Evolution of the structural stability of large Cu,Ni, Pd,and Ag clusters with size: An analysis within the embedded atom method

A study of the structural stability of clusters made up of a single component has been carried out within the Embedded Atom Method. Perfect icosahedral and cuboctahedral Cu, Ni, Pd, and Ag clusters with up to 5083 atoms have been compared. The icosahedron is found to be the stable structure for small clusters, and a change of structure from icosahedral to cuboctahedral is found as the cluster size increases. A contraction of the interatomic distances results when the cluster size decreases.     

Synthesis and performance of HPTLC plates modified with cyanopropyl- and octadecyl-trichlorosilane

Chemical modification of commercial high performance thin-layer chromatography plates with various mixtures of cyano-propyltrichlorosilane and octadecyltrichlorosilane is described. Surface coverage by different treatments is demonstrated as well as the variations in chromatographic performance. With regard to the development in aqueous media the utility of CN/ ODS plates compared to ODS plates is also shown.     

A configuration interaction study of phosphine using bonded functions

A computational study is made of the effect of basis set upon the energy, properties and inversion barrier of the phosphine molecule. The calculations are performed at both the SCF and CI level. The flexibility of the double zeta basis is discussed in the light of the results.     

Characterization of OV-1/FFAP-mixture coated glass capillary columns used for the separation of free fatty acids

As an alternative to acid pretreated UCON and FFAP capillaries for the analysis of wide-boiling free fatty acid mixtures, OV-1 : FFAP phase mixtures were used on high-temperature silylated inert glass capillary columns. The HETP-carrier gas velocity curves, peak asymmetry factors, coating efficiency, gas phase and stationary phase contributions to the mass transfer resistance were determined for various OV-1 : FFAP ratios. Mixed-phase capillaries showed optimum performance at a 2 : 1 OV-1 : FFAP ratio. The thermal and long-term stability of OV-1-stabilized FFAP columns surpassed those of the UCON and pure FFAP reference column used.     

High-Resolution,Higher-Order UV/VIS Derivative Spectrophotometry

Derivative spectrophotometry has gained increasing importance in the past two years and is currently experiencing vigorous development. Following and introduction the present article provides a review of this extremely effective method. In particular, the advantages of higher-order derivative spectrophotometry (HODS method, n > 2) are discussed on the basis of practical examples from a wide range of analytical fields. The results are achieved with the aid of a newly developed analog computer unit, whereby for the first time readily reproducible, low-noise, on-line spectra can be obtained up to the 7th order and even, in favorable cases, up to the 9th order. In practice it has proved valuable to work with spectra of the 3rd to 5th order; but even higher derivations could be profitable for the separation of strongly superposed signals or for “fingerprinting”.     

SBA-15 supported HPW: Effective catalytic performance in the alkylation of phenol

SBA-15 was synthesized using non-ionic surfactant as the structure directing agent at 40 °C. It was then impregnated with different loadings (10, 30, 50 and 70%) of phosphotungstic acid. They were characterized by XRD, N₂ adsorption, FT-IR and DRIFT techniques. The physicochemical characterization revealed that SBA-15 could accommodate discrete phosphotungstic acid due to its large pore volume and high surface area. The catalytic activity of these materials was examined in the vapour phase tert-butylation of phenol using tert-butyl alcohol as the alkylating agent. The influence of reaction parameters such as reaction temperature, reactant feed ratio, WHSV and time on stream was studied, and the results were correlated with physicochemical characteristics of the catalysts. 4-tert-Butyl phenol was observed as the major product with high selectivity. Among the catalysts, 30% phosphotungstic acid supported SBA-15 showed high phenol conversion under optimum conditions, which is significantly higher than either phosphotungstic acid loaded mesoporous AlPO or AlMCM-41.     

SNPs Feasibility of Nonlabeled Oligonucletides on Using Electrochemical Sensing

We have demonstrated an electrochemical gene chip protocol for the SNPs detection of nonlabeled DNA. Using an array consisting of streptavidin‐modified gold electrodes, probe DNA were attached through the application of a direct electric field. Electrochemical response changes originating from the hybridization of nucleic acids to protein‐bound nucleic acids using soluble mediators in K₃Fe(CN)₆ solution could then be observed. The electrochemical protocol developed showed high sensitivity and good reproducibility in the detection of DNA hybridization. Significant changes in electrochemical signals were also observed when using target DNA with a single base mismatch, indicating the applicability of this method to single nucleotide polymorphisms (SNPs) detection.     

Camdas: An automated conformational analysis system using molecular dynamics

We present an automated conformational analysis program, CAMDAS (Conformational Analyzer with Molecular Dynamics And Sampling). CAMDAS performs molecular dynamics (MD) calculations for a target molecule and samples conformers from the trajectory of the MD. The program then evaluates the similarities between each of the sampled conformers in terms of the root- mean-square deviations of the atomic positions, clusters similar conformers, and finally prints out the clustered conformers. This MD-based conformational analysis is a broadly used method, and CAMDAS is intended to provide a convenient framework for the method. CAMDAS has the ability to find the representative conformers automatically from an arbitrarily given structure of the molecule. The accuracy of the program was examined using N- acetylalanine-N-methylamide, and the obtained result was consistent with that of the systematic search method. In the test calculation of cyclodecane, CAMDAS could identify most of the known conformers and their conformational enantiomers by examining only 5000 conformers. In addition, the potential-scaled method, which we have developed previously as an accelerating technique for MD, could find two additional conformers of cyclodecane that have not been reported. CAMDAS presents a convenient way to find the energetically possible conformers of a molecule, which is needed especially in the early stage of drug design.     

Flexibility and Rigidity of Proteins and Protein–Pigment Complexes

Proteins may be rigid or flexible to various degrees as required for optimal function. Flexibility of large parts of a protein, which rearrange or move, is particularly interesting and will be discussed in this article. We differentiate between several categories, although the boundaries between them are diffuse: flexibility of peptide segments, order–disorder transitions of spatially contiguous regions, and domain motions. The domains may be flexibly linked to allow rather unrestricted motions or the motions may be constrained to certain modes. The various categories of large-scale flexibility will be illustrated with the following examples: (1) Small protein proteinase inhibitors are rather rigid molecules which provide binding surfaces complementary to their cognate proteases but show also limited segmental flexibility and adaptation. (2) Large plasma proteinase inhibitors exhibit large conformational changes after interaction with proteases probably for regulatory purposes. (3) Pancreatic serine proteases employ a disorder–order transition of their activation domain as a means to regulate enzymic activity. (4) Immunoglobulins show rather unrestricted and also hinged domain motions in different parts of the molecule probably to allow binding to antigens in different arrangements. (5) Citrate synthase adopts open and closed forms by a hinged domain motion to bind substrates and release products and to perform the catalytic condensation reaction, respectively. (6) Riboflavin synthase, a bifunctional multienzyme complex, catalyzes two consecutive reactions by means of two subunits, α and β. The β-subunits form a shell, in which the α-subunits are enclosed. Diffusional motion of the catalytic intermediates is therefore restricted. In addition, rearrangement of the N-terminal segment occurs during the assembly of the β-subunit. In contrast, rigidity is dominant in the structures of the light-harvesting complexes and the photosynthetic reaction centers involved in photosynthetic light reactions. These are large protein–pigment complexes in which the proteins serve as matrices to hold the pigments in the appropriate conformation and relative arrangement. Since motion would contribute to deactivation of the photoexcited states of the pigments and diminish the efficiency of light-energy and electron transfer, the functional role of rigidity is easy to rationalize for these proteins.