Many-body interaction analysis: algorithm development and application to large molecular clusters

A completely automated algorithm for performing many-body interaction energy analysis of clusters (MBAC) [M. J. Elrodt and R. J. Saykally, Chem. Rev. 94, 1975 (1994); S. S. Xantheas, J. Chem. Phys. 104, 8821 (1996)] at restricted Hartree-Fock (RHF)/MA Plesset 2nd order perturbation theory (MP2)/density functional theory (DFT) level of theory is reported. Use of superior guess density matrices (DM's) for smaller fragments generated from DM of the parent system and elimination of energetically insignificant higher-body combinations, leads to a more efficient performance (speed-up up to 2) compared to the conventional procedure. MBAC approach has been tested out on several large-sized weakly bound molecular clusters such as (H(2)O)(n), n=8, 12, 16, 20 and hydrated clusters of amides and aldehydes. The MBAC results indicate that the amides interact more strongly with water than aldehydes in these clusters. It also reconfirms minimization of the basis set superposition error for large cluster on using superior quality basis set. In case of larger weakly bound clusters, the contributions higher than four body are found to be repulsive in nature and smaller in magnitude. The reason for this may be attributed to the increased random orientations of the interacting molecules separated from each other by large distances.     

An ion beam spectrochemical analyser with application to the analysis of silicate minerals

Ion-beam sputtering is used to provide a new method of spectrochemical analysis of solids. The theory of quantitative analysis by this method is discussed and is shown to be applicable to the analysis of a variety of rock-forming silicates.     

Aminopropyl-silica as an advantageous alternative to nonpolar sorbents for continuous cleanup/preconcentration of vitamin D3 metabolites

Summary A new procedure for continuous cleanup and concentration of hydroxyvitamin D₃ metabolites prior to their separation by HPLC and UV-detection is reported. The process is based on the use of aminopropyl-silica as solid-phase sorbent as an alternative to the use of nonpolar sorbents. The improvement thus achieved has been tested by comparing the results with those obtained using octadecyl-C₁₈ as non-polar sorbent. The comparison has been based on the calibration graphs (linear range, detection and quantitation limits), precision and multiple standard addition method.     

Determination of rapamycin: quantification of the sodiated species by an ion trap mass spectrometer as an alternative to the ammoniated complex analysis by triple quadrupole

Rapamycin is a potent immunosuppressive drug capable of significantly reducing acute graft rejection in kidney, liver and heart transplant patients. Its immunosuppressive activity and adverse effects have been related to rapamycin concentration, and therapeutic drug monitoring of the drug is deemed appropriate. This work was aimed at developing a new quantification method based on the isolation of the [M+Na]+ ion as precursor and its further fragmentation through an ion trap mass spectrometer equipped with an electrospray ionization source. A limit of detection (LOD) of 0.7 ng/mL was obtained, while the lower limit of quantification (LLOQ) was 2.4 ng/mL. The accuracy and reproducibility of the responses were evaluated and compared with results obtained when the [M+NH4]+ ion was chosen as the precursor in a triple quadrupole mass spectrometer. In this case the LOD was 0.5 ng/mL and the LLOQ 1.7 ng/mL. Data showed that it would be possible to use the quantification of the sodiated species for the routine determination of rapamycin, as an alternative to the commonly adopted method based on the ammoniated complex.     

Global tuning of local molecular phenomena: an alternative approach to bionanoelectronics

We have applied simultaneous horizontal and vertical bias to a single molecule (2 nm(2)) in an ordered and disordered matrix to virtually isolate and tune its property without taking it out physically from its environment. Using a dedicated electrode system, we have locally tuned nanoscale properties vertically by STM, while stabilizing its environment by applying a global electric field horizontally. Using this technique, we report tuning of molecular conformations in room temperature, whose evolution of states has been statistically investigated. We have also shown control on switching of a few selected conformations by applying dual bias simultaneously. As we avoid any direct injection of charge into the system via electrode contact, this technique could be used as a generalized method to tune phenomena evolved in an environment of weak interaction from a large distance without destroying the property.     

Photochemistry of p-chloromercurobenzophenone: Photoreduction as an alternative to demercuration

p-Chloromercurobenzophenone exhibits dual reactivity during photolysis: in solvents that are hydrogen donors it is photoreduced with the formation of a mercury-containing ketyl radical, while in other solvents it undergoes demercuration. Photolysis of p-chloromercurobenzophenone by both paths occurs from the triplet excited state.Translated from Izvestiya Akademii Nauk SSSR, Seriya Khimicheskaya, No. 8, pp. 1738–1742, August, 1990.     

Secondary ion mass spectrometry depth profiling of ultrathick films using an argon gas cluster source: Crater shape implications on the analysis area as a function of depth

Argon cluster ions have enabled molecular depth profiling to unprecedented depths, with minimal loss of chemical information or changes in sputter rate. However, depth profiling of ultrathick films (>100 μm) using a commercial ion source oriented at 45° to the surface causes the crater bottom to shrink in size because of a combination of the crater wall angle, sputter rate differences along the trailing-edge crater wall, and undercutting on the leading-edge. The shrinking of the crater bottom has 2 immediate effects on dual-beam depth profiling: first is that the centering of the analysis beam inside the sputter crater will no longer ensure the best quality depth profile because the location of the flat crater bottom progressively shifts toward the leading-edge and second, the shifting of the crater bottom enforces a maximum thickness of the film that could be depth profiled. Experiments demonstrate that a time-of-flight secondary ion mass spectrometry instrument equipped with a 20 keV argon cluster source is limited to depth profiling a 180 μm-thick film when a 500 μm sputter raster is used and a 100 μm square crater bottom is to be left for analysis. In addition, depth profiling of a multilayer film revealed that the depth resolution degrades on trailing-edge side of the crater bottom presumably because of the redeposition of the sputtered flux from the crater wall onto the crater bottom.     

Partial least-squares regression on design variables as an alternative to analysis of variance

The partial least-squares (PLS) algorithm has become popular for explorative multivariate data analysis and for multivariate calibration. The same PLS algorithm can also be used for confirmatory data analysis. The discussion is limited to analysis of a single response variable. A close correspondence of PLS1 regression to classical analysis of variance (ANOVA) is demonstrated. The design of an experiment is described in terms of discrete design variables for main effects and simple interactions (dummy variables). These are used as regressors X = (x₁, x₂,…,) for modelling the response variable of the experiment, y. As in conventional use of PLS1 regression, the algorithm gives a concentrated model or diagram of the most important, y-relevant variability types in the X-data. In the present case, this gives the combination of design variables that models the variations in y. A simple plot of the resulting factor loadings immediately reveals the important design variables. Statistical tests and confidence regions in the PLS solution give additional safeguards against interpretation of spurious effects. The method is applied to two data sets. One concerns assessment of personal preference for blackcurrent juice, studied in a 2⁵ factorial experiment; these data are also studied with missing values and as fractional factorials. The other ceoncers spectrophotometric absorbance-based colour assessments of pigment in strawberry jam in a 3-factor design with 2, 2 and 3 levels in the respective factors.     

A gold-containing TiO complex: a crystalline molecular precursor as an alternative route to Au/TiO2 composites

The gold-containing titanium peroxo-complex AuCl4(NH4)7[Ti4(O2)4(Hcit)2(cit)2].12H2O 1 allows an easy reproducible access to pure Au/TiO2 composites.     

Wavelet transform analysis of ab initio molecular dynamics simulation: application to core-excitation dynamics of BF3

We propose a novel analysis method of ab initio molecular dynamics (AIMD) simulation using a continuous wavelet transform (c-WT) technique. The c-WT technique, one of the time-frequency signal analysis methods, provides a clear view of the dynamical information in time developments. Combined with the auto-correlation function of velocity by AIMD simulation, c-WT analysis enables us to well understand dynamical distribution, such as the vibrational properties following a change of electronic structure in a molecular system. As a practical application, AIMD simulation of core-excited BF(3) (B1s --> 2a(2) (')) is illustrated. AIMD simulation leads to the change of vibrational motion as well as structural deformation by core-excitation. The c-WT analysis clarifies the relationship between structural deformation and the related significant vibrational modes in core-excitation within 50 fs.     

Synthesis of a large functional cage compound based on four Ga-Ga single bonds and its application as an oligoacceptor: on the way to bio-organogallium hybrid molecules

The digallium compound R(2)Ga-GaR(2) (1; R=CH(SiMe(3))(2)) reacts with citracinic acid by the release of two equivalents of bis(trimethylsilyl)methane and the formation of a unique oligofunctional cage compound (2). Four Ga-Ga bonds in a tetrahedral arrangement are bridged by four spacer ligands that are located on the faces of the tetrahedron and bridge the gallium atoms of three different Ga-Ga bonds. Four pyridinium groups result from the shift of one of the three acidic protons of four citracinic acid molecules to the nitrogen atoms of the aromatic rings. The N-H groups are arranged in pairs and are capable of acting as chelating acceptors for the coordination of THF molecules (2(THF)(2)) or the nitrogen atoms of 1-deazapurine (3(OEt(2))(4)). In particular, the last reaction verifies the potential applicability of this relatively water- and air-resistant acceptor compound for the generation of bioorganometallic hybrid molecules.     

Highly fluorescent carbon polymer dots prepared at room temperature,and their application as a fluorescent probe for determination and intracellular imaging of ferric ion

Carbon polymer dots (CPDs) were prepared by a one-pot aqueous synthetic route from ascorbic acid and diethylenetriamine at room-temperature. The CPDs under 350-nm excitation exhibit blue fluorescence peaking at 430 nm with a quantum yield of 47%. Other features include an average diameter of 5 nm, a fluorescence that is independent of the excitation wavelength, good water dispersibility and photostability, and excellent biocompatibility. The CPDs are shown to be viable fluorescent probes for ferric ion which acts as a strong quencher. The response to Fe(III) is linear in the 0.2 to 10 μM concentration range, and the detection limit is 0.1 μM. The probe was applied to the determination of Fe(III) in environmental waters and to intracellular imaging of ferric ions in HeLa cells.

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Graphical abstract Carbon polymer dots (CPDs) are prepared from ascorbic acid and diethylenetriamine (DETA) at room-temperature (RT). The RT-CPDs exhibit excellent optical performance, biocompatibility and selectivity of quenching by ferric ions. This can be applied for determination and intracellular imaging of ferric ion.

     

不同温度下LaAlO3 : Eu的光谱分析

本文基于双层点电荷配位场(DSCPCF)模型, 计算分析了77K, 300K和500K温度下Eu^3^+离子在LaAlO3中的配位场微扰能级及其光谱行为, 结果与实验吻合较好。由于随着温度的升高,Eu^3^+点的对称性发生变化(D3→Oh), 而使计算参数的取值有微小差别, 计算得到的配位场参数也有规律性的变化, 尤其是500K时B0^2值变号, 使计算的DSCPCF能级次序稍不同于其它两个温度。     

Quantitative analysis of chloride in brackish water: an application to the hyperchromic effect of copper(II) ion with chloride ion.

A new modified method was applied to the determination of chloride anion in brackish water by using a common copper(II) sulfate solution and a spectrophotometer. The result of the quantitative analysis demonstrated that chloride concentrations were 1.61% w/v and 1.74% w/v at ebb tide and flood tide, respectively, of the Muya River. On the other hand, chloride concentrations were 1.17% w/v at ebb tide and 1.65% w/v at flood tide of the Yoshino River. The new method proved that chloride concentration corresponded well with results from Mohr and conductive methods. Therefore, the newly developed method can be exploited as common means to measure chloride concentration in aqueous solutions. Moreover, it is also valuable for application to other types of environmental samples.     

3D superposition of chemical fragments for N‐membered rings: application to conformational analysis

In this paper a procedure is suggested for the 3D superposition of chemical fragments, which is specifically designed for rings molecules and can be combined with statistical multivariate procedures to extract useful conformational information. The procedure relies on the plane introduced by Cremer and Pople ‘A general definition of ring puckering coordinates. J. Am. Chem. Soc. 1975; 97 (6): 1354–1358’ to define the celebrated puckering coordinates, and provides a measure of distance between two geometrical conformations. Real datasets are analyzed to illustrate how it can be used as input to agglomerative clustering methods, multidimensional scaling analysis and allows to compute the centroid of a group of fragments. Copyright © 2010 John Wiley & Sons, Ltd.     

3D Heteronuclear long‐range 1H–13C scalar correlation at natural abundance: application to oligosaccharide analysis

A 3D ¹H–¹³C–¹H refocused INEPT transfer experiment is proposed in which the initial coherence transfer of ¹H longitudinal to ¹³C transverse magnetization is tuned to the long‐range ¹H, ¹³C couplings while the reverse INEPT component transfers the magnetization to the directly bonded ¹H. Integration of a constant time ¹H evolution period into the long‐range coherence transfer interval provides absorption mode signals for each dimension. A ¹³C purge component at the beginning of the sequence selects for ¹²C‐bound ¹H magnetization that is then transferred to a ¹³C‐bound hydrogen, thus strongly suppressing the diagonal signals. This experiment is expected to be of particular value for situations in which resonance overlap in the ¹³C dimension renders 2D long‐range heteronuclear correlation data ambiguous. In combination with a diagonal‐suppressed 3D ¹H–¹³C–¹H TOCSY‐HSQC experiment, complete assignment of the ring resonances of the Lewis‐b hexasaccharide was obtained on a 4.2 mM sample using a conventional 500 MHz probe (0.1% ethylbenzene signal‐to‐noise ratio of 600), suggesting its applicability to sub‐millimolar samples using cryoprobe technology. Copyright © 2002 John Wiley & Sons, Ltd.     

Long-wavelength fluorimetry as an indirect detection system in immunoaffinity chromatography: application to environmental analysis

The potential of long-wavelength fluorimetry when used as the detection system in immunoaffinity chromatography is assessed for the first time by applying this approach to the analysis of water and sludge samples. Nile blue (NB) was used to synthesize a long-wavelength fluorescent tracer for linear alkylbenzenesulfonates (LASs) using the carbodiimide method, in which the amino group of NB is covalently coupled to the activated carboxylic acid group of a LAS mimic with N-hydroxysuccinimide and dicyclohexylcarbodiimide. The method consists of the injection of a pre-incubated mixture containing linear sodium 4-dodecylbenzenesulfonate (LDS; used as the LAS model), anti-LAS antibodies, and the long-wavelength tracer into a commercial Protein G column. Free and bound tracer fractions are separated in the column, and the peak height of the immunochromatogram (corresponding to the free tracer) is directly measured at 626 nm (λ _ex) and 674 nm (λ _em), and then correlated to the analyte concentration. It is not necessary to perform an elution step immediately after every sample application. The dynamic range of the method is 0.05–2.5 μg ml⁻¹ LDS, and the detection limit is 15 ng ml⁻¹. The precision, expressed as the relative standard deviation, is 4.8–6.4%. Other surfactants (sodium dodecylsulfate and Triton X-100) do not cause interference. The recoveries obtained by applying the method to the analysis of water (ground- and wastewater) and sludge (primary and activated) samples ranged from 86.0 to 111.3%. Water sample analysis included an initial solid-phase extraction step, which cleaned up the samples and improved the detection limit fivefold.     

Electrochemical irreversibility of ion transfers at liquid/liquid interfaces: Part II. Quasi-thermodynamic analysis and time dependences for single ion transfers

Structure of the double layer at immiscible liquid electrolyte interfaces is a controversial topic. and is essential to correct interpretation of ion-crossing kinetics. For single partitioned salt systems, (NR₄⁺X^? at H₂O/PhNO₂ interfaces for example. single ion free energies in each phase determine equilibrium charge and control pds in part. For non-equilibrium applied pds and currents. the overpotential may be entirely accounted for in space-charge perturbations, or as pds in compact layers in each phase, or as combinations of both. Experimental results for irreversible and quasi-reversible ion transfers, at constant current, suggest a pd across a compact layer. New results in the absence of supporting electrolyte are crucial to the argument. Log analytical plots are now available for pd dependences on time for various cases, including a compact layer whose order and capacitance depends upon charge. These plots are described and used in the analysis of experimental data.