Accurate and fast treatment of large molecular systems: Assessment of CEPA and pCCSD within the local pair natural orbital approximation

The local pair natural orbital approach, which has been combined with two post‐Hartree–Fock methods, CEPA‐1 and pCCSD‐1a, recently, is assessed for its applicability to large real‐world problems without abundant computing resources. Test cases are selected based on being representative for computational chemistry problems and availability of reliable reference data. Both methods show a good performance and can be applied easily to systems of up to 100 atoms when very accurate energies are sought after. A considerable demand for basis sets of good quality has been identified and practical guidelines to satisfy this are mapped out. © 2012 Wiley Periodicals, Inc.     

Theoretical investigation of an acid catalyst for viable release of H2 from BN nanotubes: A local pair natural orbital coupled cluster approach

Catalytic removal of H₂ from boron-nitride (BN)-based nanomaterials at ambient conditions is of paramount importance in order to develop lightweight hydrogen storage media. Here, the DLPNO-CCSD(T) technique is used to calculate accurate relative energies and activation barriers of Brønsted acid-initiated removal of H₂ from hydrogenated BN nanotubes (HBNNTs) with six different acids. Three crucial steps are identified in the mechanism: first H₂ release, catalyst regeneration via proton transfer, and second H₂ release to ensure feasibility of the dehydrogenation proposal. Our computational studies reveal that sulfonic acids with appropriate electrophilicity can facilitate dehydrogenation of HBNNT at a low free energetic cost (∆G^‡ = 17 kcal/mol). Importantly, these findings illustrate the possibility of H₂ release from BN nanomaterials at ambient conditions and provides hope for a sustainable chemical hydrogen storage strategy.     

An efficient algorithm for solving nonlinear equations with a minimal number of trial vectors: applications to atomic-orbital based coupled-cluster theory

The conjugate residual with optimal trial vectors (CROP) algorithm is developed. In this algorithm, the optimal trial vectors of the iterations are used as basis vectors in the iterative subspace. For linear equations and nonlinear equations with a small-to-medium nonlinearity, the iterative subspace may be truncated to a three-dimensional subspace with no or little loss of convergence rate, and the norm of the residual decreases in each iteration. The efficiency of the algorithm is demonstrated by solving the equations of coupled-cluster theory with single and double excitations in the atomic orbital basis. By performing calculations on H(2)O with various bond lengths, the algorithm is tested for varying degrees of nonlinearity. In general, the CROP algorithm with a three-dimensional subspace exhibits fast and stable convergence and outperforms the standard direct inversion in iterative subspace method.     

New relativistic atomic natural orbital basis sets for lanthanide atoms with applications to the Ce diatom and LuF3

New basis sets of the atomic natural orbital (ANO) type have been developed for the lanthanide atoms La-Lu. The ANOs have been obtained from the average density matrix of the ground and lowest excited states of the atom, the positive ions, and the atom in an electric field. Scalar relativistic effects are included through the use of a Douglas-Kroll-Hess Hamiltonian. Multiconfigurational wave functions have been used with dynamic correlation included using second-order perturbation theory (CASSCF/CASPT2). The basis sets are applied in calculations of ionization energies and some excitation energies. Computed ionization energies have an accuracy better than 0.1 eV in most cases. Two molecular applications are included as illustration: the cerium diatom and the LuF3 molecule. In both cases it is shown that 4f orbitals are not involved in the chemical bond in contrast to an earlier claim for the latter molecule.     

A coupled cluster approach with a hybrid treatment of connected triple excitations: implementation and applications for open-shell systems

An implementation of the coupled cluster (CC) singles, doubles, and a hybrid treatment of connected triples [denoted as CCSD(T)-h], based on the unrestricted Hartree-Fock (UHF) reference, is presented. Based on the spin-integrated formulation, we have developed a computer program to achieve the automatic derivation and implementation of the CCSD(T)-h approach. The CCSD(T)-h approach computationally scales as the seventh power of the system size, and is affordable for many medium-sized systems. The present approach has been applied to study the equilibrium geometries and harmonic vibrational frequencies in a number of open-shell diatomic molecules and bond breaking potential energy profiles in several open-shell molecules, including CH(3), NH(2), and SiH(2). For all systems under study, the overall performance of the UHF-based CCSD(T)-h approach is very close to that of the corresponding CCSDT (CC singles, doubles, and triples), and much better than that of the UHF-based CCSD(T) (CC singles, doubles, and perturbative triples).     

Microchip-based cellular biochemical systems for practical applications and fundamental research: from microfluidics to nanofluidics

By combining cell technology and microchip technology, innovative cellular biochemical tools can be created from the microscale to the nanoscale for both practical applications and fundamental research. On the microscale level, novel practical applications taking advantage of the unique capabilities of microfluidics have been accelerated in clinical diagnosis, food safety, environmental monitoring, and drug discovery. On the other hand, one important trend of this field is further downscaling of feature size to the 10¹–10³ nm scale, which we call extended-nano space. Extended-nano space technology is leading to the creation of innovative nanofluidic cellular and biochemical tools for analysis of single cells at the single-molecule level. As a pioneering group in this field, we focus not only on the development of practical applications of cellular microchip devices but also on fundamental research to initiate new possibilities in the field. In this paper, we review our recent progress on tissue reconstruction, routine cell-based assays on microchip systems, and preliminary fundamental method for single-cell analysis at the single-molecule level with integration of the burgeoning technologies of extended-nano space.     

Extended corresponding states model for fluids and fluid mixtures: II. Application to mixtures and natural gas systems

We report an extended corresponding states model optimised for accurate prediction of the thermodynamic properties and vapour–liquid equilibria of natural gases and similar mixtures. The corresponding states model uses methane as the reference fluid and employs shape factors for pure components that were reported recently [Fluid Phase Equilib. 204 (2002) 15]. The van der Waals one-fluid model is used for mixtures and, in this paper, we report two alternative temperature- and density-dependent correlations of the binary interaction parameters. Model ECSmixS1 was optimised for 19 binary systems in the wide domain 90≤T (K)≤670 with p (MPa)≤510 and is suitable for the prediction of both liquid- and gas-phase thermodynamic properties and for the solution of vapour–liquid equilibrium problems. Model ECSmixS2 was specialised for increased accuracy in the natural gas ‘custody transfer’ interval 270≤T (K)≤330 with p (MPa)≤12 and is intended for gas-phase thermodynamic properties only. For mixtures of the major components of natural gas, we obtain with Model ECSmixS1 an overall average absolute deviation (AAD) of 0.12% in calculated densities, an AAD of 0.16% in calculated speeds of sound and an AAD of 1.8% in bubble pressure. With Model ECSmixS2, we obtained improved AADs of 0.03% in density and 0.03% in speed of sound. These results compare very favourably with other commonly used mixture models. The present model may be systematically improved or extended by introducing new or improved correlations of the binary parameters.     

Evaluation of Gibbs free energy for the transfer of a highly hydrophilic ion from an acidic aqueous solution to an organic solution based on ion pair extraction

A method to determine the standard Gibbs free energy for the transfer, ΔG°_tr, of a highly hydrophilic metal ion from an aqueous solution, W, in the presence of high concentration of H⁺ to an organic solution, O, was proposed based on the theoretical consideration of the distribution process of ions between W and O. The usefulness of the proposed method was verified experimentally by comparing ΔG°_tr of Mg²⁺ determined by the method with that obtained by voltammetry for the ion transfer at the W|O interface. The O examined were nitrobenzene (NB) and 1,2-dichloroethane (DCE). By applying the proposed method, ΔG°_tr of NpO₂⁺, UO₂²⁺, NpO₂²⁺ and PuO₂²⁺ from an acidic W to NB were determined.     

Application of plug–plug technique to ACE experiments for discovery of peptides binding to a larger target protein: A model study of calmodulin‐binding fragments selected from a digested mixture of reduced BSA

To discover peptide ligands that bind to a target protein with a higher molecular mass, a concise screening methodology has been established, by applying a “plug–plug” technique to ACE experiments. Exploratory experiments using three mixed peptides, mastoparan‐X, β‐endorphin, and oxytocin, as candidates for calmodulin‐binding ligands, revealed that the technique not only reduces the consumption of the protein sample, but also increases the flexibility of the experimental conditions, by allowing the use of MS detection in the ACE experiments. With the plug–plug technique, the ACE–MS screening methodology successfully selected calmodulin‐binding peptides from a random library with diverse constituents, such as protease digests of BSA. Three peptides with K_d values between 8–147 μM for calmodulin were obtained from a Glu‐C endoprotease digest of reduced BSA, although the digest showed more than 70 peaks in its ACE–MS electropherogram. The method established here will be quite useful for the screening of peptide ligands, which have only low affinities due to their flexible chain structures but could potentially provide primary information for designing inhibitors against the target protein.     

Electronic structure of 3d[M(H2O)6](3+) ions from Sc(III) to Fe(III): a quantum mechanical study based on DFT computations and natural bond orbital analyses

The metal-donor atom bonding along the series of 3d[M(H2O)6](3+) ions from Sc(3+) to Fe(3+) has been investigated by density-functional calculations combined with natural localized bond orbital analyses. The M-OH(2) bonds were considered as donor-acceptor bonds, and the contributions coming from the metal ion's 3d sigma-, 3d pi-, and 4s sigma-interactions were treated individually. In this way, the total amount of charge transferred from the water oxygen-donor atoms toward the appropriate metal orbitals could be analyzed in a straightforward manner. One result obtained along these lines is that the overall extent of ligand-to-metal charge transfer shows a strong correlation to the hydration enthalpies of the aqua metal ions. If the contributions to the total ligand-to-metal ion charge transfer are divided into sigma- and pi-contributions, it turns out that Cr(3+) is the best sigma-acceptor, but its pi-accepting abilities are the weakest along the series. Fe(3+) is found to be the best pi-acceptor among the 3d hexaaqua ions studied. Its aptitude to accept sigma-electron density is the second weakest along the series and only slightly higher than that of Sc(3+) (the least sigma-acceptor of all ions) because of the larger involvement of the Fe(3+) 4s orbital in sigma-bonding. The strengths of the three types of bonding interactions have been correlated with the electron affinities of the different metal orbitals. Deviations from the regular trends of electron affinities along the series were found for those [M(H2O)6](3+) ions that are subject to Jahn-Teller distortions. In these cases (d(1) = [Ti(H2O)6](3+), d(2) = [V(H2O)6](3+), and d(4) = [Mn(H2O)6](3+)), ligand-to-metal charge transfer is prevented to go into those metal orbitals that contain unpaired d electrons. A lowering of the complex symmetry is observed and coupled with the following variations: The Ti(3+)- and V(3+)-hexaaqua ions switch from T(h)() to C(i)() symmetry while the Mn(3+)-hexaaqua ion moves to D(2)(h)() symmetry. The loss of orbital overlap leading to a diminished ligand-to-metal charge transfer toward the single occupied metal orbitals is compensated by amplified bonding interactions of the ligand orbitals with the unoccupied metal orbitals to some extent.     

Model experiments to test the use of a liquid membrane for separation and preconcentration of copper from natural water

The transfer and separation of Cu(II) ions across a bulk liquid membrane (BLM) containing pyridine-2-acetaldehyde benzoylhydrazone (2-APBH) as the mobile carrier dissolved in toluene has been investigated and optimised. The system was applied to the preconcentration of copper from natural waters prior to analysis by flame atomic absorption spectroscopy. The flux of copper across the membrane has been studied, and characterised as a function of analytical variables such as the carrier concentration, volume of organic phase, pH of feed and strip receiving solutions, stirring rate and temperature of solutions. The preconcentration yield at optimum conditions was 100.54±0.94%, even with a high saline matrix (30 g l⁻¹ NaCl), with good precision (1.49%). A preconcentration factor of approximately 18 times could be obtained. The detection limit of a blank sample was 0.24 μg l⁻¹ of Cu.The method was validated using a certified reference material (TMDA-62) and was applied successfully to the analysis of copper in two samples of seawater collected from the coast of Huelva (Spain). The relative errors were 2.42% for CRM and 0.48 and 3.66%, for seawaters (obtained between the results of the proposed and DPASV methods), respectively.     

A demonstration model for a selective and recyclable uptake of metals from water: Fe(III) ions complexation and release by a supported natural fluorescent chelator

We describe here the preliminary stage of development of a process aiming at the selective uptake and release of metal ions from water. The process envisioned involves the encapsulation of highly selective natural chelates secreted by bacteria or other living species in mesoporous solids that could be used as usual resins. To demonstrate the feasibility of the concept, we use a model system involving pyoverdin, a natural Fe(III) ions chelator from a Pseudomonas fluorescens strain, encapsulated in a mesoporous templated silica. For this model study, the native fluorescence of the chelator allows a simpler follow-up and quantification of the uptake and release processes.     

Application of natural compounds–based gold nanoparticles for the treatment of hemolytic anemia in an anemic mouse model: Formulation of a novel drug from relationship between the nanotechnology and hematology sciences

From time immemorial, people have tried to treat several diseases using natural compounds, including plants. Recently, researchers proposed that plants and herbal nanoparticles possess many remedial potentials. The results of this study confirmed the ability of an aqueous extract of Allium eriophyllum Boiss leaf grown under in vitro conditions for the biosynthesis of gold nanoparticles (AuNPs) and also revealed the anti-hemolytic anemia activity of AuNPs in an anemic rodent model. These nanoparticles were characterized using Fourier-transform infrared spectroscopy (FT-IR) spectroscopy, ultraviolet–visible spectroscopy, X-ray diffraction, field-emission scanning electron microscopy (FE-SEM), and transmission electron microscopy (TEM). TEM and FE-SEM images showed the biosynthesized nanoparticles as having a uniform spherical morphology and diameters in the range of 5–30 nm. In vivo design, the induction of hemolytic anemia, was done using phenylhydrazine in 40 mice. Then, the mice were randomly divided into five groups: HAuCl₄, A. eriophyllum, AuNPs, untreated, and control. AuNPs significantly (p ≤ 0.01) decreased the concentration of glucocorticoid receptors in the serum, liver, and spleen, and also alkaline phosphatase, aspartate aminotransferase, alanine aminotransferase, gamma-glutamyl transferase, total and conjugated bilirubin, cholesterol, triglyceride, low-density lipoprotein, urea, creatinine, ferrous, ferritin, and erythropoietin in the serum increased the concentrations of superoxide dismutase, catalase, and glutathione peroxidase (GPx) in the serum, liver, and spleen and also total protein, high-density lipoprotein, and albumin in serum in the control mice as compared to the anemic mice. Also, AuNPs significantly (p ≤ 0.01) increased the body weight; anti-inflammatory cytokine (IL4, IL5, IL10, IL13, and IFNα) concentration; and the total platelet, white blood cells, lymphocyte, neutrophil, monocyte, eosinophil, and basophil counts and red blood cell parameters but decreased the weight and volume of the liver and spleen and their subcompartments and decreased the concentration of pro-inflammatory cytokines (IL1, IL6, IL12, IL18, IFNY, and TNFα) compared to the untreated mice. In vitro design, using 2,2-diphenyl-1-picrylhydrazyl test, revealed similar antioxidant potentials for A. eriophyllum, AuNPs, and butylated hydroxytoluene. In addition, AuNPs were similar to A. eriophyllum and had a high cell viability dose dependently against the human umbilical vein endothelial cell line. In conclusion, the results of the chemical characterization confirm that the leaves of A. eriophyllum can be used to produce AuNPs with a remarkable amount of anti-hemolytic anemia property.     

A quasichemical lattice model for a binary mixture of hard rectangular parallelepipeds Application to systems composed of nematic and non-mesogenic molecules

The hole lattice model of rectangular parallelepipeds is presented to describe the structural and excess thermodynamic properties of nematic-non-mesogenic mixtures. The molecular attractions are taken into account within the quasi-chemical approximation. A procedure for evaluating model parameters from data on the thermodynamic characteristics of pure components and the activity coefficients of the non-mesogen at infinite dilution at the nematic-isotropic transition temperature of the mesomorphic component is proposed. The mixing functions (enthalpy and volume), activity coefficient of the non-mesogen and the order parameters of the components are calculated at a molecular level for systems composed of 4-methoxybenzylidene-4'-propylaniline and a non-mesogen (tetrachlormethane, benzene and n-heptane). The calculated results are in quite good agreement with experiment in the temperature rang from 319·2 to 335·4 K.     

Plant pathogen recognition as a natural, original and simple model for chemogenomics: a brief overview of cell-based assays to screen for peptides acting as plant defense activators

As plants lack a circulatory system and adaptive immune system, they have evolved their own defense systems distinct from animals, in which each plant cell is capable of defending itself from pathogens. Plants induce a number of defense responses, which are triggered by a variety of molecules derived from pathogenic microorganisms, referred to as microbe-associated molecular patterns (MAMPs), including peptides, proteins, lipopolysaccharide, beta-glucan, chitin, and ergosterol. The interaction between plants and chemicals in the context of plant defense represents a "natural" and simple model for chemogenomics, at the intersection between chemical and biological diversities. For protection of crop plants from diseases, it has been shown to be effective to stimulate the plant immunity by chemical compounds, the so-called "plant defense activators". Combinatorial chemistry techniques can be applied to the search for novel plant defense activators, but it is essential to establish an efficient and reliable screening system suitable for library screening. For studies of the plant immune system, it is difficult to use isolated proteins as biological targets because the receptors for MAMP recognition are largely unknown and even the receptors identified so far are transmembrane proteins. Therefore, screening for novel peptides acting on MAMP receptors from combinatorial libraries must rely on a solution-phase assay using cells as the biological targets. In this review, we introduce the cell-based lawn format assay for identification of peptides acting as plant defense activators from combinatorial peptide libraries. The requirements and limitations in constructing the screening system using combinatorial libraries in the studies of plant sciences are also discussed.     

A flexible trilinear decomposition algorithm for three-way calibration based on the trilinear component model and a theoretical extension of the algorithm to the multilinear component model

There is a great deal of interest in decompositions of multilinear component models in the field of multi-way calibration, especially the three-way case. A flexible novel trilinear decomposition algorithm of the trilinear component model as a modification of an alternating least squares algorithm for three-way calibration is proposed. The proposed algorithm (constrained alternating trilinear decomposition, CATLD) is based on an alternating approximate least-squares scheme, in which two extra terms are added to each loss function, making it more efficient and flexible. The analysis of simulated three-way data arrays shows that it converges fast, is insensitive to initialization, and is insensitive to the overestimated number of components used in the decomposition. The analysis of real excitation–emission matrix (EEM) fluorescence and real high performance liquid chromatography–photodiode array detection (HPLC–DAD) data arrays confirms the results of the simulation studies, and shows that the proposed algorithm is favorable not only for EEMs but also for HPLC–DAD data. The three-way calibration method based on the CATLD algorithm is very efficient and flexible for direct quantitative analysis of multiple analytes of interest in complex systems, even in the presence of uncalibrated interferents and varying background interferents. Additionally, a theoretical extension of the proposed algorithm to the multilinear component model (constrained alternating multilinear decomposition, CAMLD) is developed.