Uncertainty from sampling: workshop to launch a Nordtest handbook on sampling uncertainty estimation and control

A workshop on uncertainty in sampling was held in Hillerød, Denmark, on 12–13 April 2007 to launch a new handbook on sampling quality assurance and uncertainty estimation. The participants of the workshop were approximately 60 delegates from 15 European countries, representing institutions performing sampling, users of the data, research institutions, as well as accreditation bodies. Materials from the workshop, including examples, tools, and calculation aids for the work can be found at http://www.samplersguide.com. The Nordtest handbook Uncertainty from sampling will be made available on the Nordtest web site at http://www.nordicinnovation.net/nordtest.cfm under NT technical reports, report number NT tec 604. Until the final report is available on the Nordtest web site, an advance draft of the Nordtest handbook is available from http://www.samplersguide.com.     

Synthesis of a Series of Hydroxycarboxylic Acids as Standards for Oxidation of Nonanoic Acid

The synthesis of a series of nonanoic acids hydroxylated in terminal,ω-1,ω-2,ω-3 positions is described. These compounds will be employed as useful standards for the study of enzymatic and microbiological oxidation of nonanoic acid.

[Supplementary materials are available for this article. Go to the publisher's online edition of Synthetic Communications® for the following free supplemental resource(s): Full experimental and spectral details.]     

Thermochemical properties of the rare earth complexes with pyromellitic acid

Fourteen rare earth complexes with pyromellitic acid were synthesized and characterized by means of chemical and elemental analysis, and TG–DTG. The constant-volume combustion energies of complexes, Δ_cU, were measured by a precise rotating-bomb calorimeter (RBC-type II). Their standard molar enthalpies of combustion, , and standard molar enthalpies of formation, , were calculated at T = 298.15 K. The relationship of and with the atomic numbers of the elements in the lanthanide series was examined. The results show that a certain amount of covalence is present in the chemical bond between rare earth cations and the ligand.     

Mild,Selective Oxidation of Aromatic Alcohols Using β-Cyclodextrin-Functionalized Glass Microparticles: Characterization,Stability, and Application

The surface of glass microparticle (GMP) was functionalized with β-cyclodextrin (→ GMP-β-CD) and was characterized by x-ray photoelectron spectroscopy (XPS). GMP-β-CD was used to catalyze oxidation of alcohols into aldehydes and katones with excellent yield (86–92%). The modified surface of GMP-β-CD showed no change or degradation after repeated use as confirmed from XPS analysis after 10 cycles.

[Supplementary materials are available for this article. Go to the publisher's online edition of Synthetic Communications® for the following free supplemental resource(s): Full experimental and spectral details.]     

Yada: a novel tool for molecular docking calculations

Molecular docking is a computational method employed to estimate the binding between a small ligand (the drug candidate) and a protein receptor that has become a standard part of workflow in drug discovery. Generally, when the binding site is known and a molecule is similar to known ligands, the most popular docking methods are rather accurate in the prediction of the geometry. Unfortunately, when the binding site is unknown, the blind docking analysis requires large computational resources and the results are often not accurate. Here we present Yada, a new tool for molecular docking that is capable to distribute efficiently calculations onto general purposes computer grid and that combines biological and structural information of the receptor. Yada is available for Windows and Linux and it is free to download at www.yada.unisa.it.     

Theoretical mapping of new L–(N)–L family of species with donor–acceptor bonding between N and ligand L

We perform a computational mapping study of a family of new inorganic species, based on idea of donor–acceptor type bonding between N⁺ and a ligand L with a terminal electron lone pair. The nitrogen ion is seen as being in an atomic ¹D state, with empty 2p acceptor orbitals [I.S.K. Kerkines., A. Papakondylis, A. Mavridis, J. Phys. Chem. A, 2002, 106, 4435]. We consider a series of small ligands, such as PN, CCH⁻, CCCN⁻, , and others. Chemical bonding analysis confirms the suggested bonding picture as characteristic for experimentally known and as well as for most of the predicted species. A number of these new compounds is found to be thermodynamically stable with respect to the existing or . They are candidates for new synthetic targets.     

Nucleophilic and electrophilic radical attack on maleic and fumaric acids in aqueous solution

Rate coefficients (k) of CH₂OH, , and radical addition to maleic and fumaric acids were investigated between pH 1 and 8. Strong pH dependences observed were attributed to changes in protonation states of acids: H₂X, HX⁻ and X²⁻. k of CH₂OH, , addition to fumaric acid decreased in the order k_H2F>k_HF^->k_F^2- in agreement with the nucleophilic character of reaction. The electrophilic radical showed opposite tendency. With maleic acid the monoanion had the highest reactivity towards nucleophilic and the lowest one towards electrophilic radicals. This is attributed to a prevalence of steric over polar effects for HM⁻.     

Total Synthesis of (±)-Glabridin

An efficient formal synthesis of (±)-glabridin was accomplished in 10 steps from resorcinol using Raney Ni to reduce carbon–carbon double bonds in α,β-unsaturated carbonyl compound as the key step.

[Supplementary materials are available for this article. Go to the publisher's online edition of Synthetic Communications® for the following free supplemental resource(s): Full experimental and spectral details.]     

First principles study of the structure, electronic state and stability of cations

Structural and electronic properties of semiconductor binary microclusters cations have been investigated using the B3LYP-DFT method in the ranges of n=1, 2 and m=1–7. Full structural optimization, adiabatic ionization potentials calculation and frequency analysis are performed with the basis of 6-311+G(d). The charged-induced structural changes in these cations have been discussed. The strong As–As bond is also favored over Al–As bonds in the cations in comparison with corresponding neutral cluster. With As_m forming the base, adding Al atom(s) in different positions would find the stable structures of cations quickly and correctly. , , and are predicted to be species with high stabilities and possible to be produced experimentally.     

Carbon- and nitrogen-centered radicals produced from l-lysine by radiation-induced oxidation: A pulse radiolysis study

Radical species generated from the reactions of a basic amino acid, l-lysine (Lys), with hydroxyl radicals (OH) and sulfate radical anion () have been detected by the method of pulse radiolysis. On the basis of electron transfer reactivities toward tetranitromethane (TNM), it was demonstrated that reducing carbon-centered radicals are generated as a result of hydrogen abstraction from CH₂ of Lys with a G-value of 1.9 × 10⁻⁷ mol J⁻¹. On the other hand, direct oxidation of l-Lys by formed a transient species with different spectroscopic properties, most likely, the ε-N-centered Lys radical.     

Photoelectron spectroscopic study of iron–benzene cluster anions

Iron–benzene cluster anions, (n = 1–7, m = 1–4), were generated via laser vaporization and studied using mass spectrometry, anion photoelectron spectroscopy and in one case by density functional theory. Based on these studies, we propose that and Fe₁Bz₁ as well as and Fe₂Bz₁ exhibit half-sandwich structures, that and Fe₁Bz₂, and Fe₂Bz₂, as well as Fe₃Bz₂ and Fe₄Bz₂ are sandwich structures, and that and Fe₂Bz₃ and larger species form ‘rice-ball’ structures which in each case consist of benzene molecules surrounding an iron cluster core.     

Selection of Amino Acids and the Biomimetic Synthesis of Amido Bond in the Presence of β-CD

A new method was developed to construct a special amido bond in the presence of β-cyclodextrin. This process is similar to peptide synthesis in organisms. NMR experiments were performed to investigate the possible mechanism. This work has potential application in biomimetic peptide synthesis.

[Supplementary materials are available for this article. Go to the publisher's online edition of Synthetic Communications® for the following free supplemental resource(s): Full experimental and spectral details.]     

Copper(ii) ketimides in sp3 C–H amination

Commercially available benzophenone imine (HN CPh₂) reacts with β-diketiminato copper(ii) tert-butoxide complexes [Cu^II]–O^tBu to form isolable copper(ii) ketimides [Cu^II]–N CPh₂. Structural characterization of the three coordinate copper(ii) ketimide [Me₃NN]Cu–N CPh₂ reveals a short Cu-N_ketimide distance (1.700(2) Å) with a nearly linear Cu–N–C linkage (178.9(2)°). Copper(ii) ketimides [Cu^II]–N CPh₂ readily capture alkyl radicals R˙ (PhCH(˙)Me and Cy˙) to form the corresponding R–N CPh₂ products in a process that competes with N–N coupling of copper(ii) ketimides [Cu^II]–N CPh₂ to form the azine Ph₂C N–N CPh₂. Copper(ii) ketimides [Cu^II]–N CAr₂ serve as intermediates in catalytic sp³ C–H amination of substrates R–H with ketimines HN CAr₂ and ^tBuOO^tBu as oxidant to form N-alkyl ketimines R–N CAr₂. This protocol enables the use of unactivated sp³ C–H bonds to give R–N CAr₂ products easily converted to primary amines R–NH₂via simple acidic deprotection.

Commercially available benzophenone imine (HN CPh₂) reacts with β-diketiminato copper(ii) tert-butoxide complexes [Cu^II]–O^tBu to form isolable copper(ii) ketimides [Cu^II]–N CPh₂ that serve as intermediates in catalytic sp³ C−H amination via radical relay.     

Extrapolative prediction using physically-based QSAR

Surflex-QMOD integrates chemical structure and activity data to produce physically-realistic models for binding affinity prediction. Here, we apply QMOD to a 3D-QSAR benchmark dataset and show broad applicability to a diverse set of targets. Testing new ligands within the QMOD model employs automated flexible molecular alignment, with the model itself defining the optimal pose for each ligand. QMOD performance was compared to that of four approaches that depended on manual alignments (CoMFA, two variations of CoMSIA, and CMF). QMOD showed comparable performance to the other methods on a challenging, but structurally limited, test set. The QMOD models were also applied to test a large and structurally diverse dataset of ligands from ChEMBL, nearly all of which were synthesized years after those used for model construction. Extrapolation across diverse chemical structures was possible because the method addresses the ligand pose problem and provides structural and geometric means to quantitatively identify ligands within a model’s applicability domain. Predictions for such ligands for the four tested targets were highly statistically significant based on rank correlation. Those molecules predicted to be highly active (\(\hbox {pK}_i \ge 7.5\)) had a mean experimental \(\hbox {pK}_i\) of 7.5, with potent and structurally novel ligands being identified by QMOD for each target.     

Ab initio electronic and rovibrational structure of

The electronic structure of the ground state of has been investigated using relativistically-corrected CCSD(T) in conjunction with ANO-RCC (Mg) and aug-cc-pVQZ (H) basis sets. The molecular potential energy surface possessed minima corresponding to both ¹A₁ and equilibrium structures (with a ¹Σ⁺ transition state). The ¹A₁ structure possessed R_e and θ_e values of 2.0297 Å and of 22.09°, respectively. The higher-energy structure exhibited an R_e value of 2.1658 Å. Property surfaces were constructed to calculate rovibrational energies and spectral line intensities for the ground states of , (¹A′) MgHD²⁺ and . For the vibration ground state of , the vibration-averaged R_e and θ_e values were calculated to be 2.0209 Å and 22.53°, respectively. The A, B and C rotational constants were calculated to be 58.0, 2.21 and 2.11 cm⁻¹, respectively.     

A TEM investigation of the (Bi1−xSrx)FeO3−x/2, 0.2≤x≤0.67, solid solution and a suggested superspace structural description thereof

A careful transmission electron microscopy (TEM) investigation of an incommensurately modulated member of the (Bi_1−xSr_x)Fe³⁺O_3−x/2□_x/2, 0.2≤x≤0.67, solid solution has been carried out. High resolution (HR) TEM imaging is used to show the presence of at least 6-fold twinning on a rather fine (5 nm) scale. The (3+1)-d superspace group symmetry is suggested to be or one of the non-centrosymmetric sub-groups thereof, namely , , and . A superspace construction is then used to propose the nature of the local compositional ordering and, hence, of the oxygen-deficient slab that intergrows with the perovskite slab to produce the observed solid solution phase. The proposed compositional superspace atomic surfaces can be used to produce model structures at any composition within the solid solution range.     

An Expedient Approach for the Synthesis of 1-Alkyl-4-propionylpyrrolidin-2-ones

A simple and useful tandem addition–cyclization reaction of primary amines on a prepared α-functionalized propylvinyl ketone 3 in methanol at reflux is a promising route for the synthesis of a new family of 1-alkyl-4-propionylpyrrolidin-2-ones 4.

[Supplementary materials are available for this article. Go to the publisher's online edition of Synthetic Communications® for the following free supplemental resource(s): Full experimental and spectral details.]     

Self-assembly, crystal structure and photoluminescent properties of a novel organic–inorganic hybrid coordination polymer: [CdCl3(CH3)3NH]

A novel organic–inorganic coordination polymer [CdCl₃(CH₃)₃NH] 1 was synthesized by the reaction of CdCl₂ with trimethylamine (TMA) at 170 °C for 5 days in ethanol and structurally characterized by means of X-ray single diffraction. The title compound affords a one-dimensional chain structure. It crystallizes in hexagonal system space group P6(3)/m with , , , γ=120.00°, , Z=2, , F(000)=266, Mr=277.86, , the final R=0.0420 and ωR=0.1020 for 355 observed reflections with I>2σ(I). The title compound consists of cation [(CH₃)₃NH]⁺ and anion chain , and they are combined by static attracting forces in the crystal. TG–DTA, XRD and IR data for the title compound are reported and discussed. The photoluminescent properties of the compound 1 were also investigated.