Derivatives of molecular surface area and volume: simple and exact analytical formulas

The computational effort of biomolecular simulations can be significantly reduced by means of implicit solvent models in which the energy generally contains a correction depending on the surface area and/or the volume of the molecule. In this article, we present simple derivation of exact, easy-to-use analytical formulas for these quantities and their derivatives with respect to atomic coordinates. In addition, we provide an efficient, linear-scaling algorithm for the construction of the power diagram required for practical implementation of these formulas. Our approach is implemented in a C++ header-only template library.     

Zinc-rich compounds of iron and cobalt: formation of [Fe2Zn(n)] (n = 2-4) and [Co2Zn3] cores

The reactions of heteroleptic GaCp*/CO containing transition metal complexes of iron and cobalt, namely [(CO)(3)M(μ(2)-GaCp*)(m)M(CO)(3)] (Cp* = pentamethylcyclopentadienyl; M = Fe, m = 3; M = Co, m = 2) and [Fe(CO)(4)(GaCp*)], with ZnMe(2) in toluene and the presence of a coordinating co-solvent were investigated. The reaction of the iron complex [Fe(CO)(4)(GaCp*)] with ZnMe(2) in presence of tetrahydrofurane (thf) leads to the dimeric compound [(CO)(4)Fe{μ(2)-Zn(thf)(2)}(2)Fe(CO)(4)] (1). Reaction of [(CO)(3)Fe(μ(2)-GaCp*(3))Fe(CO)(3)] with ZnMe(2) and stoichiometric amounts of thf leads to the formation of [(CO)(3)Fe{μ(2)-Zn(thf)(2)}(2)(μ(2)-ZnMe)(2)Fe(CO)(3)] (2) containing {Zn(thf)(2)} as well as ZnMe ligands. Using pyridine (py) instead of thf leads to [(CO)(3)Fe{μ(2)-Zn(py)(2)}(3)Fe(CO)(3)] (3) via replacement of all GaCp* ligands by three{Zn(py)(2)} groups. In contrast, reaction of [(CO)(3)Co(μ(2)-GaCp*)(2)Co(CO)(3)] with ZnMe(2) in the presence of py or thf leads in both cases to the formation of [(CO)(3)Co{μ(2)-ZnL(2)}(μ(2)-ZnCp*)(2)Co(CO)(3)] (L = py (4), thf (5)) via replacement of GaCp* with {Zn(L)(2)} units as well as Cp* transfer from the gallium to the zinc centre. All compounds were characterised by NMR spectroscopy, IR spectroscopy, single crystal X-ray diffraction and elemental analysis.     

The rich chemistry of [Zn2Cp*2]: trapping three different types of zinc ligands in the PdZn7 complex [Pd(ZnCp*)4(ZnMe)2{Zn(tmeda)}

The synthesis, structural characterization, and bonding situation analysis of a novel, all-zinc, hepta-coordinated palladium complex [Pd(ZnCp*)(4)(ZnMe)(2){Zn(tmeda)}] (1) is reported. The reaction of the substitution labile d(10) metal starting complex [Pd(CH(3))(2)(tmeda)] (tmeda = N,N,N',N'-tetramethyl-ethane-1,2-diamine) with stoichiometric amounts of [Zn(2)Cp*(2)] (Cp* = pentamethylcyclopentadienyl) results in the formation of [Pd(ZnCp*)(4)(ZnMe)(2){Zn(tmeda)}] (1) in 35% yield. Compound 1 has been fully characterized by single-crystal X-ray diffraction, (1)H and (13)C NMR spectroscopy, IR spectroscopy, and liquid injection field desorption ionization mass spectrometry. It consists of an unusual [PdZn(7)] metal core and exhibits a terminal {Zn(tmeda)} unit. The bonding situation of 1 with respect to the properties of the three different types of Zn ligands Zn(R,L) (R = CH(3), Cp*; L = tmeda) bonded to the Pd center was studied by density functional theory quantum chemical calculations. The results of energy decomposition and atoms in molecules analysis clearly point out significant differences according to R vs L. While Zn(CH(3)) and ZnCp* can be viewed as 1e donor Zn(I) ligands, {Zn(tmeda)} is best described as a strong 2e Zn(0) donor ligand. Thus, the 18 valence electron complex 1 nicely fits to the family of metal-rich molecules of the general formula [M(ZnR)(a)(GaR)(b)] (a + 2b = n ≥ 8; M = Mo, Ru, Rh; Ni, Pd, Pt; R = Me, Et, Cp*).     

Mixed phosphine and group-13 metal ligator complexes [(PR3)(a)M(ECp*)b] (M = Mo, Ni; E = Ga, Al; R = C6H5, cyclo-C6H11, CH3)

Treatment of [Mo(N(2))(PMe(3))(5)] with two equivalents GaCp* (Cp* = η(5)-C(5)(CH(3))(5)) leads to the formation of cis-[Mo(GaCp*)(2)(PMe(3))(4)] (1), while AlCp* did not react with this precursor. In addition, [Ni(GaCp*)(2)(PPh(3))(2)] (2a), [Ni(AlCp*)(2)(PPh(3))(2)] (2b), [Ni(GaCp*)(2)(PCy(3))(2)] (3a), [Ni(GaCp*)(2)(PMe(3))(2)] (3b), [Ni(GaCp*)(3)(PCy(3))] (4) and [Ni(GaCp*)(PMe(3))(3)] (5) have been prepared in high yields by a direct synthesis from [Ni(COD)(2)] and stoichiometric amounts of the ligands PR(3) and ECp* (E = Al, Ga), respectively. All compounds have been fully characterized by (1)H, (13)C, and (31)P NMR spectroscopy, elemental analysis and single crystal X-ray diffraction studies.     

A paper-based lateral flow assay for morphine

Morphine was used as a model analyte to examine the possibility of using cellulose, physically modified by papermaking and converting techniques, as a capillary matrix in a lateral flow type of diagnostic assay. This research was directed toward low-cost, disposable, and portable paper-based diagnostics, with the aim of addressing the analytical performance of paper as a substrate in the analysis for drugs of abuse. Antibody Fab fragments were used as sensing molecules, and gold nanoparticle detection was employed. Inkjet printing was used to pattern sensing biomolecules as detection zones on paper. To validate the usefulness of paper as a diagnostic platform, the principle of a direct sandwich assay, based on immunocomplex formation between morphine and the anti-morphine Fab fragment and detection of the formed immunocomplex by another Fab fragment, was implemented. Results were compared with that achieved by using nitrocellulose as a reference material. Possible interfering from the sample matrix on assay quality was investigated with spiked oral fluid samples. Under optimized conditions, a visually assessed limit of detection for the sandwich assay was 1 ng/mL, indicating that the paper-based test devices developed in this work can perform screening for drugs of abuse and can fulfill the requirement for a sensitive assay in diagnostically relevant ranges. Fig

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Copper‐Mediated ortho‐Nitration of (Hetero)Arenecarboxylates

Various (hetero)arenecarboxylic acids were converted to the corresponding Daugulis amides and nitrated selectively in the ortho‐position in the presence of [CuNO₃(PPh₃)₂] and AgNO₂ at 50 °C. A microwave‐assisted saponification allows regenerating the carboxylate group within minutes, which may then be removed tracelessly by protodecarboxylation, or substituted by aryl‐ or alkoxy‐groups via decarboxylative cross‐coupling.     

Application of enriched stable 196Hg isotope for monitoring the stability of total mercury in water samples

A novel tool for the investigation of stability of total mercury in water samples is presented. The study focuses on the application of enriched ¹⁹⁶Hg stable isotopic reagent for the stability studies. Natural abundance of ¹⁹⁶Hg in water samples is only 0.15%. Thus, the use of the ¹⁹⁶Hg isotope spike represents a major advantage, when it can be assumed that all the measured isotope is the same as is accurately added by the analyst, and the change in its mass concentration can be followed simply and reliably. Tests were carried out with industrial waste water and two type of the natural water. Cold vapour (CV) inductively coupled plasma mass spectrometer (ICP-MS) technique was applied for the mercury measurements. Monitoring was continued for approximately 100 days. It is commonly advised that the measurement for total mercury in water samples should be carried out within 14 days. In this study the samples were observed to be stable for more than three months, if they were stored at a temperature of 4–6°C. The results of this stability study were in line with the guidance presented in EPA standard 1631. However, the samples were noticed to be stable for a much longer time than is presented in the standard method ISO 17852.     

Vibrational spectroscopy and normal-mode analysis of Fe(II) octaethylporphyrin

The normal-mode spectrum for the four-coordinated heme compound Fe(II) octaethylporphyrin, Fe(OEP), has been determined by refining force constants to the experimental Fe vibrational density of states measured with nuclear resonance vibrational spectroscopy (NRVS). Convergence of the calculated spectrum to the data was achieved by first imposing D4 symmetry on the model structure as well as the force constants, progressively including different internal coordinates of motion, then allowing the true Ci (or S2) point group symmetry of the C(i)1 Fe(OEP) crystal structure. The NRVS-refined normal modes are in good agreement with Raman and IR spectra at high frequencies. Prior density functional theory predictions for a model porphyrin are similar to the core modes computed with the best-fit force field, but significant differences between D4 and Ci modes underline the sensitivity of porphyrin Fe normal modes to structural details. Some differences between the Ci best fit and the NRVS data can be attributed to intermolecular contacts not included in the normal-mode analysis.     

Chlorine‐Enhanced Surface Mobility of Au(100)

Motivated by experimental studies of two‐dimensional Ostwald ripening on Au(100) electrodes in chlorine‐containing electrolytes, we have studied diffusion processes using density functional theory. We find that chlorine has a propensity to temporary form AuCl complexes, which diffuse significantly faster than gold adatoms. With and without chlorine, the lowest activation energy is found for the exchange mechanism. Chlorine furthermore reduces the activation energy for the detachment from kink sites. Kinetic Monte Carlo simulations were performed on the basis of extensive density functional theory calculations. The island‐decay rate obtained from these Monte Carlo simulations, as well as the decay rate obtained from the theoretical activation energies and frequency factors when inserted into analytical solutions for Ostwald ripening, are in agreement with experimental island‐decay rates in chlorine‐containing electrolytes.