituted pyridine, 2,4,6-trimethylpyridine (2,4,6-TMP). By using 1D and 2D NMR spectroscopy, we investigated adsorbed layers on silica in suspension in water/substituted-pyridine mixtures and demonstrated the existence of adsorbed species specific signals. Comparison of signals with those displayed on NMR spectra of liquid binary mixtures under various pH conditions rules out adsorption via interaction of the surface silanol group and the lone electron pair of the nitrogen atom. A mechanism of adsorption through the interaction of surface siloxane oxygen and the aromatic pi-system is proposed; it is consistent with both thermodynamic measurements and stacking of substituted pyridines within the adsorbed layer.     

Predicting mixture phase equilibria and critical behavior using the SAFT-VRX approach

The SAFT-VRX equation of state combines the SAFT-VR equation with a crossover function that smoothly transforms the classical equation into a nonanalytical form close to the critical point. By a combinination of the accuracy of the SAFT-VR approach away from the critical region with the asymptotic scaling behavior seen at the critical point of real fluids, the SAFT-VRX equation can accurately describe the global fluid phase diagram. In previous work, we demonstrated that the SAFT-VRX equation very accurately describes the pvT and phase behavior of both nonassociating and associating pure fluids, with a minimum of fitting to experimental data. Here, we present a generalized SAFT-VRX equation of state for binary mixtures that is found to accurately predict the vapor-liquid equilibrium and pvT behavior of the systems studied. In particular, we examine binary mixtures of n-alkanes and carbon dioxide + n-alkanes. The SAFT-VRX equation accurately describes not only the gas-liquid critical locus for these systems but also the vapor-liquid equilibrium phase diagrams and thermal properties in single-phase regions.     

Simultaneous determination of Amaranth and Sunset Yellow by ratio derivative voltammetry

A ratio derivative voltammetric method for resolving overlapping voltammograms without a pre-separation is described. The method is based on the use of the first derivative of ratios of the voltammograms of binary mixtures. The voltammogram of the mixture is obtained and the amplitudes of the current at appropriate potentials are divided by the corresponding amplitudes in the voltammogram of a standard solution of the components, and the first derivative of the ratio voltammogram is obtained. The concentration of the other component is then determined from a calibration graph. The method has been successfully applied for resolving binary mixtures of Amaranth and Sunset Yellow, which have overlapped adsorptive voltammograms in pH 6.0 McIlvane buffers.     

The elastic net algorithm and protein structure prediction

Predicting protein structures from their amino acid sequences is a problem of global optimization. Global optima (native structures) are often sought using stochastic sampling methods such as Monte Carlo or molecular dynamics, but these methods are slow. In contrast, there are fast deterministic methods that find near-optimal solutions of well-known global optimization problems such as the traveling salesman problem (TSP). But fast TSP strategies have yet to be applied to protein folding, because of fundamental differences in the two types of problems. Here, we show how protein folding can be framed in terms of the TSP, to which we apply a variation of the Durbin-Willshaw elastic net optimization strategy. We illustrate using a simple model of proteins with database-derived statistical potentials and predicted secondary structure restraints. This optimization strategy can be applied to many different models and potential functions, and can readily incorporate experimental restraint information. It is also fast; with the simple model used here, the method finds structures that are within 5-6 A all-Calpha-atom RMSD of the known native structures for 40-mers in about 8 s on a PC; 100-mers take about 20 s. The computer time tau scales as tau approximately n, where n is the number of amino acids. This method may prove to be useful for structure refinement and prediction.     

A modification of Newton-Raphson algorithm for phase equilibria calculations using numerical differentiation of the gibbs energy

Deiters, U.K., 1985. A modification of Newton-Raphson algorithm for phase equilibria calculations using numerical differentiation of the Gibbs energy. Fluid Phase Equilibria, 19: 287-293.For the solution of the system of nonlinear equation describing the phase equilibrium conditions in fluid mixtures a modified Newton-Raphson method is proposed, which uses numerical differentiation to obtain the chemical potentials. For binary mixtures the new algorithm a little faster, because the same intermediate results that are required for the chemical potentials are also used for the construction of the Jacobian matrix.     

Phase diagrams of binary mixtures of oppositely charged colloids

Phase diagrams of binary mixtures of oppositely charged colloids are calculated theoretically. The proposed mean-field-like formalism interpolates between the limits of a hard-sphere system at high temperatures and the colloidal crystals which minimize Madelung-like energy sums at low temperatures. Comparison with computer simulations of an equimolar mixture of oppositely charged, equally sized spheres indicate semiquantitative accuracy of the proposed formalism. We calculate global phase diagrams of binary mixtures of equally sized spheres with opposite charges and equal charge magnitude in terms of temperature, pressure, and composition. The influence of the screening of the Coulomb interaction upon the topology of the phase diagram is discussed. Insight into the topology of the global phase diagram as a function of the system parameters leads to predictions on the preparation conditions for specific binary colloidal crystals.     

Solid-fluid and solid-solid phase equilibrium in a model of n-alkane mixtures

Solid-fluid and solid-solid phase equilibrium for binary mixtures of hard sphere chains modeling n-hexane, n-heptane, and n-octane has been calculated using Monte Carlo computer simulations. Thermodynamic integration was used to calculate the Gibbs free energy and chemical potentials in the solid and fluid phases from pure component reference values. A multiple stage free energy perturbation method was used to calculate the composition derivative of the Gibbs free energy. Equation of state and free energy data for the fluid phase indicate ideal solution behavior. Nonideality is much more significant in the solid phase with only partial solubility of shorter chains in the longer chains and essentially no solubility at the other end of the composition range. The miscibility decreases with increasing chain length difference between the components. For the model of n-hexane/n-octane mixtures solid--solid phase separation has been observed directly in some of the simulations, with the components segregating between the layers of the solid structure. The behavior is similar to that seen in some binary n-alkane mixtures with longer chain lengths but comparable chain length ratios between the components. Such phase separation, although indicated thermodynamically, is not seen directly in the simulations of the n-heptane/n-octane mixture due to the difference in the pure component crystal structures.